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Yorodumi- PDB-3ndk: RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ndk | ||||||
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Title | RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG | ||||||
Components |
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Keywords | TRANSFERASE/DNA / RB69 DNA polymerase / fidelity / Mutation Frequencies / Kinetics / 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 / 3'-5'-DNA exonuclease activity / DNA replication proofreading / 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 / 3'-5'-DNA exonuclease activity / DNA replication proofreading / 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 Å | ||||||
Authors | Wang, M. / Wang, J. / Konigsberg, W.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. Authors: Xia, S. / Wang, M. / Lee, H.R. / Sinha, A. / Blaha, G. / Christian, T. / Wang, J. / Konigsberg, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ndk.cif.gz | 244.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndk.ent.gz | 186.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ndk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ndk_validation.pdf.gz | 791.7 KB | Display | wwPDB validaton report |
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Full document | 3ndk_full_validation.pdf.gz | 795.7 KB | Display | |
Data in XML | 3ndk_validation.xml.gz | 42 KB | Display | |
Data in CIF | 3ndk_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndk ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndk | HTTPS FTP |
-Related structure data
Related structure data | 3ne6C 3ngiC 3nhgC 3nciS S: Starting model for refinement 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: 104563.047 Da / Num. of mol.: 1 / Mutation: D222A, D327A, Y567A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 5541.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA strand |
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#3: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA strand |
-Non-polymers , 3 types, 883 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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 293 K / Method: micro-batch vapor-diffusion / pH: 6.5 Details: 10% (w/v) PEG 350 monomethyl ether (MME), 175 mM CaCl2, 100 mM NaCacodylate (pH 6.5), micro-batch vapor-diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 80523 / Num. obs: 76738 / % possible obs: 95.3 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.879 / Mean I/σ(I) obs: 1.18 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NCI Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.351 / SU ML: 0.119 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 28.679 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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