+Open data
-Basic information
Entry | Database: PDB / ID: 4jr4 | ||||||
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Title | Crystal structure of Mtb DsbA (Oxidized) | ||||||
Components | Possible conserved membrane or secreted protein | ||||||
Keywords | OXIDOREDUCTASE / Thiol:disulfide oxidoreductase / Thioredoxin Fold / Disulfide bond formation / Membrane-anchored | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å | ||||||
Authors | Wang, L. | ||||||
Citation | Journal: Protein Cell / Year: 2013 Title: Structure analysis of the extracellular domain reveals disulfide bond forming-protein properties of Mycobacterium tuberculosis Rv2969c. Authors: Wang, L. / Li, J. / Wang, X. / Liu, W. / Zhang, X.C. / Li, X. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jr4.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jr4.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/4jr4 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/4jr4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23458.357 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 59-255 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2969c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: O33272 #2: Chemical | ChemComp-SO4 / #3: 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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 28% PEG 2000, 0.2M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate, pH 4.3, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 6.6 % / Av σ(I) over netI: 12.64 / Number: 97878 / Rmerge(I) obs: 0.141 / Χ2: 1.06 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 14886 / % possible obs: 97.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.498→50 Å / Num. obs: 14886 / % possible obs: 97.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.498→46.793 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8611 / SU ML: 0.28 / σ(F): 0 / Phase error: 20.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.424 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.53 Å2 / Biso mean: 29.435 Å2 / Biso min: 10.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.498→46.793 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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