+Open data
-Basic information
Entry | Database: PDB / ID: 4whn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of toxin-activating acyltransferase (TAAT) | ||||||
Components | ApxC | ||||||
Keywords | TRANSFERASE / TAAT / GNAT / Toxin-activating acyltransferase / ACP binding | ||||||
Function / homology | RTX toxin-activating protein C, bacteria / RTX toxin acyltransferase family / toxin metabolic process / hemolysis in another organism / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm / CITRIC ACID / RTX-I toxin-activating lysine-acyltransferase ApxIC Function and homology information | ||||||
Biological species | Actinobacillus pleuropneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Crow, A. / Greene, N.P. / Hughes, C. / Koronakis, V. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structure of a bacterial toxin-activating acyltransferase. Authors: Greene, N.P. / Crow, A. / Hughes, C. / Koronakis, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4whn.cif.gz | 153.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4whn.ent.gz | 122.3 KB | Display | PDB format |
PDBx/mmJSON format | 4whn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4whn_validation.pdf.gz | 473.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4whn_full_validation.pdf.gz | 481.2 KB | Display | |
Data in XML | 4whn_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 4whn_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whn ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whn | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _
NCS ensembles :
|
-Components
#1: Protein | Mass: 21195.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria) Gene: apxIC, clyIC, hlyIC / Production host: Escherichia coli (E. coli) References: UniProt: P55132, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-CIT / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.34 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: Crystallisation reagent is 32% PEG300, Phosphate-citrate buffer, pH 4.4. Protein solution is 5 mg/ml ApxC in 150mM NaCl, 20 mM HEPES pH 7.5. Sitting drops formed by 2 ul Protein solution and ...Details: Crystallisation reagent is 32% PEG300, Phosphate-citrate buffer, pH 4.4. Protein solution is 5 mg/ml ApxC in 150mM NaCl, 20 mM HEPES pH 7.5. Sitting drops formed by 2 ul Protein solution and 1 ul crystallisation reagent equilibrated over 80 ul of the reagent alone. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→54.29 Å / Num. obs: 51711 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.104 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.15→54.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.424 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.981 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→54.29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|