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- PDB-7ayc: Crystal Structure of human mitochondrial 2-Enoyl Thioester Reduct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ayc | ||||||
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Title | Crystal Structure of human mitochondrial 2-Enoyl Thioester Reductase (MECR) with single mutation G165Q | ||||||
![]() | Enoyl-[acyl-carrier-protein] reductase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / Medium-chain alcohol dehydrogenase / Mitochondrial trans-2-enoyl-CoA reductase / Fatty acid synthesis | ||||||
Function / homology | ![]() enoyl-[acyl-carrier-protein] reductase (NADPH) / trans-2-enoyl-CoA reductase (NADPH) activity / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rahman, M.T. / Koski, M.K. / Autio, K.J. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration. Authors: Tanvir Rahman, M. / Kristian Koski, M. / Panecka-Hofman, J. / Schmitz, W. / Kastaniotis, A.J. / Wade, R.C. / Wierenga, R.K. / Kalervo Hiltunen, J. / Autio, K.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 | ![]() | 152.2 KB | Display | ![]() |
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PDB format | ![]() | 119 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.1 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aybC ![]() 2vcyS ![]() 7ayd C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Components
#1: Protein | Mass: 38364.074 Da / Num. of mol.: 1 Mutation: Glycine 165 (136 in this construct) is mutated to Glutamine (G165Q) Source method: isolated from a genetically manipulated source Details: Glycine 165 (136 in the construct) is mutated to Glutamine (G165Q). Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BV79, enoyl-[acyl-carrier-protein] reductase (NADPH) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1M NaCl, 16.82%w/v Polyethylene glycol 6000, 100mM Acetic Acid pH:4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→56.95 Å / Num. obs: 28740 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.013 / Rrim(I) all: 0.057 / Χ2: 0.93 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.02→2.07 Å / Rmerge(I) obs: 2.475 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2079 / CC1/2: 0.624 / Rpim(I) all: 0.568 / Rrim(I) all: 2.54 / Χ2: 0.88 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vcy Resolution: 2.02→56.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.546 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.85 Å2 / Biso mean: 89.568 Å2 / Biso min: 42.56 Å2
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Refinement step | Cycle: final / Resolution: 2.02→56.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -6.935 Å / Origin y: 22.155 Å / Origin z: -13.428 Å
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