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Open data
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Basic information
Entry | Database: PDB / ID: 4zdc | ||||||||||||
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Title | Yeast enoyl-CoA isomerase complexed with octanoyl-CoA | ||||||||||||
![]() | 3,2-trans-enoyl-CoA isomerase | ||||||||||||
![]() | ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() Beta-oxidation of very long chain fatty acids / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / ![]() ![]() ![]() 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 | ![]() | 187.1 KB | Display | ![]() |
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PDB format | ![]() | 147.2 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 ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / 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: 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-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: 66.77 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES pH 7.0, 1.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.13→47.31 Å / Num. obs: 86227 / % possible obs: 99.8 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.13→2.17 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.7 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1K39 Resolution: 2.13→47.31 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.57 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / 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: 48.095 Å2
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Refinement step | Cycle: 1 / Resolution: 2.13→47.31 Å
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Refine LS restraints |
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