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Yorodumi- PDB-3b0x: K263A mutant of PolX from Thermus thermophilus HB8 complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b0x | ||||||
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Title | K263A mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP | ||||||
Components | DNA polymerase beta family (X family) | ||||||
Keywords | TRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / POLXc / PHP / DNA polymerase / dRP lyase / 3'-5' exonuclease / AP endonuclease / DNA repair / nucleotide / DNA | ||||||
Function / homology | Function and homology information DNA-(apurinic or apyrimidinic site) lyase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 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 | 3b0x.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b0x.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/3b0x ftp://data.pdbj.org/pub/pdb/validation_reports/b0/3b0x | HTTPS FTP |
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-Related structure data
Related structure data | 3au2SC 3au6C 3auoC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64146.379 Da / Num. of mol.: 1 / Mutation: K263A 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 |
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-Non-polymers , 5 types, 559 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-DGT / | #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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2M potassium chloride, 0.01M calcium chloride, 0.005M sodium cacodylate (pH 6.0), 10% polyethylene glycol 4000 (v/v), 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: Jun 10, 2011 |
Diffraction measurement | Details: 0.50 degrees, 4.7 sec, detector distance 120.00 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: 0.044 / Number: 466387 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 125330 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 26.642 |
Reflection shell | Resolution: 1.36→1.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.009 / Rsym value: 0.258 / % possible all: 99.6 |
Cell measurement | Reflection used: 466387 |
-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: 1.36→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.445 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.057 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.16 Å2 / Biso mean: 20.4946 Å2 / Biso min: 6.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→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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