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Yorodumi- PDB-4k6x: Crystal structure of disulfide oxidoreductase from Mycobacterium ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4k6x | ||||||
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Title | Crystal structure of disulfide oxidoreductase from Mycobacterium tuberculosis | ||||||
Components | Disulfide oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / DsbA / Disulfide oxidase / VKOR / Thioredoxin fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.972 Å | ||||||
Authors | Premkumar, L. / Martin, J.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases. Authors: Premkumar, L. / Heras, B. / Duprez, W. / Walden, P. / Halili, M. / Kurth, F. / Fairlie, D.P. / Martin, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k6x.cif.gz | 228.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k6x.ent.gz | 196.9 KB | Display | PDB format |
PDBx/mmJSON format | 4k6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k6x_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 4k6x_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 4k6x_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4k6x_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/4k6x ftp://data.pdbj.org/pub/pdb/validation_reports/k6/4k6x | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22275.945 Da / Num. of mol.: 2 / Fragment: UNP residues 52-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2969c / Production host: Escherichia coli (E. coli) / References: UniProt: O33272 #2: Chemical | ChemComp-EPE / | #3: Chemical | ChemComp-DIO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Na Malonate, 1,4-dioxane and polyvinylpyrrolidone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | ||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2012 | ||||||||||||||||||
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.97→85.6 Å / Num. all: 35185 / Num. obs: 35185 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.9 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.972→59.324 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 17.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.972→59.324 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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