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Yorodumi- PDB-3s9h: RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s9h | ||||||
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Title | RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) ternary complex with dUpNpp and a dideoxy-terminated primer in the presence of Ca2+ | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA binding / 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: 1.95 Å | ||||||
Authors | Wang, M. / Wang, J. / Konigsberg, W.H. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Authors: Xia, S. / Wang, M. / Blaha, G. / Konigsberg, W.H. / Wang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s9h.cif.gz | 439.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s9h.ent.gz | 351.3 KB | Display | PDB format |
PDBx/mmJSON format | 3s9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s9h_validation.pdf.gz | 831.5 KB | Display | wwPDB validaton report |
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Full document | 3s9h_full_validation.pdf.gz | 842.5 KB | Display | |
Data in XML | 3s9h_validation.xml.gz | 47 KB | Display | |
Data in CIF | 3s9h_validation.cif.gz | 73.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/3s9h ftp://data.pdbj.org/pub/pdb/validation_reports/s9/3s9h | HTTPS FTP |
-Related structure data
Related structure data | 3scxC 3si6C 3sjjC 3snnC 3spyC 3spzC 3sq0C 3sq1C 1ig9S 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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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: template DNA strand |
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#2: DNA chain | Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer DNA strand |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 104490.945 Da / Num. of mol.: 1 / Mutation: D222A,D327A,L561A,S565G,Y567A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Plasmid: pET 21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 1163 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-DUP / | #6: 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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch vapor diffusion / pH: 6.5 Details: 150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.21448 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.21448 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→100 Å / Num. all: 86562 / Num. obs: 83597 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.73 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 0.934 / Num. unique all: 9629 / % possible all: 57.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IG9 Resolution: 1.95→63.63 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.858 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.16 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
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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: 33.447 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→63.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 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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