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Yorodumi- PDB-1jr3: Crystal Structure of the Processivity Clamp Loader Gamma Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jr3 | ||||||
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Title | Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA Polymerase III | ||||||
Components |
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Keywords | TRANSFERASE / DNA Polymerase / Processivity / Processivity clamp / clamp loader / AAA+ ATPASE | ||||||
Function / homology | Function and homology information DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å | ||||||
Authors | Jeruzalmi, D. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2001 Title: Crystal structure of the processivity clamp loader gamma (gamma) complex of E. coli DNA polymerase III. Authors: Jeruzalmi, D. / O'Donnell, M. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jr3.cif.gz | 350.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jr3.ent.gz | 281.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jr3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jr3 ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jr3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 41510.855 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase #2: Protein | | Mass: 38745.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase #3: Protein | | Mass: 36980.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase #4: Chemical | ChemComp-ZN / #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.35 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Polyethylene glycol, ammonium sulphate, dithiothreitol, dimethylacetamide, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Oct 17, 2000 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→500 Å / Num. all: 552088 / Num. obs: 60657 / % possible obs: 83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 13.6 |
Reflection shell | Resolution: 2.7→1000 Å / Num. unique all: 60657 / Rsym value: 13.6 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 500 Å / % possible obs: 83 % / Num. measured all: 552088 / Rmerge(I) obs: 0.136 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.7→500 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→500 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 500 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.268 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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