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- PDB-4zdf: Crystal structure of yeast enoyl-CoA isomerase helix-10 deletion ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zdf | ||||||
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Title | Crystal structure of yeast enoyl-CoA isomerase helix-10 deletion (ScECI2-H10) mutant | ||||||
![]() | 3,2-trans-enoyl-CoA isomerase | ||||||
![]() | ISOMERASE / Crotonase / enoyl-CoA isomerase / beta-oxidation | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Onwukwe, G.U. / Koski, M.K. / Wierenga, R.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the ...Title: Structures of yeast peroxisomal Delta (3), Delta (2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole. Authors: Onwukwe, G.U. / Koski, M.K. / Pihko, P. / 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 | ![]() | 124 KB | Display | ![]() |
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PDB format | ![]() | 95.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zdbC ![]() 4zdcC ![]() 4zddC ![]() 4zdeC ![]() 1k39S 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 4 - 267 / Label seq-ID: 24 - 287
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Components
#1: Protein | Mass: 32471.053 Da / Num. of mol.: 2 / Mutation: Deleted R269-L280 Source method: isolated from a genetically manipulated source Details: CYS212 was oxidized to CME due to the presence of BME in the purification buffers Source: (gene. exp.) ![]() ![]() Gene: ECI1, YLR284C / Production host: ![]() ![]() References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM imidazole pH 6.5, 1 M NaAcetate |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / 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: 1.81→48.94 Å / Num. obs: 64106 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.064 / Mean I/σ(I) obs: 1.6 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K39 Resolution: 1.81→48.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.428 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / 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: 35.875 Å2
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Refinement step | Cycle: 1 / Resolution: 1.81→48.94 Å
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Refine LS restraints |
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