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25 hits found for Ravishankar Ramachandran

SASDJK4 – RNA polymerase core complex

DNA-directed RNA polymerase subunit alphaDNA-directed RNA polymerase subunit betaDNA-directed RNA polymerase subunit beta'DNA-directed RNA polymerase subunit omega experimental SAS data
DAMFILT model
Sample: DNA-directed RNA polymerase subunit alpha dimer, 78 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit beta monomer, 129 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit beta' monomer, 147 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit omega monomer, 12 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2018 Mar 8
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 5.1 nm
Dmax 19.3 nm
VolumePorod 262 nm3

SASDJL4 – RNA polymerase core subunit in complex with ATP-dependent DNA helicase UvrD1

DNA-directed RNA polymerase subunit alphaDNA-directed RNA polymerase subunit betaDNA-directed RNA polymerase subunit beta'DNA-directed RNA polymerase subunit omegaATP-dependent DNA helicase UvrD1 experimental SAS data
DAMMIF model
Sample: DNA-directed RNA polymerase subunit alpha dimer, 75 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit beta monomer, 129 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit beta' monomer, 147 kDa Mycobacterium tuberculosis protein
DNA-directed RNA polymerase subunit omega monomer, 12 kDa Mycobacterium tuberculosis protein
ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2018 Mar 11
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 7.5 nm
Dmax 22.2 nm
VolumePorod 898 nm3

SASDJM4 – ATP-dependent DNA helicase UvrD1 (Apo-UvrD)

ATP-dependent DNA helicase UvrD1 experimental SAS data
DAMFILT model
Sample: ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2020 Feb 28
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 3.4 nm
Dmax 8.4 nm
VolumePorod 132 nm3

SASDJN4 – ATP-dependent DNA helicase UvrD-ATP complex

ATP-dependent DNA helicase UvrD1 experimental SAS data
DAMFILT model
Sample: ATP-dependent DNA helicase UvrD1 monomer, 85 kDa Mycobacterium tuberculosis protein
Buffer: 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2020 Feb 28
Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair
Ravishankar Ramachandran
RgGuinier 3.5 nm
Dmax 9.5 nm
VolumePorod 101 nm3

SASDFE6 – Sliding beta clamp

Beta sliding clamp experimental SAS data
GASBOR model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 15
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
...Ramachandran R
RgGuinier 3.7 nm
Dmax 10.3 nm
VolumePorod 186 nm3

SASDFF6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex

Beta sliding clampProbable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) monomer, 33 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 15
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
...Ramachandran R
RgGuinier 3.5 nm
Dmax 11.3 nm
VolumePorod 98 nm3

SASDFG6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex

Beta sliding clampProbable exodeoxyribonuclease III protein XthADNA ligase A experimental SAS data
DAMMIF model
Sample: Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
...Ramachandran R
RgGuinier 5.8 nm
Dmax 25.3 nm
VolumePorod 501 nm3

SASDFH6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp, DNA ligase-A tricomplex in the presence of DNA substrate

Probable exodeoxyribonuclease III protein XthADNA ligase ABeta sliding clampDNA ligase A nicked DNA substrate experimental SAS data
DAMMIF model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 31 kDa Mycobacterium tuberculosis protein
DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Beta sliding clamp dimer, 86 kDa Mycobacterium tuberculosis protein
DNA ligase A nicked DNA substrate dimer, 16 kDa DNA
Buffer: 50 mM Tris pH 8.0, 200 mM NaCl , 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 17
Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex International Journal of Biological Macromolecules (2022)
...Ramachandran R
RgGuinier 5.8 nm
Dmax 19.1 nm
VolumePorod 496 nm3

SASDJM7 – Iron-sulfur cluster assembly protein (IscU)

Iron-sulfur cluster assembly protein experimental SAS data
DAMFILT model
Sample: Iron-sulfur cluster assembly protein trimer, 42 kDa Plasmodium falciparum (isolate … protein
Buffer: 50 mM Tris-Cl, 300 mM NaCl, 5% Glycerol, pH: 7.5
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 May 5
[Fe-S] cluster biogenesis and unusual assembly of the ISC scaffold complex in Plasmodium falciparum mitochondrion
Ravishankar Ramachandran
RgGuinier 5.4 nm
Dmax 11.1 nm
VolumePorod 177 nm3

