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Yorodumi- PDB-7ayb: Crystal Structure of wild type human mitochondrial 2-Enoyl Thioes... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ayb | ||||||
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Title | Crystal Structure of wild type human mitochondrial 2-Enoyl Thioester Reductase (MECR) | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / Medium-chain alcohol dehydrogenase / Mitochondrial trans-2-enoyl-CoA reductase / Fatty acid synthesis | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase (NADPH) / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / ceramide biosynthetic process / fatty acid metabolic process / fatty acid biosynthetic process / intracellular iron ion homeostasis / mitochondrial matrix / mitochondrion / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Rahman, M.T. / Koski, M.K. / Autio, K.J. / Kastaniotis, A.J. / Wierenga, R.K. / Hiltunen, J.K. | ||||||
Funding support | Finland, 1items
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Citation | Journal: Nat Commun / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ayb.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ayb.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ayb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ayb_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 7ayb_full_validation.pdf.gz | 460.3 KB | Display | |
Data in XML | 7ayb_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7ayb_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/7ayb ftp://data.pdbj.org/pub/pdb/validation_reports/ay/7ayb | HTTPS FTP |
-Related structure data
Related structure data | 7aycC 2vcyS 7ayd C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38293.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Wild type / Source: (gene. exp.) Homo sapiens (human) / Gene: MECR, NBRF1, CGI-63 / Production host: Escherichia coli (E. coli) / Strain (production host): BL 21 Star (DE3) pLysS References: UniProt: Q9BV79, enoyl-[acyl-carrier-protein] reductase (NADPH) |
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-Non-polymers , 5 types, 209 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-PO4 / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.05 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 1.85→61.89 Å / Num. obs: 37465 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.011 / Rrim(I) all: 0.048 / Χ2: 0.95 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 15.1 % / Rmerge(I) obs: 1.894 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2722 / CC1/2: 0.703 / Rpim(I) all: 0.497 / Rrim(I) all: 1.959 / Χ2: 0.81 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2vcy Resolution: 1.85→61.89 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.904 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.124 / 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: 141.41 Å2 / Biso mean: 58.952 Å2 / Biso min: 31.98 Å2
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Refinement step | Cycle: final / Resolution: 1.85→61.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -58.591 Å / Origin y: 66.508 Å / Origin z: 10.486 Å
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