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Yorodumi- PDB-2hhu: C:O6-methyl-guanine in the polymerase postinsertion site (-1 base... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hhu | |||||||||
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Title | C:O6-methyl-guanine in the polymerase postinsertion site (-1 basepair position) | |||||||||
Components |
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Keywords | Transferase/DNA / DNA polymerase I / DNA replication / Klenow fragment / Protein-DNA complex / O6-methyl-guanine / Transferase-DNA COMPLEX | |||||||||
Function / homology | Function and homology information 5'-3' exonuclease activity / double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å | |||||||||
Authors | Warren, J.J. / Forsberg, L.J. / Beese, L.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: The structural basis for the mutagenicity of O6-methyl-guanine lesions. Authors: Warren, J.J. / Forsberg, L.J. / Beese, L.S. | |||||||||
History |
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Remark 999 | SEQUENCE THE DNA POLYMERASE GENE WAS CLONED FROM AN ORGANISM THAT WAS CLASSIFIED AS A THERMOSTABLE ...SEQUENCE THE DNA POLYMERASE GENE WAS CLONED FROM AN ORGANISM THAT WAS CLASSIFIED AS A THERMOSTABLE STRAIN OF BACILLUS STEAROTHERMOPHILUS BY RIBOSOMAL RNA SEQUENCING. HOWEVER, THIS PARTICULAR GENE HAS MUCH GREATER HOMOLOGY WITH THE ANALOGOUS GENE FROM GEOBACILLUS KAUSTOPHILUS, UNP ACCESSION, Q5KWC1_GEOKA. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hhu.cif.gz | 159.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hhu.ent.gz | 117.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hhu ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hhu | HTTPS FTP |
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-Related structure data
Related structure data | 2hhqC 2hhsC 2hhtC 2hhvC 2hhwC 2hhxC 2hvhC 2hviC 2hw3C 2hhy 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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Details | The asymmetric unit contains one biological assembly |
-Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3319.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized |
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#2: DNA chain | Mass: 4953.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized |
-Protein / Sugars , 2 types, 3 molecules A
#3: Protein | Mass: 66230.953 Da / Num. of mol.: 1 Fragment: residues 299-876 (analogous to E Coli Klenow Fragment) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: polA / Plasmid: PUC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5KWC1, DNA-directed DNA polymerase |
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#4: Polysaccharide |
-Non-polymers , 4 types, 425 molecules
#5: Chemical | ChemComp-DCP / | ||||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-MG / | #8: 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: 2.92 Å3/Da / Density % sol: 57.95 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 45% saturated ammonium sulfate, 2.5% MPD, 100mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 9, 2005 / Details: Yale mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 80388 / Num. obs: 80388 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Redundancy: 7.1 % / Rsym value: 0.099 / Χ2: 1.042 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 7841 / Rsym value: 0.765 / Χ2: 0.897 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→50 Å / Isotropic thermal model: isotropic / σ(F): 0
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Solvent computation | Bsol: 40.973 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.597 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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Xplor file |
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