SASDJN7 – Cysteine desulfurase, Iron-sulfur cluster assembly protein (IscS_IscU) complex

Iron-sulfur cluster assembly proteinCysteine desulfurase, putative experimental SAS data
DAMMIF model
Sample: Iron-sulfur cluster assembly protein tetramer, 56 kDa Plasmodium falciparum (isolate … protein
Cysteine desulfurase, putative tetramer, 204 kDa Plasmodium falciparum (isolate … protein
Buffer: 50 mM Tris-Cl, 300 mM NaCl, 5% Glycerol, pH: 7.5
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Sep 4
[Fe-S] cluster biogenesis and unusual assembly of the ISC scaffold complex in Plasmodium falciparum mitochondrion
Ravishankar Ramachandran
RgGuinier 6.4 nm
Dmax 17.6 nm
VolumePorod 1100 nm3

SASDJP7 – Cysteine desulfurase, Iron-sulfur cluster assembly protein, Protein ISD11 (IscS_IscU_Isd11) complex

Cysteine desulfurase, putativeIron-sulfur cluster assembly proteinProtein ISD11 experimental SAS data
DAMMIF model
Sample: Cysteine desulfurase, putative tetramer, 204 kDa Plasmodium falciparum (isolate … protein
Iron-sulfur cluster assembly protein tetramer, 56 kDa Plasmodium falciparum (isolate … protein
Protein ISD11 tetramer, 43 kDa Plasmodium falciparum (isolate … protein
Buffer: 50 mM Tris-Cl, 300 mM NaCl, 5% Glycerol, pH: 7.5
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Sep 19
[Fe-S] cluster biogenesis and unusual assembly of the ISC scaffold complex in Plasmodium falciparum mitochondrion
Ravishankar Ramachandran
RgGuinier 7.1 nm
Dmax 17.9 nm
VolumePorod 950 nm3

SASDKP7 – Probable transcriptional regulatory protein Lrp/AsnC protein Rv2324

Probable transcriptional regulatory protein (Probably AsnC-family) experimental SAS data
DAMMIF model
Sample: Probable transcriptional regulatory protein (Probably AsnC-family) dimer, 36 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris, 150 mM NaCl, 2 mM EDTA, pH: 7.5
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Mar 1
Mycobacterium tuberculosis Rv2324 is a multifunctional feast/famine regulatory protein involved in growth, DNA replication and damage control. Int J Biol Macromol 252:126459 (2023)
...Ramachandran R
RgGuinier 2.7 nm
Dmax 11.6 nm
VolumePorod 156 nm3

SASDKQ7 – Probable transcriptional regulatory protein Lrp/AsnC protein Rv2324 in the presence of methionine

Probable transcriptional regulatory protein (Probably AsnC-family) experimental SAS data
DAMMIF model
Sample: Probable transcriptional regulatory protein (Probably AsnC-family) octamer, 143 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 20 mM Tris, 150 mM NaCl, 2 mM EDTA, 2 mM methionine, pH: 7.5
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Dec 5
Mycobacterium tuberculosis Rv2324 is a multifunctional feast/famine regulatory protein involved in growth, DNA replication and damage control. Int J Biol Macromol 252:126459 (2023)
...Ramachandran R
RgGuinier 4.0 nm
Dmax 13.8 nm
VolumePorod 246 nm3

SASDEU5 – Adenylation domain of DNA ligase A

DNA ligase A experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 38 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Sep 27
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are import... Acta Crystallographica Section D Structural Biology 77(6) (2021)
...Ramachandran R
RgGuinier 2.4 nm
Dmax 8.8 nm
VolumePorod 69 nm3

SASDHU5 – Heat shock protein 70 (PfHSP70-1)

Heat shock protein 70Peptide experimental SAS data
DAMFILT model
Sample: Heat shock protein 70 monomer, 74 kDa Plasmodium falciparum protein
Peptide monomer, 1 kDa synthetic construct protein
Buffer: 50mM Tris, 5mM MgCl2, 500mM KCl, 5mM Bme, 5% glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Oct 24
Structural-functional diversity of malaria parasite's PfHSP70-1 and PfHSP40 chaperone pair gives an edge over human orthologs in chaperone-assisted protein folding. Biochem J 477(18):3625-3643 (2020)
...Ramachandran R, Kumar N
RgGuinier 5.3 nm
Dmax 16.6 nm
VolumePorod 450 nm3

