+Open data
-Basic information
Entry | Database: PDB / ID: 6wvf | |||||||||||||||||||||
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Title | E.coli DsbB C104S with ubiquinone | |||||||||||||||||||||
Components | Green fluorescent protein,Disulfide bond formation protein B,Green fluorescent protein | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Disulfide bond formation protein B(DsbB) / Disulfide bond / Disulfide oxidoreductase | |||||||||||||||||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor / protein-disulfide reductase activity / ubiquinone binding / serine-type endopeptidase inhibitor activity / protein folding / response to heat / electron transfer activity / extracellular space / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Aequorea victoria (jellyfish) Escherichia coli (E. coli) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Liu, S. / Li, W. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Sci Adv / Year: 2020 Title: Termini restraining of small membrane proteins enables structure determination at near-atomic resolution. Authors: Liu, S. / Li, S. / Yang, Y. / Li, W. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wvf.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wvf.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 6wvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wvf_validation.pdf.gz | 665.9 KB | Display | wwPDB validaton report |
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Full document | 6wvf_full_validation.pdf.gz | 672.2 KB | Display | |
Data in XML | 6wvf_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6wvf_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/6wvf ftp://data.pdbj.org/pub/pdb/validation_reports/wv/6wvf | HTTPS FTP |
-Related structure data
Related structure data | 6wvdC 6wveC 2b3pS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 45408.066 Da / Num. of mol.: 1 / Mutation: C8A,C49V,C104S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Escherichia coli (E. coli) Gene: GFP, dsbB, roxB, ycgA, b1185, JW5182 / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: P0A6M2 |
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#2: Chemical | ChemComp-UQ1 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-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: 51.63 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / Details: 34% PEG 400, 60 mM NaCl, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.68→46.23 Å / Num. obs: 13571 / % possible obs: 97.6 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.082 / Rrim(I) all: 0.203 / Net I/σ(I): 9.1 / Num. measured all: 79211 / Scaling rejects: 6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 2.9→46.23 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 245.24 Å2 / Biso mean: 113.0847 Å2 / Biso min: 57.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→46.23 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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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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