+Open data
-Basic information
Entry | Database: PDB / ID: 2v5g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the mutated N263A YscU C-terminal domain | ||||||
Components | YSCU | ||||||
Keywords | MEMBRANE PROTEIN / PLASMID / AUTOCLEAVAGE / RECOGNITION PROTEIN / TYPE III SECRETION SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | YERSINIA ENTEROCOLITICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Wiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of the Type III Secretion Recognition Protein Yscu from Yersinia Enterocolitica Authors: Wiesand, U. / Sorg, I. / Amstutz, M. / Wagner, S. / Van Den Heuvel, J. / Luehrs, T. / Cornelis, G.R. / Heinz, D.W. #1: Journal: J.Bacteriol. / Year: 1994 Title: Yscu, a Yersinia Enterocolitica Inner Membrane Protein Involved in Yop Secretion. Authors: Allaoui, A. / Woestyn, S. / Sluiters, C. / Cornelis, G.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v5g.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v5g.ent.gz | 27.9 KB | Display | PDB format |
PDBx/mmJSON format | 2v5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v5g_validation.pdf.gz | 427.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v5g_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 2v5g_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 2v5g_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5g ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16994.943 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 211-354 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA ENTEROCOLITICA (bacteria) / Strain: W22703 / Plasmid: PGEX-6-P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: Q56844 |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROP METHOD USING 3 UL OF A 8 MG/ML PROTEIN SOLUTION MIXED WITH 3UL RESERVOIR BUFFER (1.6 M (NH4)2SO4, 0.2 M NACL, 0.1 M HEPES PH 7.5) IN THE DROPLET. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.97854 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 26, 2007 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97854 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 10836 / % possible obs: 99.9 % / Observed criterion σ(I): 2.2 / Redundancy: 13.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2→29.84 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.549 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES 211-221 AND 343-354 DUE TO WEAK DENSITY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→29.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|