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Yorodumi- PDB-1k39: The structure of yeast delta3-delta2-enoyl-COA isomerase complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k39 | ||||||
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Title | The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA | ||||||
Components | d3,d2-enoyl CoA isomerase ECI1 | ||||||
Keywords | ISOMERASE / beta-beta-alpha spiral | ||||||
Function / homology | Function and homology information Beta-oxidation of very long chain fatty acids / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Peroxisomal protein import / fatty acid beta-oxidation / peroxisomal matrix / peroxisome Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å | ||||||
Authors | Mursula, A.M. / Geerlof, A. / Hiltunen, J.K. / Wierenga, R.K. | ||||||
Citation | #1: Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structure of delta3-delta2-enoyl-CoA isomerase Authors: Mursula, A.M. / van Aalten, D.M.F. / Hiltunen, J.K. / Wierenga, R.K. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and X-ray diffraction analysis of peroxisomal Delta3-Delta2-enoyl-CoA isomerase from Saccharomyces cerevisiae Authors: Mursula, A.M. / van Aalten, D.M.F. / Modis, Y. / Hiltunen, J.K. / Wierenga, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k39.cif.gz | 172.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k39.ent.gz | 138 KB | Display | PDB format |
PDBx/mmJSON format | 1k39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/1k39 ftp://data.pdbj.org/pub/pdb/validation_reports/k3/1k39 | HTTPS FTP |
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-Related structure data
Related structure data | 1hnuS 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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Details | The biological assembly is a hexamer generated from the trimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 31718.369 Da / Num. of mol.: 3 / Mutation: M25I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ECI1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase #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: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M TEA, 1.3 M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.946 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 2000 |
Radiation | Monochromator: bendable mirror and asymmetrically cut Si(111) monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.946 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. all: 23549 / Num. obs: 22527 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.3→3.42 Å / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HNU Resolution: 3.29→20 Å / SU B: 17.906 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.628 Å2
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Refinement step | Cycle: LAST / Resolution: 3.29→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.286→3.369 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Origin x: -11.499 Å / Origin y: 10.513 Å / Origin z: 146.123 Å
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Refinement TLS group |
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