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Yorodumi- PDB-3auo: DNA polymerase X from Thermus thermophilus HB8 ternary complex wi... -
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-Basic information
Entry | Database: PDB / ID: 3auo | ||||||
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Title | DNA polymerase X from Thermus thermophilus HB8 ternary complex with 1-nt gapped DNA and ddGTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / RSGI / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / POLXc domain / PHP domain / DNA polymerase / dRP lyase / AP endonuclease / 3'-5' exonuclease / DNA repair / DNA binding / nucleotide binding / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information phosphoric ester hydrolase activity / bacterial-type flagellum-dependent swarming motility / DNA-(apurinic or apyrimidinic site) lyase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Nakane, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA. Authors: Nakane, S. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3auo.cif.gz | 266.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3auo.ent.gz | 209.2 KB | Display | PDB format |
PDBx/mmJSON format | 3auo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3auo_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3auo_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3auo_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 3auo_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3auo ftp://data.pdbj.org/pub/pdb/validation_reports/au/3auo | HTTPS FTP |
-Related structure data
Related structure data | 3au2SC 3au6C 3b0xC 3b0yC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 4 molecules ABDE
#1: Protein | Mass: 64204.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: PolX, TTHA1150 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2/pLysS / References: UniProt: Q5SJ64, DNA-directed DNA polymerase #2: DNA chain | Mass: 8843.667 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 142 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: 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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 25, 2010 |
Diffraction measurement | Details: 0.50 degrees, 11.2 sec, detector distance 270.00 mm Method: \w scans |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.136 / Number: 276998 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 37457 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 15.619 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 3.524 / Rsym value: 0.567 / % possible all: 100 |
Cell measurement | Reflection used: 276998 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AU2 Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.232 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.167 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.5 Å2 / Biso mean: 34.1472 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 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: 20
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