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Yorodumi- PDB-2vwk: Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vwk | ||||||
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Title | Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q polymerase variant | ||||||
Components | DNA POLYMERASE | ||||||
Keywords | DNA REPLICATION / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / TRANSFERASE / EXONUCLEASE / DNA-BINDING / DNA POLYMERASE / URACIL / ARCHAEA / NUCLEASE / HYDROLASE / DNA REPAIR | ||||||
Function / homology | Function and homology information exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | THERMOCOCCUS GORGONARIUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Firbank, S.J. / Wardle, J. / Heslop, P. / Lewis, R.J. / Connolly, B.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Uracil Recognition in Archaeal DNA Polymerases Captured by X-Ray Crystallography. Authors: Firbank, S.J. / Wardle, J. / Heslop, P. / Lewis, R.J. / Connolly, B.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vwk.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vwk.ent.gz | 127.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwk ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwk | HTTPS FTP |
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-Related structure data
Related structure data | 2vwjC 1tgoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89965.305 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS GORGONARIUS (archaea) / Plasmid: PET 17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56689, DNA-directed DNA polymerase | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | V93 MUTATED TO GLUTAMINE - A MUTATION WHICH PREVENTS THE RECOGNITION OF URACIL BY THE POLYMERASE. ...V93 MUTATED TO GLUTAMINE - A MUTATION WHICH PREVENTS THE RECOGNITIO | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.8 % Description: ESSENTIALLY ISOMORPHOUS WITH 1TGO, THEREFORE 1TGO USED AS STARTING MODEL FOR RIGID BODY REFINEMENT. |
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Crystal grow | pH: 5.5 / Details: 1.9M AMMONIUM SULPHATE, 100MM BIS-TRIS, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Details: DIAMOND AND GE(220) |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→62 Å / Num. obs: 29945 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TGO Resolution: 2.6→51 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.87 / SU B: 11.314 / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.738 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→51 Å
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Refine LS restraints |
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