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- PDB-3hp6: Crystal structure of fragment DNA polymerase I from Bacillus stea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hp6 | |||||||||
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Title | Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus F710Y mutant bound to G:T mismatch | |||||||||
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![]() | TRANSFERASE/DNA / protein-DNA complex / DNA polymerase I / DNA replication / DNA-binding / DNA-directed DNA polymerase / Hydrolase / Nuclease / Nucleotidyltransferase / Transferase / 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 | ![]() ![]() ![]() | |||||||||
![]() | Wu, E.Y. / Beese, L.S. | |||||||||
![]() | ![]() Title: The structure of a high fidelity DNA polymerase bound to a mismatched nucleotide reveals an "ajar" intermediate conformation in the nucleotide selection mechanism. Authors: Wu, E.Y. / 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 | ![]() | 293.4 KB | Display | ![]() |
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PDB format | ![]() | 228.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3hpoC ![]() 3ht3C ![]() 2hviS 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 biological unit is a complex of enzyme and DNA. There are two biological units in the asymmetric unit (chains A,B,C and chains D,E,F). |
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Components
-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 2724.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic oligonucleotide DNA template strand #3: DNA chain | Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic oligonucleotide DNA primer strand |
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-Protein / Sugars , 2 types, 4 molecules AD
#1: Protein | Mass: 66220.961 Da / Num. of mol.: 2 / Fragment: Residues 297-876 / Mutation: D598A, F710Y Source method: isolated from a genetically manipulated source Details: Isolate from Idaho hot spring Source: (gene. exp.) ![]() ![]() Gene: DPO1 / Plasmid: pET30a / Production host: ![]() ![]() References: UniProt: Q5KWC1*PLUS, DNA-directed DNA polymerase #4: Polysaccharide | |
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-Non-polymers , 4 types, 876 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.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: 2.65 Å3/Da / Density % sol: 53.66 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 50% Saturated ammonium sulfate, 0.1M MES, 2.5% v/v MPD, 10mM Magnesium sulfate, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→42.84 Å / Num. all: 140976 / Num. obs: 139378 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.25 Å2 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.81→1.86 Å / Redundancy: 5 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.61 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2HVI Resolution: 1.81→42.84 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.809 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.473 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→42.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.857 Å / Total num. of bins used: 20
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