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Yorodumi- PDB-1rep: CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rep | ||||||
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Title | CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI-F PLASMID COMPLEXED WITH AN ITERON DNA | ||||||
Components |
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Keywords | REPLICATION/DNA / REPLICATION INITIATOR / DNA-BINDING / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å | ||||||
Authors | Komori, H. / Matsunaga, F. / Higuchi, Y. / Ishiai, M. / Wada, C. / Miki, K. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution. Authors: Komori, H. / Matsunaga, F. / Higuchi, Y. / Ishiai, M. / Wada, C. / Miki, K. #1: Journal: J.Biochem.(Tokyo) / Year: 1999 Title: Crystallization and preliminary X-ray diffraction studies of a replication initiator protein (RepE54) of the mini-F plasmid complexed with iteron DNA Authors: Komori, H. / Sasai, N. / Matsunaga, F. / Wada, C. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rep.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rep.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1rep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1rep ftp://data.pdbj.org/pub/pdb/validation_reports/re/1rep | 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: DNA chain | Mass: 6687.328 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6807.401 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 29343.527 Da / Num. of mol.: 1 / Mutation: R118P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: HIS-TAGGED PROTEIN / Production host: Escherichia coli (E. coli) / References: UniProt: P03856 |
#4: Chemical | ChemComp-MG / |
#5: 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: 3.12 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 12 % PEG 400, 200 MM MGCL2, 100 MM TRIS-HCL, PH8.0, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS Density % sol: 60.6 % | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Komori, H., (1999) J.Biochem.(Tokyo), 125, 24. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35 Å / Num. obs: 15208 / % possible obs: 88.7 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.8 / % possible all: 65 |
Reflection | *PLUS Num. measured all: 57565 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.6→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 30.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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