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Yorodumi- PDB-2r8h: Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r8h | |||||||||
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Title | Selectivity of Nucleoside Triphosphate Incorporation Opposite 1,N2-Propanodeoxyguanosine (PdG) by the Sulfolobus solfataricus DNA Polymerase Dpo4 Polymerase | |||||||||
Components |
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Keywords | REPLICATION / TRANSFERASE/DNA / exocyclic adducts / replication bypass / translesion / polymerase / frameshifting / TRANSFERASE-DNA COMPLEX | |||||||||
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: 2.48 Å | |||||||||
Authors | Wang, Y. / Saleh, S. / Marnette, L.J. / Egli, M. / Stone, M.P. | |||||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Insertion of dNTPs opposite the 1,N2-propanodeoxyguanosine adduct by Sulfolobus solfataricus P2 DNA polymerase IV Authors: Wang, Y. / Musser, S.K. / Saleh, S. / Marnett, L.J. / Egli, M. / Stone, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r8h.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r8h.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 2r8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r8h ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r8h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules PT
#1: DNA chain | Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 5412.545 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 40257.879 Da / Num. of mol.: 1 / Mutation: R332A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) Description: purified using heat denaturation, Ni2+-nitriloacetate chromatography, and ion-exchange chromatography Gene: dbh, dpo4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 102 molecules
#4: Chemical | #5: Chemical | ChemComp-DGT / | #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: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→50 Å / Num. all: 23739 / Num. obs: 15421 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→50 Å
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Refinement step | Cycle: LAST / Resolution: 2.48→50 Å
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Refine LS restraints |
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