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Yorodumi- PDB-2vqh: Crystal structure of PorB from Corynebacterium glutamicum (crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vqh | ||||||
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Title | Crystal structure of PorB from Corynebacterium glutamicum (crystal form II) | ||||||
Components | PUTATIVE UNCHARACTERIZED PROTEIN CGL0972 | ||||||
Keywords | MEMBRANE PROTEIN / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CORYNEBACTERIUM GLUTAMICUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vqh.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vqh.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/2vqh ftp://data.pdbj.org/pub/pdb/validation_reports/vq/2vqh | HTTPS FTP |
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-Related structure data
-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
#1: Protein | Mass: 10643.550 Da / Num. of mol.: 2 / 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 #2: Chemical | ChemComp-ZN / #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.58 Å3/Da / Density % sol: 65.68 % / 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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→70.53 Å / Num. obs: 7663 / % possible obs: 99.2 % / Observed criterion σ(I): 3 / Redundancy: 20.3 % / Rsym value: 0.08 / Net I/σ(I): 28.8 |
Reflection shell | Redundancy: 21.4 % / Mean I/σ(I) obs: 8.1 / Rsym value: 0.48 / % possible all: 100 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→70.53 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.913 / SU B: 21.338 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.482 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→70.53 Å
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Refine LS restraints |
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