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- PDB-2hhw: ddTTP:O6-methyl-guanine pair in the polymerase active site, in th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hhw | ||||||||||||
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Title | ddTTP:O6-methyl-guanine pair in the polymerase active site, in the closed conformation | ||||||||||||
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![]() | Transferase/DNA / DNA polymerase I / DNA replication / Klenow fragment / DNA-protein complex / O6-methyl-guanine / Transferase-DNA COMPLEX | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Warren, J.J. / Forsberg, L.J. / Beese, L.S. | ||||||||||||
![]() | ![]() 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 SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF ...SEQUENCE THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT UNP SEQUENCE DATABASE AT THE TIME OF PROCESSING. THE SEQUENCE OF THIS PROTEIN IS ANALOGOUS TO GEOBACILLUS KAUSTOPHILUS, UNP ACCESSION, Q5KWC1_GEOKA. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 288.7 KB | Display | ![]() |
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PDB format | ![]() | 223.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2hhqC ![]() 2hhsC ![]() 2hhtC ![]() 2hhuC ![]() 2hhvC ![]() 2hhxC ![]() 2hvhC ![]() 2hviC ![]() 2hw3C ![]() 1lv5S ![]() 2hhy C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The asymmetric unit contains two biological assemblies, each consisting of one protein molecule, two strands of DNA, and an incoming dideoxy thymidine triphosphate. Chains A, B, C, and G constitute one assembly, and chains D, E, F, and G constitute the second. |
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Components
-DNA chain , 2 types, 4 molecules EBFC
#1: DNA chain | Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized #2: DNA chain | Mass: 4030.650 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized |
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-Protein / Sugars , 2 types, 4 molecules AD
#3: Protein | Mass: 66144.836 Da / Num. of mol.: 2 Fragment: residues 299-876 (analogous to E coli Klenow fragment) Mutation: D598A, F710Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: polA / Plasmid: PUC / Species (production host): Escherichia coli / Production host: ![]() ![]() #4: Polysaccharide | |
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-Non-polymers , 4 types, 801 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/SO4.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.49 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 50% 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: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Dec 14, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→50 Å / Num. all: 120016 / Num. obs: 120016 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.111 / Χ2: 1.046 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 11633 / Rsym value: 0.782 / Χ2: 1.025 / % possible all: 93.6 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1LV5 Resolution: 1.88→50 Å / Isotropic thermal model: isotropic / σ(F): 0
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Solvent computation | Bsol: 45.062 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.212 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.88→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.95 Å
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Xplor file |
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