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Yorodumi- PDB-3cfr: Structure of the replicating complex of a POL Alpha family DNA Po... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cfr | ||||||
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Title | Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 2 | ||||||
Components |
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Keywords | Transferase/DNA / DNA POLYMERASE / CATALYTIC COMPLEX / FIDELITY / TWO METAL ION MECHANISM / 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 | BACTERIOPHAGE RB69 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Wang, J. / Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H. | ||||||
Citation | Journal: To be Published Title: Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant Authors: Klimenko, D. / Wang, M. / Steitz, T.A. / Konigsberg, W.H. / Wang, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: Crystal structure of a POL Alpha family replicative DNA Polymerase from bacteriophage RB69 Authors: Wang, J. / Sattar, A.K. / Wang, C.C. / Karam, J.D. / Konigsberg, W.H. / Steitz, T.A. / Franklin, M.C. #2: Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Structure of the replication complex of a POL Alpha family DNA Polymerase Authors: Franklin, M.C. / Wang, J. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cfr.cif.gz | 231.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cfr.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cfr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cfr_validation.pdf.gz | 800.9 KB | Display | wwPDB validaton report |
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Full document | 3cfr_full_validation.pdf.gz | 817.3 KB | Display | |
Data in XML | 3cfr_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 3cfr_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cf/3cfr ftp://data.pdbj.org/pub/pdb/validation_reports/cf/3cfr | HTTPS FTP |
-Related structure data
Related structure data | 3cfoC 3cfpC 1ig9S 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
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 5525.592 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SYNTHEsized by W.M. KECK FACILITY AT YALE UNIVERSITY |
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#2: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: SYNTHEsized by W.M. KECK FACILITY AT YALE UNIVERSITY |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 105407.852 Da / Num. of mol.: 1 / Mutation: L561A, S565G, Y567A Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE RB69 (virus) / Gene: 43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-Non-polymers , 4 types, 636 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-TTP / | #7: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.73 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7% PEG350 monomethyl ether, 0.1M NA CACODYLATE, 0.1 M CA2CL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A |
Detector | Detector: CCD / Date: Aug 2, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 46306 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.187 |
Reflection shell | Resolution: 2.4→2.7 Å / Redundancy: 6.3 % / Num. unique all: 13614 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IG9 Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 17.685 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.452 / ESU R Free: 0.289 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.912 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.466 Å / Total num. of bins used: 20
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