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Yorodumi- PDB-3ey8: Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ey8 | ||||||
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Title | Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1 | ||||||
Components | Biphenyl-2,3-diol 1,2-dioxygenase III-related protein | ||||||
Keywords | OXIDOREDUCTASE / Integron Cassette protein / Dioxygenase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. ...Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure from the mobile metagenome of V. Pseudocholerae. VPC_CASS1 Authors: Harrop, S.J. / Deshpande, C.N. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Chang, C. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Curmi, P.M.G. / Mabbutt, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ey8.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ey8.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ey8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3ey8 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3ey8 | HTTPS FTP |
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-Related structure data
Related structure data | 3ey7S S: Starting model for refinement |
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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: 14963.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0328, VC_A0341, VC_A0463 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q9K3D3 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.75 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: 25% Peg 3350 0.2M LiSo4 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 7, 2008 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26.23 Å / Num. obs: 27068 / % possible obs: 84.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.5 / Redundancy: 7 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 40.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 17.4 / Num. unique all: 1755 / Rsym value: 0.089 / % possible all: 38.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EY7 Resolution: 1.6→26.228 Å / SU ML: 0.14 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.508 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→26.228 Å
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LS refinement shell |
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