+Open data
-Basic information
Entry | Database: PDB / ID: 2hi7 | ||||||
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Title | Crystal structure of DsbA-DsbB-ubiquinone complex | ||||||
Components |
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Keywords | OXIDOREDUCTASE / disulfide bond / redox / DsbB / membrane protein / ubiquinone / oxidative protein folding | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / cellular response to antibiotic / protein disulfide isomerase activity / ubiquinone binding / protein-disulfide reductase activity / protein folding / outer membrane-bounded periplasmic space / response to heat / electron transfer activity / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.7 Å | ||||||
Authors | Inaba, K. / Murakami, S. / Suzuki, M. / Nakagawa, A. / Yamashita, E. / Okada, K. / Ito, K. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Crystal Structure of the DsbB-DsbA Complex Reveals a Mechanism of Disulfide Bond Generation Authors: Inaba, K. / Murakami, S. / Suzuki, M. / Nakagawa, A. / Yamashita, E. / Okada, K. / Ito, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hi7.cif.gz | 74 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hi7.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hi7 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hi7 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 21122.959 Da / Num. of mol.: 1 / Mutation: C33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE70 (QIAGEN) / Production host: Escherichia coli (E. coli) References: UniProt: P0AEG4, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor |
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#2: Protein | Mass: 20106.982 Da / Num. of mol.: 1 / Mutation: C8A,C49V,C130S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pQE70 (QIAGEN) / Production host: Escherichia coli (E. coli) References: UniProt: P0A6M2, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-UQ1 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.471755 Å3/Da / Density % sol: 77.52092 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: JeffamimeED2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Sep 22, 2005 / Details: Rh-coated mirror |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→61.2 Å / Num. obs: 10332 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 6.9 % / Biso Wilson estimate: 140.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3.7→3.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1450 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.7→20 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.901 / SU B: 54.5 / SU ML: 0.835 / Cross valid method: THROUGHOUT / ESU R Free: 0.705 / 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: 185.155 Å2
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Refinement step | Cycle: LAST / Resolution: 3.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.7→4.039 Å / Total num. of bins used: 6
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