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- PDB-4euf: Crystal structure of Clostridium acetobutulicum trans-2-enoyl-CoA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4euf | ||||||
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Title | Crystal structure of Clostridium acetobutulicum trans-2-enoyl-CoA reductase in complex with NAD | ||||||
![]() | Putative reductase CA_C0462 | ||||||
![]() | OXIDOREDUCTASE / TER / biofuel / synthetic biology / reductase / catalytic mechanism / substrate specificity | ||||||
Function / homology | ![]() trans-2-enoyl-CoA reductase (NAD+) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, K. / Zhao, M. / Zhang, T. / Yang, S. / Ding, J. | ||||||
![]() | ![]() Title: Structures of trans-2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola: insights into the substrate specificity and the catalytic mechanism Authors: Hu, K. / Zhao, M. / Zhang, T. / Zha, M. / Zhong, C. / Jiang, Y. / Ding, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.2 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 730.6 KB | Display | ![]() |
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Full document | ![]() | 740.7 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4eueSC ![]() 4euhC ![]() 4fbgC 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
#1: Protein | Mass: 47891.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787 Gene: CA_C0462 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: Q97LU2, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-NAD / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M ammonium citrate tribasic, 20% PEG 3350, pH 7.0, temperature 289K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 11837 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4.5 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4EUE Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.9 Å2 / Biso mean: 45.5651 Å2 / Biso min: 5.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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