+Open data
-Basic information
Entry | Database: PDB / ID: 6a2q | ||||||
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Title | Mycobacterium tuberculosis LexA C-domain I | ||||||
Components | LexA repressorRepressor lexA | ||||||
Keywords | HYDROLASE / Mycobacterium tuberculosis / LexA / SOS response | ||||||
Function / homology | Function and homology information repressor LexA / SOS response / peptidoglycan-based cell wall / DNA replication / response to antibiotic / serine-type endopeptidase activity / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Chandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Biochemical characterization of Mycobacterium tuberculosis LexA and structural studies of its C-terminal segment. Authors: Chandran, A.V. / Srikalaivani, R. / Paul, A. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a2q.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a2q.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 6a2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/6a2q ftp://data.pdbj.org/pub/pdb/validation_reports/a2/6a2q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12826.729 Da / Num. of mol.: 1 / Fragment: LexA C-domain I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: lexA, Rv2720, MTCY05A6.41 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHR7, repressor LexA |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.63 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / Details: Tris-Hcl, Glycerol, Pentaerythritol ethoxylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→22.82 Å / Num. obs: 21096 / % possible obs: 99.7 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.48→1.48 Å / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 14.5 / Num. unique obs: 2992 / CC1/2: 0.917 / Rpim(I) all: 0.275 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IUMU Resolution: 1.48→22.82 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.864 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.567 Å2
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Refinement step | Cycle: 1 / Resolution: 1.48→22.82 Å
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Refine LS restraints |
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