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Yorodumi- PDB-2w9a: Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w9a | ||||||
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Title | Ternary complex of Dpo4 bound to N2,N2-dimethyl-deoxyguanosine modified DNA with incoming dGTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE DNA COMPLEX / N2-DIMETHYL-G / METAL-BINDING / MUTATOR PROTEIN / NUCLEOTIDYLTRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA DAMAGE / DNA REPAIR / DNA-BINDING / TRANSFERASE / DNA REPLICATION / DNA / DPO4 / ADDUCT / CYTOPLASM / MAGNESIUM / POLYMERASE / 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 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Eoff, R.L. / Zhang, H. / Kosekov, I.D. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure-Function Relationships in Miscoding by Sulfolobus Solfataricus DNA Polymerase Dpo4: Guanine N2,N2-Dimethyl Substitution Produces Inactive and Miscoding Polymerase Complexes. Authors: Zhang, H. / Eoff, R.L. / Kozekov, I.D. / Rizzo, C.J. / 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 | 2w9a.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w9a.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w9a ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w9a | HTTPS FTP |
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-Related structure data
Related structure data | 2w9bC 2w9cC 2jefS 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41086.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Y-FAMILY DNA POLYMERASE FROM SULFOLOBUS SOLFATARICUS Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PET22B / 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: 4369.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 14 BASE PRIMER DNA 5'-GGG GGA AGG ATT C(DOC) -3' |
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#3: DNA chain | Mass: 5400.534 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 18 BASE TEMPLATE DNA 5'-TCA C(O2G)G AAT CCT TCC CCC-3' |
-Non-polymers , 3 types, 70 molecules
#4: Chemical | ChemComp-DGT / | ||
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#5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
-Details
Sequence 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: 2.44 Å3/Da / Density % sol: 53.74 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: DPO4\: DNA COMPLEX (1\:1.2 MOLAR RATIO, 150 MICROMOLAR), 20 MM TRIS HCL (PH 7.4), 15% POLYETHYLENE GLYCOL 3350 (W/V), 60 MM SODIUM CHLORIDE, 5 MM MAGNESIUM CHLORIDE, 1 MM DGTP. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID / Wavelength: 0.97857 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→19.94 Å / Num. obs: 16285 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.3 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JEF Resolution: 2.6→19.94 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 68406.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.36 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.94 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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