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Yorodumi- PDB-4oce: Crystal structure of the disulfide oxidoreductase DsbA from Prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oce | ||||||
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Title | Crystal structure of the disulfide oxidoreductase DsbA from Proteus mirabilis | ||||||
Components | Thiol:disulfide interchange protein | ||||||
Keywords | OXIDOREDUCTASE / Oxidative folding protein / virulence factor maturation protein / disulfide oxidoreductase / Thioredoxin fold / DsbA / Dithiol exchange / DsbB / Periplasmic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Proteus mirabilis HI4320 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 Å | ||||||
Authors | Kurth, F. / Martin, J.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Crystal Structure of the Dithiol Oxidase DsbA Enzyme from Proteus Mirabilis Bound Non-covalently to an Active Site Peptide Ligand. Authors: Kurth, F. / Duprez, W. / Premkumar, L. / Schembri, M.A. / 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 | 4oce.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oce.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 4oce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oce_validation.pdf.gz | 425.5 KB | Display | wwPDB validaton report |
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Full document | 4oce_full_validation.pdf.gz | 425.5 KB | Display | |
Data in XML | 4oce_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 4oce_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/4oce ftp://data.pdbj.org/pub/pdb/validation_reports/oc/4oce | HTTPS FTP |
-Related structure data
Related structure data | 4ocfC 4od7C 1dsbS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 21027.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis HI4320 (bacteria) / Strain: HI4320 / Gene: dsbA, PMI2828 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B4EZ68 |
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#2: Chemical | ChemComp-MLI / |
#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: 2.54 Å3/Da / Density % sol: 51.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG3350, Sodium Malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2011 |
Radiation | Monochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 |
Reflection | Resolution: 1.768→42.64 Å / Num. all: 22817 / Num. obs: 22817 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.768→1.86 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3207 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DSB Resolution: 1.768→37.53 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 13.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.768→37.53 Å
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Refine LS restraints |
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LS refinement shell |
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