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Yorodumi- PDB-3hpo: Crystal structure of fragment DNA polymerase I from Bacillus stea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpo | |||||||||
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Title | Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch | |||||||||
Components |
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Keywords | 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 | Function and homology information Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Wu, E.Y. / Beese, L.S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hpo.cif.gz | 167.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpo.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpo ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpo | HTTPS FTP |
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-Related structure data
Related structure data | 3hp6C 3ht3C 1l3uS C: citing same article (ref.) S: Starting model for refinement |
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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 biological unit is a complex of enzyme and DNA. The asymmetric unit is the same as the biological assembly. |
-Components
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 2684.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide primer strand |
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#3: DNA chain | Mass: 3101.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic oligonucleotide template strand |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 66128.859 Da / Num. of mol.: 1 / Fragment: Residues 297-876 / Mutation: D329A, Y714S Source method: isolated from a genetically manipulated source Details: Isolate from Idaho hot spring Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: DPO1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: DNA-directed DNA polymerase |
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#4: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose / |
-Non-polymers , 4 types, 727 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-TTP / |
#7: Chemical | ChemComp-SO4 / |
#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: 3.1 Å3/Da / Density % sol: 60.34 % | ||||||||||||||||||||||||||||||||||||
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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 Methylpentanediol, 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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 1, 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: 1.74→45.98 Å / Num. all: 92241 / Num. obs: 83554 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 29.055 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.66 |
Reflection shell | Resolution: 1.74→1.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 53772 / Num. unique all: 11929 / Num. unique obs: 11929 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L3U Resolution: 1.75→45.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.845 / SU B: 2.4 / SU ML: 0.077 / SU R Cruickshank DPI: 0.116 / SU Rfree: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.36 Å2 / Biso mean: 25.3 Å2 / Biso min: 6.78 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→45.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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