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- PDB-1hkq: PPS10 plasmid DNA replication initiator protein RepA. Replication... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hkq | ||||||
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Title | PPS10 plasmid DNA replication initiator protein RepA. Replication inactive, dimeric N-terminal domain. | ||||||
![]() | REPLICATION PROTEIN | ||||||
![]() | DNA BINDING PROTEIN / WINGED-HELIX / PPS10 PLASMID / REPLICATION INITIATOR DIMER. | ||||||
Function / homology | ![]() DNA replication initiation / DNA-directed DNA polymerase activity / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Giraldo, R. / Fernandez-Tornero, C. / Evans, P.R. / Diaz-Orejas, R. / Romero, A. | ||||||
![]() | ![]() Title: A Conformational Switch between Transcriptional Repression and Replication Initiation in Repa Dimerization Domain Authors: Giraldo, R. / Fernandez-Tornero, C. / Evans, P.R. / Diaz-Orejas, R. / Romero, A. #1: Journal: J.Biol.Chem. / Year: 2003 Title: Structural Changes in Repa, a Plasmid Replication Initiator, Upon Binding to Origin DNA Authors: Diaz-Lopez, T. / Lages-Gonzalo, M. / Serrano-Lopez, A. / Alfonso, C. / Rivas, G. / Diaz-Orejas, R. / Giraldo, R. #2: Journal: Fems Microbiol.Rev. / Year: 2003 Title: Common Domains in the Initiators of DNA Replication in Bacteria, Archaea and Eukarya: Combined Structural, Functional and Phylogenetic Perspectives Authors: Giraldo, R. #3: Journal: Embo J. / Year: 1998 Title: Protein Domains and Conformational Changes in the Activation of Repa, a DNA Replication Initiator Authors: Giraldo, R. / Andreu, J.M. / Diaz-Orejas, R. #4: Journal: J.Mol.Biol. / Year: 1992 Title: Genetic and Functional Analysis of the Basic Replicon of Pps10, a Plasmid Specific for Pseudomonas Isolated from Pseudomonas Syringae, Patovar Savastanoi Authors: Nieto, C. / Giraldo, R. / Fernandez-Tresguerres, M.E. / Diaz, R. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 48.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 468 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 16.6 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.05164, 0.99822, 0.02989), Vector: |
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Components
#1: Protein | Mass: 15180.649 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN DIMER, RESIDUES 2-133 Source method: isolated from a genetically manipulated source Details: PPS10 PLASMID DNA REPLICATION INITIATOR, REPLICATION INACTIVE, DIMERIC SPECIES Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-HG / #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Sequence details | CLONED REPA STARTS WITH A SINGLE MET RESIDUE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.17 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: VAPOUR DIFFUSION (HANGING DROPS), WELLS: 500 MICROLITRES (14% PEG4000, 6% MPD), DROPS: 5 MICROLITRES PROTEIN (5 MG/ML IN 50 MM K2HPO4/ KH2PO4, PH= 6.2),5 MICROLITRES WELL SOL. PLUS 1 ...Details: VAPOUR DIFFUSION (HANGING DROPS), WELLS: 500 MICROLITRES (14% PEG4000, 6% MPD), DROPS: 5 MICROLITRES PROTEIN (5 MG/ML IN 50 MM K2HPO4/ KH2PO4, PH= 6.2),5 MICROLITRES WELL SOL. PLUS 1 MICROLITRE OF P-CL-MERCURIBENZOATE (=1 MM IN WATER), THIN LARGE CRYSTAL PRISMS APPEAR AT 295 DEGREES KELVIN IN 1 MONTH., pH 6.20 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 2000 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.75→48.2 Å / Num. obs: 8343 / % possible obs: 97.7 % / Observed criterion σ(I): 2.1 / Redundancy: 5.2 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 8 | |||||||||
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 97.8 | |||||||||
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 48.2 Å / Num. measured all: 44839 / Rmerge(I) obs: 0.081 | |||||||||
Reflection shell | *PLUS % possible obs: 97.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE ELECTRON DENSITY FOR RESIDUES SER B36 - LYS B42 IN CHAIN B IS DISCONTINUOUS, INTERPRETED TO BE PARTIALLY DISORDERED. THUS IT HAS BEEN MODELLED BASED ON STEREOCHEMICAL RESTRAINTS.
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Solvent computation | Solvent model: FLAT / Bsol: 27.2205 Å2 / ksol: 0.305183 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→27.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.9 Å |