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Yorodumi- PDB-1zbp: X-Ray Crystal Structure of Protein VPA1032 from Vibrio parahaemol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zbp | ||||||
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Title | X-Ray Crystal Structure of Protein VPA1032 from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium Target VpR44 | ||||||
Components | hypothetical protein VPA1032Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information Type VI secretion system accessory component TagJ / ImpE protein / : / Tetratricopeptide repeat domain / TPR repeat region circular profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Vibrio parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Forouhar, F. / Yong, W. / Vorobiev, S.M. / Ciao, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.STRUCT.FUNCT.GENOM. / Year: 2007 Title: Functional insights from structural genomics. Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zbp.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zbp.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 1zbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/1zbp ftp://data.pdbj.org/pub/pdb/validation_reports/zb/1zbp | HTTPS FTP |
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-Related structure data
Related structure data | 1rtyC 1sqsC 1tm0C 2hd3C 2nv4C 2oysC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30829.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q87HD3 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM sodium cacodylate, 20% PEG8K, 200 mM magnesium acetate, 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 28906 / Num. obs: 28733 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.036 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 3.71 / Rsym value: 0.314 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.4→25.06 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 356841.5 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.6572 Å2 / ksol: 0.321776 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→25.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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