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- PDB-4m3r: RB69 DNA polymerase ternary complex with dT/dG at position n-1 of... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m3r | ||||||
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Title | RB69 DNA polymerase ternary complex with dT/dG at position n-1 of primer/template duplex | ||||||
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![]() | HYDROLASE/DNA / RB69 pol / quadruple / dT/dG / n-1 / RB69 / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xia, S. / Konigsberg, W.H. | ||||||
![]() | ![]() Title: Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant. Authors: Xia, S. / Konigsberg, W.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 416.5 KB | Display | ![]() |
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PDB format | ![]() | 333.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.1 KB | Display | ![]() |
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Full document | ![]() | 808.5 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 53.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m3tC ![]() 4m3uC ![]() 4m3wC ![]() 4m3xC ![]() 4m3yC ![]() 4m3zC ![]() 4m41C ![]() 4m42C ![]() 4m45C C: citing same article ( |
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Similar structure data |
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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: 104448.867 Da / Num. of mol.: 1 / Mutation: D222A,D327A,L415A,L561A,S565G,Y567A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 4938.215 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Oligo was synthesized at keck facilities. (Yale University) |
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#3: DNA chain | Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Oligo was synthesized at keck facilities. (Yale University) |
-Non-polymers , 3 types, 440 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ATP / | ||
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#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 150 mM CaCl2, 12% (w/v) PEG 350 monomethyl ether (MME), and 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2012 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. all: 74231 / Num. obs: 63924 / % possible obs: 86.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 |
Reflection shell | Resolution: 2.07→2.15 Å / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 34.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→47.53 Å
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Refine LS restraints |
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