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- PDB-4zdb: Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zdb | ||||||
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Title | Yeast enoyl-CoA isomerase (ScECI2) complexed with acetoacetyl-CoA | ||||||
![]() | 3,2-trans-enoyl-CoA isomerase | ||||||
![]() | ISOMERASE / Crotonase / acetoacetyl-CoA / 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 / mitochondrion 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 | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 148.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 51.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zdcC ![]() 4zddC ![]() 4zdeC ![]() 4zdfC ![]() 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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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: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 4 - 270 / Label seq-ID: 24 - 290
NCS ensembles :
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Components
#1: Protein | Mass: 33965.848 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Cysteine 212 was oxidized to CME (S,S-(2-HYDROXYETHYL)THIOCYSTEINE) in the structure due to the presence of beta-mecarptoethanol. Source: (gene. exp.) ![]() ![]() Gene: ECI1, YLR284C / Production host: ![]() ![]() References: UniProt: Q05871, Delta3-Delta2-enoyl-CoA isomerase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES pH 6.5, 1.6 M (NH4)2SO4, 10% dioxane |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.945 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→103.1 Å / Num. obs: 83764 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1k39 Resolution: 2.14→103.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.219 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.123 / 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: 40.968 Å2
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Refinement step | Cycle: 1 / Resolution: 2.14→103.1 Å
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Refine LS restraints |
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