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Yorodumi- PDB-2v1l: Structure of the conserved hypothetical protein VC1805 from patho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v1l | ||||||
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Title | Structure of the conserved hypothetical protein VC1805 from pathogenicity island VPI-2 of Vibrio cholerae O1 biovar eltor str. N16961 shares structural homology with the human P32 protein | ||||||
Components | HYPOTHETICAL PROTEIN | ||||||
Keywords | UNKNOWN FUNCTION / PATHOGENICITY ISLAND / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Protein of unknown function DUF2787 / Protein of unknown function DUF2787 / Protein of unknown function (DUF2787) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | VIBRIO CHOLERAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.13 Å | ||||||
Authors | Sheikh, M.A. / Potter, J.A. / Johnson, K.A. / Boyd, E.F. / Taylor, G.L. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal Structure of Vc1805, a Conserved Hypothetical Protein from a Vibrio Cholerae Pathogenicity Island, Reveals Homology to Human P32. Authors: Sheikh, M.A. / Potter, J.A. / Johnson, K.A. / Sim, R.B. / Boyd, E.F. / Taylor, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v1l.cif.gz | 34.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v1l.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 2v1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1l ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1l | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16846.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: O1 / Variant: BIOVAR ELTOR STR. N16961 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KR41 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→39.16 Å / Num. obs: 8131 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.13→2.25 Å / Redundancy: 9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 6.4 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.13→39.16 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.871 / SU B: 6.663 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.21 Å2
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Refinement step | Cycle: LAST / Resolution: 2.13→39.16 Å
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Refine LS restraints |
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