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Yorodumi- PDB-2uvv: Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2uvv | |||||||||
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Title | Crystal structures of mutant Dpo4 DNA polymerases with 8-oxoG containing DNA template-primer constructs | |||||||||
Components |
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Keywords | TRANSFERASE / DNA-DIRECTED DNA POLYMERASE / P2 DNA POLYMERASE IV / NUCLEOTIDYLTRANSFERASE / 7 / MAGNESIUM / DNA DAMAGE / DNA REPAIR / DNA-BINDING / TRANSLESION DNA POLYMERASE / METAL-BINDING / 8-DIHYDRO-8- OXODEOXYGUANOSINE / METAL- BINDING / MUTATOR PROTEIN / DNA REPLICATION | |||||||||
Function / homology | Function and homology information error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Irimia, A. / Egli, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with a Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus DNA Polymerase Dpo4. Authors: Eoff, R.L. / Irimia, A. / Angel, K.C. / Egli, M. / Guengerich, F.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uvv.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvv.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2uvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uvv_validation.pdf.gz | 794.5 KB | Display | wwPDB validaton report |
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Full document | 2uvv_full_validation.pdf.gz | 803.7 KB | Display | |
Data in XML | 2uvv_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 2uvv_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvv ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvv | HTTPS FTP |
-Related structure data
Related structure data | 2uvrSC 2uvuC 2uvwC 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: 41058.672 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: R332E MUTANT OF DPO4 / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Description: GENE DPO4 / Plasmid: PET22B/DPO4-NHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules PT
#2: DNA chain | Mass: 4385.852 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GGG GGA AGG ATT CC |
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#3: DNA chain | Mass: 5388.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T C A C 8OG G A A T C C T T C C C C C |
-Non-polymers , 3 types, 186 molecules
#4: Chemical | ChemComp-DGT / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | ENGINEERED |
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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: 2.6 Å3/Da / Density % sol: 55.3 % Description: THE MODEL POSITION WAS OPTIMIZED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT. |
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Crystal grow | pH: 7.3 Details: 7% PEG 4000, 10 MM HEPES PH 7.3, 50 MM CA(CH3CO2)2, 50MM NACL, 3.5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.32 Å / Num. obs: 27480 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 6.38 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.61 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.57 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.41 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UVR Resolution: 2.2→29.32 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1331600.58 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.1682 Å2 / ksol: 0.373696 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→29.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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