[English] 日本語
Yorodumi- PDB-3tg2: Crystal structure of the ISC domain of VibB in complex with isoch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tg2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ISC domain of VibB in complex with isochorismate | ||||||
Components | Vibriobactin-specific isochorismatase | ||||||
Keywords | HYDROLASE / isochorismatase | ||||||
Function / homology | Function and homology information vibriobactin biosynthetic process / isochorismatase / isochorismatase activity Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 Å | ||||||
Authors | Liu, S. / Zhang, C. / Niu, B. / Li, N. / Liu, X. / Liu, M. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural insight into the ISC domain of VibB from Vibrio cholerae at atomic resolution: a snapshot just before the enzymatic reaction Authors: Liu, S. / Zhang, C. / Li, N. / Niu, B. / Liu, M. / Liu, X. / Wei, T. / Zhu, D. / Huang, Y. / Xu, S. / Gu, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3tg2.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3tg2.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 3tg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tg2_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3tg2_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 3tg2_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 3tg2_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/3tg2 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/3tg2 | HTTPS FTP |
-Related structure data
Related structure data | 3tb4SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 24838.283 Da / Num. of mol.: 1 / Fragment: ISC domain, UNP residues 1-215 / Mutation: D35N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor Inaba N16961 / Gene: VC_0771, vibB / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6D3, isochorismatase |
---|---|
#2: Chemical | ChemComp-ISC / ( |
#3: Chemical | ChemComp-PGE / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50mM CaCl2, 0.1M Bis-Tris pH 6.5, 28% PEG MME 500, 40mM MgCl2, 2.4mM chorismate, 0.02mg/ml EntC (isochrismate synthase from Escherichia coli O157) , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. all: 87374 / Num. obs: 87374 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 44 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.528 / % possible all: 95 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TB4 Resolution: 1.101→25.21 Å / SU ML: 0.09 / σ(F): 0 / Phase error: 12.03 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.628 Å2 / ksol: 0.432 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.101→25.21 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|