+Open data
-Basic information
Entry | Database: PDB / ID: 5yoa | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of KAS III from Acinetobacter baumannii | ||||||
Components | 3-Oxoacyl-[acyl-carrier-(ACP)] synthase III C terminal family protein | ||||||
Keywords | TRANSFERASE / thiolase | ||||||
Function / homology | Function and homology information beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Model details | C155A mutant in complex with CoA | ||||||
Authors | Lee, W.C. / Jung, M. / Lee, J. / Kim, Y. | ||||||
Funding support | Korea, Republic Of, 1items
| ||||||
Citation | Journal: to be published Title: Crystal structure of a novel KAS III from Acinetobacter baumannii Authors: Lee, W.C. / Jung, M. / Lee, J. / Kim, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5yoa.cif.gz | 161.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5yoa.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 5yoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yoa_validation.pdf.gz | 686 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5yoa_full_validation.pdf.gz | 696.8 KB | Display | |
Data in XML | 5yoa_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 5yoa_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/5yoa ftp://data.pdbj.org/pub/pdb/validation_reports/yo/5yoa | HTTPS FTP |
-Related structure data
Related structure data | 5yo9C 5yzuC 3ledS 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: 40428.465 Da / Num. of mol.: 2 / Mutation: C155A, C264A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: KAS III / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: V5VGF8, beta-ketoacyl-[acyl-carrier-protein] synthase III, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-CO8 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.99 % / Mosaicity: 0.808 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 0.2M calcium acetate, , 0.1M Tris pH 7.0, 20% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→50 Å / Num. obs: 35771 / % possible obs: 93.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.69 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Χ2: 2.554 / Net I/σ(I): 12.5 / Num. measured all: 236848 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LED Resolution: 2.33→29.908 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.24
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.94 Å2 / Biso mean: 31.4738 Å2 / Biso min: 10.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.33→29.908 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
|