[English] 日本語
Yorodumi- PDB-2ntz: Structure of a ParB-DNA complex reveals a double B-box interaction -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ntz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a ParB-DNA complex reveals a double B-box interaction | ||||||
Components |
| ||||||
Keywords | CELL CYCLE/DNA / partition / segregation / parb / para / CELL CYCLE-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage P1 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Schumacher, M.A. / Mansoor, A. / Funnell, B.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structure of a four-way bridged ParB-DNA complex provides insight into P1 segrosome assembly. Authors: Schumacher, M.A. / Mansoor, A. / Funnell, B.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ntz.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ntz.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ntz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ntz_validation.pdf.gz | 465.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ntz_full_validation.pdf.gz | 506.2 KB | Display | |
Data in XML | 2ntz_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2ntz_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/2ntz ftp://data.pdbj.org/pub/pdb/validation_reports/nt/2ntz | HTTPS FTP |
-Related structure data
Related structure data | 1zx4S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 4892.194 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 4905.176 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 22227.596 Da / Num. of mol.: 2 / Fragment: 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) / References: UniProt: Q38420 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.42 % | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, MES 6.5, Magnesium chloride, sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.989 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2004 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.989 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→129.1 Å / Num. all: 15990 / Num. obs: 15703 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 89 Å2 / Rsym value: 0.049 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.35→3.5 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2177 / Rsym value: 0.333 / % possible all: 94 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1zx4 Resolution: 3.35→66.72 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 5132409.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.6469 Å2 / ksol: 0.175069 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 145.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→66.72 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.35→3.56 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
| |||||||||||||||||||||||||
Xplor file |
|