+Open data
-Basic information
Entry | Database: PDB / ID: 1qht | ||||||
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Title | DNA POLYMERASE FROM THERMOCOCCUS SP. 9ON-7 ARCHAEON | ||||||
Components | PROTEIN (DNA POLYMERASE) | ||||||
Keywords | TRANSFERASE / DNA POLYMERASE / ARCHAEA / HYPERTHERMOSTABLE / FAMILY B POLYMERASE / POL ALPHA FAMILY POLYMERASE | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus sp. (archaea) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.1 Å | ||||||
Authors | Park, H.-W. / Rodriguez, A.C. / Beese, L.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. Authors: Rodriguez, A.C. / Park, H.W. / Mao, C. / Beese, L.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary Diffraction Analysis of a Hyperthermostable DNA Polymerase from a Thermococcus Archaeon Authors: Zhou, M. / Mao, C. / Rodriguez, A.C. / Kiefer, J.R. / Kucera, R.B. / 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 | 1qht.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qht.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 1qht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qht_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 1qht_full_validation.pdf.gz | 468.9 KB | Display | |
Data in XML | 1qht_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 1qht_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/1qht ftp://data.pdbj.org/pub/pdb/validation_reports/qh/1qht | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 89826.570 Da / Num. of mol.: 1 / Mutation: D141A,E143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus sp. (archaea) / Strain: 9oN-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56366, DNA-directed DNA polymerase |
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#2: 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: 2.9 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / pH: 9 Details: MICRODIALYSIS AT 291 K: 4-7% PEG 1500, 10 MM NICL2, 100 MM GLYCINE-NAOH, PH 9.0 OR 9.1; 25 MICROLITERS OF 3.9 MG/ML PROTEIN | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: microdialysis | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. obs: 58956 / % possible obs: 94.2 % / Redundancy: 11 % / Rsym value: 0.055 |
Reflection | *PLUS Num. measured all: 652420 / Rmerge(I) obs: 0.055 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.1→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Rfactor Rfree: 0.308 / Rfactor Rwork: 0.239 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.26 |