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Yorodumi- PDB-3fy6: Structure from the mobile metagenome of V. Cholerae. Integron cas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fy6 | ||||||
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Title | Structure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS3 | ||||||
Components | Integron cassette protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel / Integron cassette protein / Vibrio cholerae / Oyster pond / Woodshole / USA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Integron cassette protein fold / Integron cassette protein superfamily / 2-Layer Sandwich / Alpha Beta / Integron cassette protein Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Tan, K. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Tan, K. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Integron gene cassettes: a repository of novel protein folds with distinct interaction sites. Authors: Sureshan, V. / Deshpande, C.N. / Boucher, Y. / Koenig, J.E. / Stokes, H.W. / Harrop, S.J. / Curmi, P.M. / 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 | 3fy6.cif.gz | 212.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fy6.ent.gz | 179.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/3fy6 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/3fy6 | HTTPS FTP |
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-Related structure data
Related structure data | 3fuyC 3fxhC 3if4C 3imoC 3jrtC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15325.311 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OPVCH_OP8A / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1E6*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.68 % |
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Crystal grow | Method: vapor diffusion / pH: 4.6 Details: 0.1M sodium acetate , 2.0M sodium Formate, pH 4.6, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→74.43 Å / Num. all: 33584 / Num. obs: 33584 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.992 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.13 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3 / Rsym value: 0.508 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.867 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 0.94 / Phase error: 20.65 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.126 Å2 / ksol: 0.389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.867 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain D |