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Yorodumi- PDB-2v4r: Non-productive complex of the Y-family DNA polymerase Dpo4 with d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v4r | ||||||
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Title | Non-productive complex of the Y-family DNA polymerase Dpo4 with dGTP skipping the M1dG adduct to pair with the next template cytosine | ||||||
Components |
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Keywords | TRANSFERASE / DNA-DIRECTED DNA POLYMERASE / DNA-BINDING / METAL-BINDING / DNA REPLICATION / MUTATOR PROTEIN / NUCLEOTIDYLTRANSFERASE / DNA ADDUCT / DNA DAMAGE / DNA REPAIR / DPO4 / M1DG / CYTOPLASM / MAGNESIUM | ||||||
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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Eoff, R.L. / Stafford, J.B. / Szekely, J. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. / Marnett, L.J. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family DNA Polymerase Dpo4-Catalyzed Bypass of the Malondialdehyde-Deoxyguanosine Adduct. Authors: Eoff, R.L. / Stafford, J.B. / Szekely, J. / Rizzo, C.J. / Egli, M. / Guengerich, F.P. / Marnett, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v4r.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v4r.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/2v4r ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v4r | HTTPS FTP |
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-Related structure data
Related structure data | 2v4qC 2bqrS 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: 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: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13 BASE PRIMER DNA 5'-GGG GGA AGG ATT C-3' / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5408.513 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 18 BASE TEMPLATE DNA 5'-TCA C(M1G)G AAT CCT TCC CCC-3' Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 138 molecules
#4: Chemical | ChemComp-DGT / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | N TERMINAL HEXA-HISTIDINE TAG AND MISSING LAST 11 RESIDUES |
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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: 3.1 Å3/Da / Density % sol: 59.5 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.4 Details: 7.5% POLYETHYLENE GLYCOL 3350, 100 MM CALCIUM ACETATE, 25 MM TRIS HCL (PH 7.4), 100 MM SODIUM CHLORIDE, 2.5% GLYCEROL, 1 MM DGTP, 5 MM CALCIUM CHLORIDE. |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.987 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 17552 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.89 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BQR Resolution: 2.5→29.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 72280.94 / 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: 49.9285 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.6 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: WATER.TOP |