+Open data
-Basic information
Entry | Database: PDB / ID: 1qqc | ||||||
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Title | CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK | ||||||
Components | DNA POLYMERASE II | ||||||
Keywords | TRANSFERASE / DNA POLYMERASE / THERMOSTABLE / EXONUCLEASE / RBD DOMAIN | ||||||
Function / homology | Function and homology information exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfurococcus sp. Tok (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Zhao, Y. / Jeruzalmi, D. / Leighton, L. / Lasken, R. / Kuriyan, J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of an archaebacterial DNA polymerase Authors: Zhao, Y. / Jeruzalmi, D. / Moarefi, I. / Leighton, L. / Lasken, R. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qqc.cif.gz | 158.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqc.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqc ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqc | HTTPS FTP |
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-Related 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: 90128.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfurococcus sp. Tok (archaea) / Plasmid: PET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG7, DNA-directed DNA polymerase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 3.07 Å3/Da / Density % sol: 59.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 400, PEG 4000, AMMONIUM SULFATE, MAGNESIUM SULFATE, TRIS, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: OTHER / Detector: CCD / Date: Dec 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 34977 / Num. obs: 31591 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Redundancy: 5 % / Biso Wilson estimate: 47.08 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.6→50 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.156 / % possible all: 57.8 |
Reflection | *PLUS Num. obs: 32909 / % possible obs: 93.9 % |
Reflection shell | *PLUS % possible obs: 57.8 % |
-Processing
Software |
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Refinement | Resolution: 2.6→50 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: CNS PACKAGE
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.242 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d |