[English] 日本語
Yorodumi- PDB-2vwj: Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vwj | ||||||
---|---|---|---|---|---|---|---|
Title | Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. | ||||||
Components |
| ||||||
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: 2.78 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vwj.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vwj.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/2vwj ftp://data.pdbj.org/pub/pdb/validation_reports/vw/2vwj | HTTPS FTP |
---|
-Related structure data
Related structure data | 2vwkC 1tgoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 89936.305 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOCOCCUS GORGONARIUS (archaea) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56689, DNA-directed DNA polymerase | ||||||
---|---|---|---|---|---|---|---|
#2: DNA chain | Mass: 8005.138 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | MUTATION OF D215 TO ALANINE TO REMOVE EXONUCLEAS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 76 % / Description: NONE |
---|---|
Crystal grow | pH: 8.3 / Details: 0.2M TRIPOTASSIUM CITRATE PH8.3, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD Details: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→30 Å / Num. obs: 45193 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.78→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TGO Resolution: 2.78→67.73 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.645 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 52.83 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→67.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|