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Yorodumi- PDB-3jrt: Structure from the mobile metagenome of V. paracholerae: Integron... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jrt | ||||||
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Title | Structure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2 | ||||||
Components | Integron cassette protein Vpc_cass2 | ||||||
Keywords | Structural Genomics / Unknown function / Integron cassette protein / Vibrio paracholerae / Mobile metagenome / PSI-2 Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Four Helix Bundle (Hemerythrin (Met), subunit A) - #1060 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | Vibrio paracholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Harrop, S.J. / Deshpande, C. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Cuff, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. ...Harrop, S.J. / Deshpande, C. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Cuff, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / 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 | 3jrt.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jrt.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jrt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jrt_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 3jrt_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 3jrt_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3jrt_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/3jrt ftp://data.pdbj.org/pub/pdb/validation_reports/jr/3jrt | HTTPS FTP |
-Related structure data
Related structure data | 3fuyC 3fxhC 3fy6C 3if4C 3imoC 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: 22282.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio paracholerae (bacteria) / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL |
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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: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 20% PEG3350, 0.2 M disodium tartrate. In situ proteolysis with chymotrypsin, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-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 25, 2008 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.003 Å / Num. all: 8801 / Num. obs: 8801 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / Num. measured all: 18536 / Num. unique all: 1281 / Rsym value: 0.473 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→27.99 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.31 / Isotropic thermal model: TLS and individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 22.09 / 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: 60.884 Å2 / ksol: 0.305 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 396.66 Å2 / Biso mean: 66.901 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 14.2965 Å / Origin y: 29.3796 Å / Origin z: 15.5965 Å
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Refinement TLS group |
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