SASDDD8 – class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III

Probable exodeoxyribonuclease III protein XthA experimental SAS data
DAMMIF model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 32 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 12
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 2.4 nm
Dmax 7.3 nm
VolumePorod 56 nm3

SASDHR5 – Heat shock protein 40, subfamily A (PfHSP40)

HSP40, subfamily A experimental SAS data
DAMMIF model
Sample: HSP40, subfamily A dimer, 97 kDa Plasmodium falciparum protein
Buffer: 50 mM Tris, 5 mM MgCl2, 300 mM KCl, 1 mM β-mercaptoethanol, 5% glycerol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 Oct 24
Structural-functional diversity of malaria parasite's PfHSP70-1 and PfHSP40 chaperone pair gives an edge over human orthologs in chaperone-assisted protein folding. Biochem J 477(18):3625-3643 (2020)
...Ramachandran R, Kumar N
RgGuinier 4.3 nm
Dmax 15.0 nm
VolumePorod 339 nm3

SASDEC6 – Adenylation Domain of DNA ligase A with NAD+

DNA ligase A experimental SAS data
DAMMIF model
Sample: DNA ligase A monomer, 38 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Oct 6
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are import... Acta Crystallographica Section D Structural Biology 77(6) (2021)
...Ramachandran R
RgGuinier 2.4 nm
Dmax 6.2 nm
VolumePorod 94 nm3

SASDDN9 – Mycobacterium tuberculosis DNA Ligase A

DNA ligase A experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 5.2 nm
Dmax 16.7 nm
VolumePorod 870 nm3

SASDG65 – Adenylation domain of DNA ligase A (LigA)

DNA ligase A experimental SAS data
GASBOR model
Sample: DNA ligase A monomer, 37 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2019 May 21
Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are import... Acta Crystallographica Section D Structural Biology 77(6) (2021)
...Ramachandran R
RgGuinier 2.7 nm
Dmax 8.9 nm
VolumePorod 68 nm3

SASDDV9 – Mycobacterium tuberculosis DNA LigaseA with Nicked DNA

DNA ligase ANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Nicked DNA dimer, 16 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 4.4 nm
Dmax 14.8 nm
VolumePorod 262 nm3

SASDEW3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA)

DNA ligase AProbable exodeoxyribonuclease III protein XthA experimental SAS data
DAMMIF model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 6.2 nm
Dmax 23.9 nm
VolumePorod 662 nm3

SASDEX3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA

DNA ligase AProbable exodeoxyribonuclease III protein XthANicked DNA experimental SAS data
DAMFILT model
Sample: DNA ligase A monomer, 76 kDa Mycobacterium tuberculosis protein
Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
Nicked DNA monomer, 8 kDa DNA
Buffer: 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2017 May 13
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 4.5 nm
Dmax 17.1 nm
VolumePorod 117 nm3

SASDDQ8 – The complex formed between the class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III (XthA) bound to the BRCT domain from Mycobacterium tuberculosis DNA ligase

Probable exodeoxyribonuclease III protein XthAM. tb. LigA BRCT domain experimental SAS data
DAMFILT model
Sample: Probable exodeoxyribonuclease III protein XthA monomer, 33 kDa Mycobacterium tuberculosis protein
M. tb. LigA BRCT domain monomer, 15 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at BM29, ESRF on 2018 Mar 9
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 3.7 nm
Dmax 18.5 nm
VolumePorod 112 nm3

SASDD88 – The BRCT domain from Mycobacterium tuberculosis DNA ligase

M.tb. LigA BRCT domain (DNA ligase A) experimental SAS data
DAMMIN model
Sample: M.tb. LigA BRCT domain (DNA ligase A) monomer, 13 kDa Mycobacterium tuberculosis protein
Buffer: 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH: 8
Experiment: SAXS data collected at Anton Paar SAXSpace, CSIR-Central Drug Research Institute on 2018 Jun 2
M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision re... Nucleic Acids Res (2020)
...Ramachandran R
RgGuinier 1.6 nm
Dmax 3.7 nm
VolumePorod 23 nm3