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- PDB-3b0y: K263D mutant of PolX from Thermus thermophilus HB8 complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b0y | ||||||
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Title | K263D mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP | ||||||
![]() | DNA polymerase beta family (X family) | ||||||
![]() | 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 | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Nakane, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.5 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.8 KB | Display | ![]() |
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Full document | ![]() | 787.1 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 42.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3au2SC ![]() 3au6C ![]() 3auoC ![]() 3b0xC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64190.387 Da / Num. of mol.: 1 / Mutation: K263D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 528 molecules ![](data/chem/img/DGT.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DGT / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.78 % |
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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: ![]() ![]() ![]() |
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: 0.04 / Number: 387360 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 103603 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 3.081 / Rsym value: 0.322 / % possible all: 100 |
Cell measurement | Reflection used: 387360 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AU2 Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.211 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.938 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.069 / 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: 56.54 Å2 / Biso mean: 21.4292 Å2 / Biso min: 7.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→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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