+Open data
-Basic information
Entry | Database: PDB / ID: 1v33 | ||||||
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Title | Crystal structure of DNA primase from Pyrococcus horikoshii | ||||||
Components | DNA primase small subunitPrimase | ||||||
Keywords | TRANSFERASE / Nucleotidyl transferase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information primosome complex / DNA primase activity / DNA-directed RNA polymerase complex / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ito, N. / Nureki, O. / Shirouzu, M. / Yokoyama, S. / Hanaoka, F. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Genes Cells / Year: 2003 Title: Crystal structure of the Pyrococcus horikoshii DNA primase-UTP complex: implications for the mechanism of primer synthesis. Authors: Ito, N. / Nureki, O. / Shirouzu, M. / Yokoyama, S. / Hanaoka, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v33.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v33.ent.gz | 64.7 KB | Display | PDB format |
PDBx/mmJSON format | 1v33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v33 ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v33 | 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: 42643.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET 15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CODON PLUS References: UniProt: O57934, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PO4 / |
#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: 51.85 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, AMMONIUM SULFATE, POTASSIUM PHOSPHATE, SODIUM CACODYLATE, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 38381 / % possible obs: 90.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.09 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1561 / % possible all: 75.8 |
Reflection shell | *PLUS % possible obs: 75.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.1 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.12 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→33.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 37304 / % reflection Rfree: 5 % / Rfactor Rfree: 0.244 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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