+Open data
-Basic information
Entry | Database: PDB / ID: 1w8d | ||||||
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Title | Binary structure of human DECR. | ||||||
Components | 2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR | ||||||
Keywords | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE / REDUCTASE / SELENOMETHIONINE / SAD / DIENOYL-COA | ||||||
Function / homology | Function and homology information 2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / fatty acid beta-oxidation / catalytic complex / NADPH binding / positive regulation of cold-induced thermogenesis / mitochondrial matrix / mitochondrion / nucleoplasm ...2,4-dienoyl-CoA reductase [(3E)-enoyl-CoA-producing] / 2,4-dienoyl-CoA reductase (NADPH) activity / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / fatty acid beta-oxidation / catalytic complex / NADPH binding / positive regulation of cold-induced thermogenesis / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å | ||||||
Authors | Alphey, M.S. / Byres, E. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structure and Reactivity of Human Mitochondrial 2,4-Dienoyl-Coa Reductase: Enzyme-Ligand Interactions in a Distinctive Short-Chain Reductase Active Site Authors: Alphey, M.S. / Yu, W. / Byres, E. / Li, D. / Hunter, W.N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w8d.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w8d.ent.gz | 190.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w8d_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1w8d_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1w8d_validation.xml.gz | 45.7 KB | Display | |
Data in CIF | 1w8d_validation.cif.gz | 61.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w8d ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w8d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32690.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organelle: MITOCHONDRIA / Plasmid: PLM1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q16698, 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing] #2: Chemical | #3: Chemical | ChemComp-NAP / #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: 2.2 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | pH: 7.4 / Details: pH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 7, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→2.32 Å / Num. obs: 56224 / % possible obs: 96.9 % / Observed criterion σ(I): 1.5 / Redundancy: 3.8 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.2→70.71 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.838 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.245 / 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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→70.71 Å
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Refine LS restraints |
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