+Open data
-Basic information
Entry | Database: PDB / ID: 5vxf | ||||||
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Title | Crystal structure of Xanthomonas campestris OleA E117Q | ||||||
Components | 3-oxoacyl-[ACP] synthase III | ||||||
Keywords | TRANSFERASE / Thiolase / Condensation | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å | ||||||
Authors | Jensen, M.R. / Wilmot, C.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem. J. / Year: 2017 Title: OleA Glu117 is key to condensation of two fatty-acyl coenzyme A substrates in long-chain olefin biosynthesis. Authors: Jensen, M.R. / Goblirsch, B.R. / Christenson, J.K. / Esler, M.A. / 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 | 5vxf.cif.gz | 270.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vxf.ent.gz | 217.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vxf_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 5vxf_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 5vxf_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 5vxf_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/5vxf ftp://data.pdbj.org/pub/pdb/validation_reports/vx/5vxf | HTTPS FTP |
-Related structure data
Related structure data | 5vxdC 5vxeC 5vxgC 5vxhC 5vxiC 4ku3S C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
#1: Protein | Mass: 38841.457 Da / Num. of mol.: 2 / Mutation: E117Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria) Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: fabH, XCC0212 / Plasmid: pET28b+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q8PDX2, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-GOL / #3: 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: 2.43 Å3/Da / Density % sol: 49.36 % / Mosaicity: 0.539 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 17% PEG 8000, 105 mM potassium phosphate dibasic, 100 mM sodium citrate pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 27, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 73521 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Χ2: 1.044 / Net I/σ(I): 10.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4KU3 Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.194 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.57 Å2 / Biso mean: 31.651 Å2 / Biso min: 15.08 Å2
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Refinement step | Cycle: final / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.753→1.799 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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