[English] 日本語
Yorodumi- PDB-2vh2: Crystal structure of cell divison protein FtsQ from Yersinia ente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vh2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cell divison protein FtsQ from Yersinia enterecolitica | ||||||
Components | CELL DIVISION PROTEIN FTSQ | ||||||
Keywords | CELL CYCLE / FTSQ / POTRA / CELL DIVISION | ||||||
Function / homology | Function and homology information cell septum assembly / FtsZ-dependent cytokinesis / cell division site / plasma membrane => GO:0005886 Similarity search - Function | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | van den Ent, F. / Vinkenvleugel, T. / Ind, A. / West, P. / Veprintsev, D. / Nanninga, N. / den Blaauwen, T. / Lowe, J. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2008 Title: Structural and Mutational Analysis of Cell Division Protein Ftsq Authors: van den Ent, F. / Vinkenvleugel, T. / Ind, A. / West, P. / Veprintsev, D. / Naninga, N. / den Blaauwen, T. / Lowe, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vh2.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vh2.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vh2 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vh2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2vh1SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (1), |
-Components
#1: Protein | Mass: 29011.756 Da / Num. of mol.: 2 / Fragment: RESIDUES 54-285 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A1JJJ6 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE |
---|---|
Crystal grow | Details: 1.5M LICL2, 10% PEG6000, 100 MM BICINE, PH8.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→20 Å / Num. obs: 11190 / % possible obs: 99.6 % / Observed criterion σ(I): 3.9 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.9 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VH1 Resolution: 3.4→35 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1282359.79 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELYHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 109.247 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 150 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.61 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
|