+Open data
-Basic information
Entry | Database: PDB / ID: 3kz5 | ||||||
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Title | Structure of cdomain | ||||||
Components | Protein sopB | ||||||
Keywords | DNA BINDING PROTEIN / partition / segregation / F plasmid / DNA-binding protein / DNA-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.58 Å | ||||||
Authors | Schumacher, M.A. | ||||||
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 | 3kz5.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kz5.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kz5_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 3kz5_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 3kz5_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 3kz5_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kz5 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kz5 | HTTPS FTP |
-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: Protein | Mass: 5802.745 Da / Num. of mol.: 3 / Fragment: UNP residues 276-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 Description: sopB(272-323) artificial gene for expression in pET15b Gene: B, ECOK12F047, sopB / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62558 #2: Chemical | ChemComp-ACT / | #3: Water | ChemComp-HOH / | |
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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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, sodium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.08 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→43.85 Å / Num. all: 19742 / Num. obs: 18124 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 10.1 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.58→43.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 991750.05 / 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: 54.0656 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.58→43.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.58→1.68 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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