+Open data
-Basic information
Entry | Database: PDB / ID: 3mkw | ||||||
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Title | Structure of sopB(155-272)-18mer complex, I23 form | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / segregation / sopB / F plasmid / centromere / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Schumacher, M.A. / Piro, K. / Xu, W. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2010 Title: Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes. Authors: Schumacher, M.A. / Piro, K.M. / Xu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mkw.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mkw.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/3mkw ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mkw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5517.566 Da / Num. of mol.: 2 / Fragment: 18 mer sopC repeat / Source method: obtained synthetically / Details: The DNA was chemically synthesized. #2: Protein | Mass: 15157.027 Da / Num. of mol.: 2 / Fragment: SopB(UNP residues 155-272) Source method: isolated from a genetically manipulated source Details: artificial gene, codon optimized for e. coli expression Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: B, ECOK12F047, F plasmid, sopB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62558 #3: Chemical | ChemComp-SO4 / |
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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: 8.12 Å3/Da / Density % sol: 84.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25.5% PEG 4000, 0.17 M lithium sulphate, 0.1 M Tris pH 8.0, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å |
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Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 12, 2008 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→100 Å / Num. all: 26809 / Num. obs: 26809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 0.2 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.99→3.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2 / Num. unique all: 2800 / Rsym value: 0.448 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the FL SopB-18mer I23 Resolution: 2.99→100.23 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 500.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.0147 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.99→100.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.99→3.18 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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