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- PDB-2vwk: Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray ... -
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Open data
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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 | ||||||
![]() | DNA POLYMERASE | ||||||
![]() | DNA REPLICATION / MULTIFUNCTIONAL ENZYME / NUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / TRANSFERASE / EXONUCLEASE / DNA-BINDING / DNA POLYMERASE / URACIL / ARCHAEA / NUCLEASE / HYDROLASE / DNA REPAIR | ||||||
Function / homology | ![]() nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Firbank, S.J. / Wardle, J. / Heslop, P. / Lewis, R.J. / Connolly, B.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.5 KB | Display | ![]() |
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PDB format | ![]() | 127.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.4 KB | Display | ![]() |
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Full document | ![]() | 445.5 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vwjC ![]() 1tgoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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