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Yorodumi- PDB-2bab: Crystal structure of CLA-producing fatty acid isomerase from P. acnes -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bab | ||||||
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Title | Crystal structure of CLA-producing fatty acid isomerase from P. acnes | ||||||
Components | putative aminooxidase | ||||||
Keywords | ISOMERASE / conjugated linoleic acid / fad | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Propionibacterium acnes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rudolph, M.G. / Liavonchanka, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Structure and mechanism of the Propionibacterium acnes polyunsaturated fatty acid isomerase Authors: Liavonchanka, A. / Hornung, E. / Feussner, I. / Rudolph, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bab.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bab.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 2bab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/2bab ftp://data.pdbj.org/pub/pdb/validation_reports/ba/2bab | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49081.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Propionibacterium acnes (bacteria) / Plasmid: pGEX 6-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 50842522, UniProt: Q6A8X5*PLUS |
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-Non-polymers , 5 types, 567 molecules
#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | ChemComp-ODD / ( | #5: Chemical | #6: 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: 3.59 Å3/Da / Density % sol: 65.75 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2% 1,4-butanediol, 0.02M Bis-Tris, 2M lithium sulphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 46145 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rsym value: 0.104 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.533 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.148 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.971 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→26.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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