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Yorodumi- PDB-3px4: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3px4 | ||||||
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Title | Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar Conformation | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / TRANSFERASE-DNA complex / Cytosine-Adenine / closed conformation | ||||||
Function / homology | Function and homology information 5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.582 Å | ||||||
Authors | Wang, W. / Beese, L.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Authors: Wang, W. / Hellinga, H.W. / Beese, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3px4.cif.gz | 505.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3px4.ent.gz | 409.5 KB | Display | PDB format |
PDBx/mmJSON format | 3px4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3px4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3px4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3px4_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 3px4_validation.cif.gz | 89.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3px4 ftp://data.pdbj.org/pub/pdb/validation_reports/px/3px4 | HTTPS FTP |
-Related structure data
Related structure data | 3pv8C 3px0C 3px6C 3tanC 3tapC 3taqC 3tarC 3thvC 3ti0C 2hviS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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 , 1 types, 2 molecules AD
#1: Protein | Mass: 67490.289 Da / Num. of mol.: 2 Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment) Mutation: D598A, F710Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: polA, GK2730 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5KWC1, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 2635.751 Da / Num. of mol.: 2 / Fragment: DNA primer strand / Source method: obtained synthetically #3: DNA chain | Mass: 4040.647 Da / Num. of mol.: 2 / Fragment: DNA template strand / Source method: obtained synthetically |
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-Non-polymers , 4 types, 1473 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLU |
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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: 2.59 Å3/Da / Density % sol: 52.58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Ammonium Sulfate, MPD, MgSO4, MES, pH 5.8, vapor diffusion, hanging drop, temperature 290K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→100 Å / Num. all: 210662 / Num. obs: 200999 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 21.94 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 680-717 deleted Resolution: 1.582→71.099 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.47 / σ(F): 2.35 / Phase error: 22.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.522 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.582→71.099 Å
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Refine LS restraints |
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LS refinement shell |
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