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Yorodumi- PDB-2oyq: Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP op... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oyq | ||||||
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Title | Crystal structure of RB69 gp43 in complex with DNA with 5-NIMP opposite an abasic site analog | ||||||
Components |
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Keywords | transferase/DNA / DNA POLYMERASE / ABASIC SITE / DNA LESION / NUCLEOTIDE BINDING / 5-NITP / 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 / 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 | Enterobacteria phage RB69 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Isomorphous Replacement / Resolution: 2.86 Å | ||||||
Authors | Zahn, K.E. / Belrhali, H. / Wallace, S.S. / Doublie, S. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Caught bending the a-rule: crystal structures of translesion DNA synthesis with a non-natural nucleotide. Authors: Zahn, K.E. / Belrhali, H. / 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 | 2oyq.cif.gz | 730.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oyq.ent.gz | 576 KB | Display | PDB format |
PDBx/mmJSON format | 2oyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oyq_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2oyq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2oyq_validation.xml.gz | 123.1 KB | Display | |
Data in CIF | 2oyq_validation.cif.gz | 169.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/2oyq ftp://data.pdbj.org/pub/pdb/validation_reports/oy/2oyq | HTTPS FTP |
-Related structure data
Related structure data | 2ozmC 2ozsC 2p5gC 1rv2 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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2 |
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4 |
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Unit cell |
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-Components
-DNA chain , 2 types, 8 molecules EGIKFHJL
#1: DNA chain | Mass: 6300.051 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: DNA chain | Mass: 4661.042 Da / Num. of mol.: 4 / Source method: obtained synthetically |
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-Protein , 1 types, 4 molecules ABCD
#3: Protein | Mass: 104655.141 Da / Num. of mol.: 4 / Mutation: D222A, D327A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: 43 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q38087, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 657 molecules
#4: Chemical | #5: Chemical | ChemComp-N5P / #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: 2.88 Å3/Da / Density % sol: 57.28 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 2000 MME, sodium acetate, magnesium sulfate, beta-mercaptoethanol, HEPES 7.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.99187 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 3, 2006 / Details: mirrors |
Radiation | Monochromator: DCM - pair of flat Si crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→30 Å / Num. all: 121231 / Num. obs: 121231 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.86→2.96 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2 / % possible all: 97.3 |
-Processing
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Refinement | Method to determine structure: Isomorphous Replacement Starting model: 1RV2 1rv2 Resolution: 2.86→30 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.872 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.755 Å2
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Refinement step | Cycle: LAST / Resolution: 2.86→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→2.934 Å / Total num. of bins used: 20
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