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Open data
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Basic information
Entry | Database: PDB / ID: 2hvi | |||||||||
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Title | ddCTP:G pair in the polymerase active site (0 position) | |||||||||
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![]() | Transferase/DNA / DNA Polymerase I / DNA replication / Klenow Fragment / Protein-DNA complex / closed conformation / Transferase-DNA COMPLEX | |||||||||
Function / homology | ![]() 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 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.5 KB | Display | ![]() |
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PDB format | ![]() | 222.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 50.8 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hhqC ![]() 2hhsC ![]() 2hhtC ![]() 2hhuC ![]() 2hhvC ![]() 2hhwC ![]() 2hhxC ![]() 2hvhC ![]() 2hw3C ![]() 1lv5S ![]() 2hhy S: Starting model for refinement C: citing same article ( |
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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 complete biological assemblies, each with a DNA polymerase molecule, a primer and template DNA, and an incoming ddCTP+Mg. |
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Components
-DNA chain , 2 types, 4 molecules BECF
#1: DNA chain | Mass: 2675.775 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA primer strand #2: DNA chain | Mass: 4016.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand |
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-Protein / Sugars , 2 types, 4 molecules AD
#3: Protein | Mass: 66202.945 Da / Num. of mol.: 2 Fragment: residues 299-876 (analogous to E Coli Klenow Fragment) 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, 658 molecules ![](data/chem/img/DCT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.67 % | ||||||||||||||||||||||||||||||||||||
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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, 10 mM MgSO4, 100 mM 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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 9, 2004 / 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: 1.98→50 Å / Num. all: 93220 / Num. obs: 93220 / % possible obs: 87.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.084 / Χ2: 1.023 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.87 / Num. unique all: 8751 / Rsym value: 0.638 / Χ2: 0.941 / % possible all: 82.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1LV5 Resolution: 1.98→50 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 48.527 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.399 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.05 Å
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Xplor file |
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