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Yorodumi- PDB-3gk6: Crystal structure from the mobile metagenome of Vibrio cholerae. ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gk6 | ||||||
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Title | Crystal structure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS2. | ||||||
Components | Integron cassette protein VCH_CASS2 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel / Integron cassette protein / Vibrio cholerae / Oyster pond / Woods hole / USA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Chang, C. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Chang, C. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module. Authors: Deshpande, C.N. / Harrop, S.J. / Boucher, Y. / Hassan, K.A. / Leo, R.D. / Xu, X. / Cui, H. / Savchenko, A. / Chang, C. / Labbate, M. / Paulsen, I.T. / Stokes, H.W. / 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 | 3gk6.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gk6.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gk6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/3gk6 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/3gk6 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 19482.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: OPVCH_OP4G / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX23*PLUS |
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#2: Chemical | ChemComp-PE4 / |
#3: 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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 0.1M Citric acid, 25% PEG 3350, pH 3.5, 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: 0.97953 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.89 Å / Num. all: 34832 / Num. obs: 34832 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 27.219 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.079 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2650 / Rsym value: 0.624 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→35.041 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.411 Å2 / ksol: 0.408 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→35.041 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: 13
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Refinement TLS params. | Method: refined / Origin x: 15.3857 Å / Origin y: 29.826 Å / Origin z: 29.2665 Å
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Refinement TLS group | Selection details: chain A |