+Open data
-Basic information
Entry | Database: PDB / ID: 2qwv | ||||||
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Title | Crystal structure of unknown function protein VCA1059 | ||||||
Components | UPF0217 protein VC_A1059 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Vibrio cholerae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information tRNA methyltransferase activity / tRNA methylation / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Chang, C. / Sather, A. / Moy, S. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of unknown function protein VCA1059. Authors: Chang, C. / Sather, A. / Moy, S. / Freeman, L. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qwv.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qwv.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 2qwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/2qwv ftp://data.pdbj.org/pub/pdb/validation_reports/qw/2qwv | 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: 23551.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar eltor str. N16961 (bacteria) Species: Vibrio cholerae / Strain: El Tor Inaba N16961 / Gene: VC_A1059 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KKP3 #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: 2.68 Å3/Da / Density % sol: 54.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 35% Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2007 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 30250 / Num. obs: 28834 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 59.191 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 35.58 |
Reflection shell | Resolution: 2.6→2.62 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 6.19 / Num. unique all: 319 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→41.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 14.271 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Bijvoet differences were used for phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.333 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→41.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.665 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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