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Yorodumi- PDB-4dto: RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dto | ||||||
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Title | RB69 DNA Polymerase Ternary Complex with dCTP Opposite an Abasic Site and ddA/dT as the Penultimate Base-pair | ||||||
Components |
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Keywords | Transferase/DNA / abasic site / THF / RB69pol / dATP / Transferase-DNA complex | ||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage RB69 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Xia, S. / Wang, J. / Konigsberg, W.H. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Authors: Xia, S. / Vashishtha, A. / Bulkley, D. / Eom, S.H. / Wang, J. / Konigsberg, W.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dto.cif.gz | 421.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dto.ent.gz | 336.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dto_validation.pdf.gz | 819.1 KB | Display | wwPDB validaton report |
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Full document | 4dto_full_validation.pdf.gz | 823.6 KB | Display | |
Data in XML | 4dto_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 4dto_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/4dto ftp://data.pdbj.org/pub/pdb/validation_reports/dt/4dto | HTTPS FTP |
-Related structure data
Related structure data | 4dtjC 4dtmC 4dtnC 4dtpC 4dtrC 4dtsC 4dtuC 4dtxC C: citing same article (ref.) |
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Similar structure data |
-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: 104490.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 5063.276 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#3: DNA chain | Mass: 3991.610 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 568 molecules
#4: Chemical | ChemComp-DCP / | ||
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#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM CaCl2, 15% (w/v) PEG 350 monomethyl ether (MME), 100 mM Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97198 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Oct 15, 2011 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97198 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. all: 78651 / Num. obs: 74651 / % possible obs: 94.9 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 1.3 |
Reflection shell | Resolution: 2.05→2.12 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.728 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 35.561 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.081 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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