+Open data
-Basic information
Entry | Database: PDB / ID: 3gil | ||||||
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Title | Dpo4 extension ternary complex with oxoG(anti)-T(anti) pair | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA POLYMERASE / 8-OXOGUANINE / Y-FAMILY / LESION BYPASS / DNA damage / DNA repair / DNA replication / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Transferase / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information SOS response / error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus P2 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Rechkoblit, O. / Malinina, L. / Patel, D.J. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases. Authors: Rechkoblit, O. / Malinina, L. / Cheng, Y. / Geacintov, N.E. / Broyde, S. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gil.cif.gz | 189.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gil.ent.gz | 143.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/3gil ftp://data.pdbj.org/pub/pdb/validation_reports/gi/3gil | HTTPS FTP |
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-Related structure data
Related structure data | 3giiC 3gijSC 3gikC 3gimC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38945.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / DSM 1617 / JCM 11322 / Gene: dbh, dpo4, SSO2448 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL(STRATAGENE) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 4 molecules DHEJ
#2: DNA chain | Mass: 4061.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer strand #3: DNA chain | Mass: 5405.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA OXOG-modified template strand |
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-Non-polymers , 3 types, 127 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #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: 3.07 Å3/Da / Density % sol: 59.96 % | ||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, 100 mM Calcium acetate, 10% PEG 4000, pH 7.0, 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: 24-ID-C / Wavelength: 0.97922 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 22, 2005 Details: 6144 x 6144 pixel elements with an effective pixel size less than 60x60 micron and resolution of order 90x90 micron | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97922 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→20 Å / Num. obs: 31388 / % possible obs: 99.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.113 / Χ2: 1.016 / Net I/σ(I): 12.553 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GIJ Resolution: 2.71→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 23.232 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.979 / ESU R Free: 0.346 / 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 max: 88.2 Å2 / Biso mean: 51.444 Å2 / Biso min: 21.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.71→2.78 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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