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Yorodumi- PDB-2va3: Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2va3 | ||||||
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Title | Complex structure of Sulfolobus solfataricus DPO4 and DNA duplex containing a hydrophobic thymine isostere 2,4-difluorotoluene nucleotide in the template strand | ||||||
Components |
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Keywords | TRANSFERASE / DNA-DIRECTED DNA POLYMERASE / P2 DNA POLYMERASE IV / NUCLEOTIDYLTRANSFERASE / MUTATOR PROTEIN / DNA REPLICATION / 2 / 4-DIFLUOROTOLUENE / DNA REPAIR / DNA-BINDING / METAL-BINDING / TRANSLESION DNA POLYMERASE / DGTP / CYTOPLASM / MAGNESIUM / DNA DAMAGE | ||||||
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: 2.98 Å | ||||||
Authors | Irimia, A. / Pallan, P.S. / Egli, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structure and Activity of Y-Class DNA Polymerase Dpo4 from Sulfolobus Solfataricus with Templates Containing the Hydrophobic Thymine Analog 2,4-Difluorotoluene. Authors: Irimia, A. / Eoff, R.L. / Pallan, P.S. / Guengerich, F.P. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2va3.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2va3.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 2va3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2va3 ftp://data.pdbj.org/pub/pdb/validation_reports/va/2va3 | HTTPS FTP |
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-Related structure data
Related structure data | 2v9wC 2va2C 2uvvS 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: DPO4 / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / 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: 4105.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 13-MER PRIMER |
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#3: DNA chain | Mass: 5355.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 18-MER TEMPLATE |
-Non-polymers , 3 types, 67 molecules
#4: Chemical | ChemComp-DGT / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.2 % Description: THE POSITION OF THE INITIAL MODEL WAS OPTIMISED BY SEVERAL ROUNDS OF RIGID BODY REFINEMENT WHILE GRADUALLY INCREASING THE RESOLUTION OF THE DIFFRACTION DATA |
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Crystal grow | pH: 7.5 Details: 30 MM NACL, 2%GLYCEROL, 10 MM TRIS PH 7.5, 2.5 MM CACL2, 0.5 MM DDCTP, 6% PEG 3350, 0.05 CALCIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 3, 2007 / Details: PT-COATED TOROIDAL MIRROR |
Radiation | Monochromator: SI-111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→30.17 Å / Num. obs: 9628 / % possible obs: 84.5 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 77.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.05 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2UVV Resolution: 2.98→30.17 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1062732.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.279 Å2 / ksol: 0.292993 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.98→30.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.98→3.17 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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