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- PDB-1rep: CRYSTAL STRUCTURE OF REPLICATION INITIATOR PROTEIN REPE54 OF MINI... -
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Open data
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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 | ||||||
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![]() | REPLICATION/DNA / REPLICATION INITIATOR / DNA-BINDING / REPLICATION-DNA COMPLEX | ||||||
Function / homology | ![]() plasmid maintenance / DNA replication initiation / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Komori, H. / Matsunaga, F. / Higuchi, Y. / Ishiai, M. / Wada, C. / Miki, K. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.1 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 381.3 KB | Display | ![]() |
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Full document | ![]() | 396.4 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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