+Open data
-Basic information
Entry | Database: PDB / ID: 1wn7 | ||||||
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Title | Crystal structure of archaeal family B DNA polymerase mutant | ||||||
Components | Family B DNA Polymerase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Kuroita, T. / Matsumura, H. / Yokota, N. / Hashimoto, H. / Imanaka, T. / Inoue, T. / Kai, Y. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural Mechanism for Coordination of Proofreading and Polymerase Activities in Archaeal DNA Polymerases Authors: Kuroita, T. / Matsumura, H. / Yokota, N. / Kitabayashi, M. / Hashimoto, H. / Inoue, T. / Imanaka, T. / Kai, Y. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 Authors: Hashimoto, H. / Nishioka, M. / Fujiwara, S. / Takagi, M. / Imanaka, T. / Inoue, T. / Kai, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wn7.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wn7.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/1wn7 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/1wn7 | HTTPS FTP |
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-Related structure data
Related structure data | 1gcx 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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-Components
#1: Protein | Mass: 90153.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Plasmid: PET-8C / Production host: Escherichia coli (E. coli) References: UniProt: D0VWU9*PLUS, DNA-directed DNA polymerase |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.57 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1450, NiCl2, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 17, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→33.26 Å / Num. obs: 22320 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.75→2.92 Å / % possible all: 79.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCX 1gcx Resolution: 2.75→33.26 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.57 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→33.26 Å
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LS refinement shell | Resolution: 2.75→2.92 Å
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