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Yorodumi- PDB-3s20: Crystal structure of cerulenin bound Xanthomonas campestri OleA (soak) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s20 | ||||||
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Title | Crystal structure of cerulenin bound Xanthomonas campestri OleA (soak) | ||||||
Components | 3-oxoacyl-[ACP] synthase III | ||||||
Keywords | TRANSFERASE / Non-decarboxylative Claisen Condensation Reaction | ||||||
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: 1.8796 Å | ||||||
Authors | Goblirsch, B.R. / Wilmot, C.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal Structures of Xanthomonas campestris OleA Reveal Features That Promote Head-to-Head Condensation of Two Long-Chain Fatty Acids. Authors: Goblirsch, B.R. / Frias, J.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 | 3s20.cif.gz | 280.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s20.ent.gz | 225.6 KB | Display | PDB format |
PDBx/mmJSON format | 3s20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s20_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
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Full document | 3s20_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 3s20_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 3s20_validation.cif.gz | 47.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/3s20 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/3s20 | HTTPS FTP |
-Related structure data
Related structure data | 3rowSC 3s1zC 3s21C 3s23C 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: 37306.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Gene: fabH, XCC0212 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PDX2 #2: Chemical | #3: Chemical | #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: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 18% PEG 8000, 80 mM potassium phosphate dibasic, 100 mM sodium citrate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.8796→50 Å / Num. all: 59154 / Num. obs: 59154 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 40.7 |
Reflection shell | Resolution: 1.8796→1.91 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3ROW Resolution: 1.8796→30.487 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 18.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.547 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8796→30.487 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -12.1328 Å / Origin y: 15.2037 Å / Origin z: -14.4082 Å
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Refinement TLS group | Selection details: (chain 'A') or (chain 'B') |