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- PDB-1xc9: Structure of a high-fidelity polymerase bound to a benzo[a]pyrene... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xc9 | |||||||||
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Title | Structure of a high-fidelity polymerase bound to a benzo[a]pyrene adduct that blocks replication | |||||||||
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![]() | TRANSFERASE/DNA / DNA polymerase I / DNA replication / klenow fragment / benzo[a]pyrene / benzopyrene / DNA lesion / translation replication / 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 / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hsu, G.W. / Huang, X. / Luneva, N.P. / Geacintov, N.E. / Beese, L.S. | |||||||||
![]() | ![]() Title: Structure of a High Fidelity DNA Polymerase Bound to a Benzo[a]pyrene Adduct That Blocks Replication Authors: Hsu, G.W. / Huang, X. / Luneva, N.P. / Geacintov, N.E. / Beese, L.S. #1: ![]() Title: Observing translation synthesis of an aromatic amine DNA adduct by a high-fidelity DNA polymerase Authors: Hsu, G.W. / Kiefer, J.R. / Becherel, O.J. / Fuchs, R.P.P. / Beese, L.S. #2: ![]() Title: Structures of Mismatch Replication Errors Observed in a DNA Polymerase Authors: Johnson, S.J. / Beese, L.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.7 KB | Display | ![]() |
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PDB format | ![]() | 114.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lv5S 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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Unit cell |
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Details | Exists as a monomer. One molecule per asymmetric unit |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3141.052 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4449.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: see remark 400 |
-Protein / Sugars , 2 types, 2 molecules A
#3: Protein | Mass: 66172.844 Da / Num. of mol.: 1 / Fragment: analogous to the E. coli klenow fragment Source method: isolated from a genetically manipulated source Details: see remark 400 Source: (gene. exp.) ![]() ![]() Plasmid: pet-30A(+) / Production host: ![]() ![]() |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
-Non-polymers , 4 types, 379 molecules ![](data/chem/img/BAP.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-BAP / | ||||
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#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Ammonium Sulfate, Magnesium Sulfate, MPD, 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: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 5, 2001 |
Radiation | Monochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.76 Å / Num. all: 71966 / Num. obs: 71966 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1LV5 Resolution: 1.9→42.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2634280.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.8031 Å2 / ksol: 0.385435 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→42.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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