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Yorodumi- PDB-2z9o: Crystal structure of the dimeric form of RepE in complex with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z9o | ||||||
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Title | Crystal structure of the dimeric form of RepE in complex with the repE operator DNA | ||||||
Components |
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Keywords | REPLICATION/DNA / REPLICATION INITIATOR / AUTOGENOUS REPRESSOR / PROTEIN-DNA COMPLEX / WINGED HELIX-TURN-HELIX / DNA replication / 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 / MOLECULAR REPLACEMENT / Resolution: 3.14 Å | ||||||
Authors | Nakamura, A. / Wada, C. / Miki, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural basis for regulation of bifunctional roles in replication initiator protein Authors: Nakamura, A. / Wada, C. / Miki, K. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z9o.cif.gz | 139.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z9o.ent.gz | 104.8 KB | Display | PDB format |
PDBx/mmJSON format | 2z9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z9o_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 2z9o_full_validation.pdf.gz | 501.8 KB | Display | |
Data in XML | 2z9o_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 2z9o_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/2z9o ftp://data.pdbj.org/pub/pdb/validation_reports/z9/2z9o | HTTPS FTP |
-Related structure data
Related structure data | 1repS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 10087.534 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 10207.605 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 31134.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: repE / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P03856 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.61 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 10% PEG 4000, 200mM Sodium Chloride, 5mM Samarium Chloride, 100mM HEPES-NaOH, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→50 Å / Num. obs: 16535 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.067 / Net I/σ(I): 11 |
Reflection shell | Resolution: 3.14→3.25 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.15 / % possible all: 73.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1REP Resolution: 3.14→45.03 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 276022.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10.4121 Å2 / ksol: 0.198433 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.14→45.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.14→3.34 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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