+Open data
-Basic information
Entry | Database: PDB / ID: 4ktm | ||||||
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Title | Crystal Structure of C143S Xanthomonas campestris OleA | ||||||
Components | 3-oxoacyl-[ACP] synthase III | ||||||
Keywords | TRANSFERASE / Thiolase | ||||||
Function / homology | Function and homology information acyl-CoA:acyl-CoA alkyltransferase / secondary metabolite biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.36 Å | ||||||
Authors | Goblirsch, B.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Substrate Trapping in Crystals of the Thiolase OleA Identifies Three Channels That Enable Long Chain Olefin Biosynthesis. Authors: Goblirsch, B.R. / Jensen, M.R. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ktm.cif.gz | 280.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ktm.ent.gz | 227.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ktm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ktm_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 4ktm_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | 4ktm_validation.xml.gz | 29 KB | Display | |
Data in CIF | 4ktm_validation.cif.gz | 41.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4ktm ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4ktm | HTTPS FTP |
-Related structure data
Related structure data | 4ktiC 4ku2C 4ku3C 4ku5C 3rowS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetric unit of the structure corresponds to the biological assembly. |
-Components
#1: Protein | Mass: 36880.250 Da / Num. of mol.: 2 / Mutation: C143S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Strain: ATCC 33913 / NCPPB 528 / LMG 568 / Gene: fabH, XCC0212 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDX2 #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 15% PEG 8000, 80 mM potassium phosphate dibasic, 100 mM sodium citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→50 Å / Num. all: 211791 / Num. obs: 211791 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.36→2.4 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.1 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3ROW Resolution: 2.36→32.828 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→32.828 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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