+Open data
-Basic information
Entry | Database: PDB / ID: 6b2s | |||||||||
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Title | Crystal structure of Xanthomonas campestris OleA H285N | |||||||||
Components | 3-oxoacyl-[ACP] synthase III | |||||||||
Keywords | TRANSFERASE / Thiolase / OleA / 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: 2 Å | |||||||||
Authors | Jensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / Mohamed, F.A. / Wackett, L.P. / Wilmot, C.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: FEBS Lett. / Year: 2018 Title: The role of OleA His285 in orchestration of long-chain acyl-coenzyme A substrates. Authors: Jensen, M.R. / Goblirsch, B.R. / Esler, M.A. / Christenson, J.K. / 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 | 6b2s.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b2s.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 6b2s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/6b2s ftp://data.pdbj.org/pub/pdb/validation_reports/b2/6b2s | HTTPS FTP |
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-Related structure data
Related structure data | 6b2rC 6b2tC 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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-Components
#1: Protein | Mass: 38834.402 Da / Num. of mol.: 2 / Mutation: H285N 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 (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8PDX2, beta-ketoacyl-[acyl-carrier-protein] synthase I #2: Chemical | ChemComp-GOL / #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: 2.39 Å3/Da / Density % sol: 48.6 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 18% PEG 8000, 100 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-D / Wavelength: 1.03322 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.72 Å / Num. obs: 48443 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 29.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.036 / Rrim(I) all: 0.077 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.506 / Num. unique obs: 3318 / CC1/2: 0.813 / Rpim(I) all: 0.28 / Rrim(I) all: 0.581 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3ROW Resolution: 2→29.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.75 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.153 / 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: 103.04 Å2 / Biso mean: 34.409 Å2 / Biso min: 16.79 Å2
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Refinement step | Cycle: final / Resolution: 2→29.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 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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