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Yorodumi- PDB-2vqk: Crystal structure of PorB from Corynebacterium glutamicum (crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqk | ||||||
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Title | Crystal structure of PorB from Corynebacterium glutamicum (crystal form IV) | ||||||
Components | UNCHARACTERIZED PROTEIN CGL0972 | ||||||
Keywords | MEMBRANE PROTEIN / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT | ||||||
Function / homology | Porin PorB/PorC / Alpha-helical PorB/PorC / Alpha helical Porin B / metal ion binding / CACODYLATE ION / PorB Function and homology information | ||||||
Biological species | CORYNEBACTERIUM GLUTAMICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Ziegler, K. / Benz, R. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: A Putative Alpha-Helical Porin from Corynebacterium Glutamicum. Authors: Ziegler, K. / Benz, R. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vqk.cif.gz | 21.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqk.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vqk_validation.pdf.gz | 430.9 KB | Display | wwPDB validaton report |
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Full document | 2vqk_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 2vqk_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 2vqk_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqk ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqk | HTTPS FTP |
-Related 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: 10643.550 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-126 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CORYNEBACTERIUM GLUTAMICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8NRS3 | ||
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#2: Chemical | #3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.95 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1.072 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→52.705 Å / Num. obs: 1307 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 18.7 % / Rsym value: 0.12 / Net I/σ(I): 16.3 |
Reflection shell | Redundancy: 20.3 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.55 / % possible all: 100 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→52.705 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 87.137 Å2 / ksol: 0.386603 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4.2→52.705 Å
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Refine LS restraints |
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Xplor file |
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