+Open data
-Basic information
Entry | Database: PDB / ID: 1zx4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of ParB bound to DNA | ||||||
Components |
| ||||||
Keywords | CELL CYCLE / partition / P1 / plasmid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.98 Å | ||||||
Authors | Schumacher, M.A. / Funnell, B.E. | ||||||
Citation | Journal: Nature / Year: 2005 Title: Structures of ParB bound to DNA reveal mechanism of partition complex formation. Authors: Schumacher, M.A. / Funnell, B.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1zx4.cif.gz | 108 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1zx4.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 1zx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zx4_validation.pdf.gz | 476.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1zx4_full_validation.pdf.gz | 516.7 KB | Display | |
Data in XML | 1zx4_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 1zx4_validation.cif.gz | 28.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/1zx4 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zx4 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
| ||||||||||
Details | ParB(142-333) is a dimer |
-Components
#1: DNA chain | Mass: 7707.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: W-strand | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 7649.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C-strand | ||||
#3: Protein | Mass: 22212.584 Da / Num. of mol.: 2 / Fragment: P1 ParB / Mutation: residues 142-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage P1 (virus) / Genus: P1-like viruses / Gene: parb / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q38420 #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium citrate, imidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.006 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2005 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.006 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→65.9 Å / Num. all: 19627 / Num. obs: 18057 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 98 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.09 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.98→3.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3000 / Rsym value: 0.44 / % possible all: 92 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.98→50.61 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3864998.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 125.7 Å2 / ksol: 0.444336 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.98→50.61 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.98→3.15 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|