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Yorodumi- PDB-1hnu: CRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hnu | ||||||
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Title | CRYSTAL STRUCTURE OF PEROXISOMAL DELTA3-DELTA2-ENOYL-COA ISOMERASE FROM SACCHAROMYCES CEREVISIAE | ||||||
Components | D3,D2-ENOYL COA ISOMERASE ECI1 | ||||||
Keywords | ISOMERASE / alpha/beta | ||||||
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 / MAD / Resolution: 2.15 Å | ||||||
Authors | Mursula, A.M. / van Aalten, D.M.F. / Hiltunen, J.K. / Wierenga, R.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: The crystal structure of delta(3)-delta(2)-enoyl-CoA isomerase. Authors: Mursula, A.M. / van Aalten, D.M. / Hiltunen, J.K. / Wierenga, R.K. #1: 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. / 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 | 1hnu.cif.gz | 68.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hnu.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hnu_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 1hnu_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 1hnu_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 1hnu_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hn/1hnu ftp://data.pdbj.org/pub/pdb/validation_reports/hn/1hnu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31718.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.48 % | ||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: MES, ammonium sulfate, 1,4-dioxane, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.1765, 1.1773, 1.1697, 1.1836 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 26, 1999 | |||||||||||||||
Radiation | Monochromator: synchrotron / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→30 Å / Num. all: 27191 / Num. obs: 27191 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.97 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16 | |||||||||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2651 / % possible all: 99.7 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å | |||||||||||||||
Reflection shell | *PLUS % possible obs: 99.7 % / Num. unique obs: 2651 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.15→20 Å / Isotropic thermal model: individual isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.95 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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