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Yorodumi- PDB-1iqp: Crystal Structure of the Clamp Loader Small Subunit from Pyrococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iqp | ||||||
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Title | Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus | ||||||
Components | RFCS | ||||||
Keywords | REPLICATION / CLAMP LOADER / EXTENDED AAA-ATPASE DOMAIN / COMPLEX WITH ADP | ||||||
Function / homology | Function and homology information four-way junction helicase activity / intein-mediated protein splicing / endonuclease activity / DNA recombination / DNA replication / DNA repair / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å | ||||||
Authors | Oyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus Authors: Oyama, T. / Ishino, Y. / Cann, I.K.O. / Ishino, S. / Morikawa, K. #1: Journal: J.BACTERIOL. / Year: 2001 Title: Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus Authors: Cann, I.K.O. / Ishino, S. / Yuasa, M. / Daiyasu, H. / Toh, H. / Ishino, Y. #2: Journal: To be Published Title: Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus Authors: Mayanagi, K. / Miyata, T. / Oyama, T. / Ishino, Y. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iqp.cif.gz | 389.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iqp.ent.gz | 322.6 KB | Display | PDB format |
PDBx/mmJSON format | 1iqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/1iqp ftp://data.pdbj.org/pub/pdb/validation_reports/iq/1iqp | HTTPS FTP |
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-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: 37458.531 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rfcs / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U4J3 #2: Chemical | ChemComp-ADP / #3: Water | ChemComp-HOH / | |
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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: 3.66 Å3/Da / Density % sol: 66.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: MPD, glycerol, sodium chloride, acetic acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jul 8, 1999 / Details: mirros |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→65 Å / Num. all: 80855 / Num. obs: 76556 / % possible obs: 93.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.5 / Num. unique all: 6221 / % possible all: 78.7 |
Reflection | *PLUS Lowest resolution: 65 Å / Num. measured all: 260398 |
Reflection shell | *PLUS % possible obs: 78.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.8→15 Å / Isotropic thermal model: isotripic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 1 / % reflection Rfree: 5.35 % / Rfactor obs: 0.224 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.16 |