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Yorodumi- PDB-1g8y: CRYSTAL STRUCTURE OF THE HEXAMERIC REPLICATIVE HELICASE REPA OF P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g8y | ||||||
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Title | CRYSTAL STRUCTURE OF THE HEXAMERIC REPLICATIVE HELICASE REPA OF PLASMID RSF1010 | ||||||
Components | REGULATORY PROTEIN REPA | ||||||
Keywords | TRANSCRIPTION / P-loop | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Niedenzu, T. / Roeleke, D. / Bains, G. / Scherzinger, E. / Saenger, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of the hexameric replicative helicase RepA of plasmid RSF1010. Authors: Niedenzu, T. / Roleke, D. / Bains, G. / Scherzinger, E. / Saenger, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g8y.cif.gz | 547.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g8y.ent.gz | 453.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g8y ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g8y | 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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2 |
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Unit cell |
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Details | The biological assembly is one of the two hexamers in the asymmetric unit: chains a-f or g-l |
-Components
#1: Protein | Mass: 29945.189 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: REPA ON PLASMID INCQ RSF1010 / Plasmid: PTACREP-A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P20356 #2: 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: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 5000 monomethyl ether, 2-methyl-2,4-pentanediol, NaCl, sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9059 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998 |
Radiation | Monochromator: bent single-crystal germanium triangular monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9059 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 149192 / Num. obs: 149192 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.53 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 6.9 / Num. unique all: 8579 / % possible all: 81.7 |
Reflection | *PLUS Num. measured all: 377676 / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 81.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.02
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 2.1 % / Rfactor obs: 0.221 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.5 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.32 / Rfactor Rwork: 0.261 |