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Yorodumi- PDB-3rmc: Crystal Structure of a replicative DNA polymerase bound to DNA co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rmc | ||||||
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Title | Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA LESION / THYMINE GLYCOL / PROTEIN-DNA 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 / 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 / Resolution: 3 Å | ||||||
Authors | Aller, P. / Duclos, S. / Wallace, S.S. / Doublie, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex. Authors: Aller, P. / Duclos, S. / Wallace, S.S. / Doublie, S. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007 Title: A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol. Authors: Aller, P. / Rould, M.A. / Hogg, M. / Wallace, S.S. / Doublie, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rmc.cif.gz | 781.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rmc.ent.gz | 632.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rmc_validation.pdf.gz | 543 KB | Display | wwPDB validaton report |
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Full document | 3rmc_full_validation.pdf.gz | 760 KB | Display | |
Data in XML | 3rmc_validation.xml.gz | 150.4 KB | Display | |
Data in CIF | 3rmc_validation.cif.gz | 203.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/3rmc ftp://data.pdbj.org/pub/pdb/validation_reports/rm/3rmc | HTTPS FTP |
-Related structure data
Related structure data | 3rmaC 3rmbC 3rmdC 2dy4S 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 105069.586 Da / Num. of mol.: 4 / Mutation: D222A, D327A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Gene: 43, gp43 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase #2: DNA chain | Mass: 5575.606 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA template #3: DNA chain | Mass: 4271.778 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA primer #4: 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: 2.94 Å3/Da / Density % sol: 58.13 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR ...Details: 4.5 % PEG 20,000, 150 mM Na acetate, 125 mM Mg acetate, 100 mM TrisHCl, 1% glycerol, 10mM Phenol and 2 mM beta-mercaptoethanol, vapor diffusion, hanging drop, temperature 297K, pH 6.8, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. all: 107108 / Num. obs: 107001 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.085 / Χ2: 1.049 / Net I/σ(I): 12.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: pdb entry 2DY4 Resolution: 3→50 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 49.8317 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 189.19 Å2 / Biso mean: 92.6036 Å2 / Biso min: 15.59 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Xplor file |
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