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- PDB-2vqk: Crystal structure of PorB from Corynebacterium glutamicum (crysta... -

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Basic information

Entry
Database: PDB / ID: 2vqk
TitleCrystal structure of PorB from Corynebacterium glutamicum (crystal form IV)
ComponentsUNCHARACTERIZED PROTEIN CGL0972
KeywordsMEMBRANE PROTEIN / TRANSMEMBRANE / PORIN / MEMBRANE / TRANSPORT / ION TRANSPORT
Function / homologyPorin PorB/PorC / Alpha-helical PorB/PorC / Alpha helical Porin B / metal ion binding / CACODYLATE ION / PorB
Function and homology information
Biological speciesCORYNEBACTERIUM GLUTAMICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsZiegler, K. / Benz, R. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A Putative Alpha-Helical Porin from Corynebacterium Glutamicum.
Authors: Ziegler, K. / Benz, R. / Schulz, G.E.
History
DepositionMar 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UNCHARACTERIZED PROTEIN CGL0972
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,44710
Polymers10,6441
Non-polymers8039
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.370, 81.370, 80.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-1094-

ZN

21A-1095-

ZN

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Components

#1: Protein UNCHARACTERIZED PROTEIN CGL0972 / PORB / ANION-SPECIFIC PORIN / ANION-SPECIFIC PORIN PRECURSOR


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
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.95 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1.072
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 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 shellRedundancy: 20.3 % / Mean I/σ(I) obs: 6.9 / Rsym value: 0.55 / % possible all: 100

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→52.705 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.4186 --
obs0.4186 1307 98.9 %
Solvent computationBsol: 87.137 Å2 / ksol: 0.386603 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.019 Å25.286 Å20 Å2
2--0.019 Å20 Å2
3----0.038 Å2
Refinement stepCycle: LAST / Resolution: 4.2→52.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms531 0 21 0 552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3CACPARAMETERFILE.PARAM

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