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Yorodumi- PDB-3lzi: RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lzi | ||||||
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Title | RB69 DNA Polymerase (Y567A) ternary complex with dATP Opposite 7,8-dihydro-8-oxoguanine | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / replication fidelity / 7 / 8-dihydro-8-oxoguanine / Polymerase-DNA-dNTP ternary complex / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / 3'-5' exonuclease activity / DNA replication / 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: 2.3 Å | ||||||
Authors | Wang, M. / Beckman, J. / Blaha, G. / Wang, J. / Konigsberg, W.H. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Substitution of Ala for Tyr567 in RB69 DNA polymerase allows dAMP to be inserted opposite 7,8-dihydro-8-oxoguanine . Authors: Beckman, J. / Wang, M. / Blaha, G. / 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 | 3lzi.cif.gz | 222.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lzi.ent.gz | 171.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/3lzi ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lzi | HTTPS FTP |
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-Related structure data
Related structure data | 3lzjC 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
-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: pET 21b / 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: 5557.591 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, 182 molecules
#4: Chemical | ChemComp-DTP / | ||
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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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 293.15 K / Method: micro-batch vapor-diffusion / pH: 6.5 Details: 150 mM CaCl2, 11%(w/v) PEG 350 monomethyl ether MME, and 100 mM Na Cacodylate pH 6.5 , micro-batch 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: 1.075 Å |
Detector | Type: Q315 / Detector: CCD / Date: Oct 1, 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: 2.3→50 Å / Num. obs: 51799 / % possible obs: 95.3 % / Observed criterion σ(I): 0.95 / Redundancy: 4.2 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.32 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.945 / Num. unique all: 4177 / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1IG9 Resolution: 2.3→38.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.337 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.251 / 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: 40.606 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→38.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 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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