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- PDB-4u19: Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4u19 | ||||||
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Title | Crystal structure of human peroxisomal delta3,delta2, enoyl-CoA isomerase V349A mutant (ISOA-ECI2) | ||||||
![]() | Enoyl-CoA delta isomerase 2 | ||||||
![]() | ISOMERASE / PECI / enoy-CoA isomerase / crotonase / beta-oxidation | ||||||
Function / homology | ![]() Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle ...Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / Beta-oxidation of very long chain fatty acids / fatty-acyl-CoA binding / fatty acid catabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / intracellular membrane-bounded organelle / mitochondrion / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Onwukwe, G.U. / Koski, M.K. / Wierenga, R.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human Delta (3) , Delta (2) -enoyl-CoA isomerase, type 2: a structural enzymology study on the catalytic role of its ACBP domain and helix-10. Authors: Onwukwe, G.U. / Kursula, P. / Koski, M.K. / Schmitz, W. / Wierenga, R.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.3 KB | Display | ![]() |
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PDB format | ![]() | 126.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.1 KB | Display | ![]() |
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Full document | ![]() | 471.6 KB | Display | |
Data in XML | ![]() | 29.6 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u18C ![]() 4u1aC ![]() 2f6qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 103 - 348 / Label seq-ID: 24 - 269
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 30536.844 Da / Num. of mol.: 3 / Fragment: UNP residues 138-390 / Mutation: yes Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75521, Delta3-Delta2-enoyl-CoA isomerase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM HEPES pH 7.5, 10% PEG 6000, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→47.61 Å / Num. obs: 62659 / % possible obs: 99.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.88→1.95 Å / Redundancy: 7 % / Rmerge(I) obs: 1.441 / Mean I/σ(I) obs: 1.5 / % possible all: 96.8 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2F6Q Resolution: 1.88→47.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.046 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.144 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.45 Å2
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Refinement step | Cycle: 1 / Resolution: 1.88→47.6 Å
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Refine LS restraints |
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