+Open data
-Basic information
Entry | Database: PDB / ID: 7vw0 | ||||||
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Title | Structure of a dimeric periplasmic protein | ||||||
Components | DUF305 domain-containing protein | ||||||
Keywords | METAL BINDING PROTEIN / Copper binding protein / Metal homeostasis | ||||||
Function / homology | Domain of unknown function DUF305, CopM-like / Domain of unknown function (DUF305) / Ferritin-like / DUF305 domain-containing protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.447 Å | ||||||
Authors | Yang, J. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Inorg.Biochem. / Year: 2022 Title: Structural basis of copper binding by a dimeric periplasmic protein forming a six-helical bundle. Authors: Yang, J. / Gao, M. / Wang, J. / He, C. / Wang, X. / Liu, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vw0.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vw0.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vw0_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 7vw0_full_validation.pdf.gz | 432.8 KB | Display | |
Data in XML | 7vw0_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 7vw0_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/7vw0 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/7vw0 | HTTPS FTP |
-Related structure data
Related structure data | 7vw1C 7vw2C 5ffbS 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: 12089.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: O2R_94 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6EME5 #2: 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: 2.07 Å3/Da / Density % sol: 40.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: MES, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.447→50 Å / Num. obs: 35568 / % possible obs: 97.3 % / Redundancy: 12.5 % / Biso Wilson estimate: 21.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.035 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Num. unique obs: 3440 / CC1/2: 0.87 / Rpim(I) all: 0.328 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FFB Resolution: 1.447→20.435 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.1 / 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: 108.79 Å2 / Biso mean: 36.4367 Å2 / Biso min: 18.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.447→20.435 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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