+Open data
-Basic information
Entry | Database: PDB / ID: 2a1t | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the human MCAD:ETF E165betaA complex | ||||||
Components |
| ||||||
Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / electron transfer / domain dynamics / conformational sampling / protein:protein complex / fatty acid b-degradation / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information electron transfer flavoprotein complex / medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase ...electron transfer flavoprotein complex / medium-chain fatty acid catabolic process / mitochondrial fatty acid beta-oxidation of unsaturated fatty acids / carnitine metabolic process, CoA-linked / medium-chain acyl-CoA dehydrogenase / Beta oxidation of octanoyl-CoA to hexanoyl-CoA / Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA / medium-chain fatty acyl-CoA dehydrogenase activity / carnitine biosynthetic process / fatty acid beta-oxidation using acyl-CoA dehydrogenase / medium-chain fatty acid metabolic process / acyl-CoA dehydrogenase activity / amino acid catabolic process / Respiratory electron transport / cardiac muscle cell differentiation / glycogen biosynthetic process / regulation of gluconeogenesis / fatty acid beta-oxidation / response to starvation / Protein methylation / respiratory electron transport chain / response to cold / post-embryonic development / liver development / mitochondrial membrane / PPARA activates gene expression / flavin adenine dinucleotide binding / electron transfer activity / oxidoreductase activity / mitochondrial matrix / axon / mitochondrion / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Toogood, H.S. / Van Thiel, A. / Scrutton, N.S. / Leys, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Stabilization of Non-productive Conformations Underpins Rapid Electron Transfer to Electron-transferring Flavoprotein Authors: Toogood, H.S. / van Thiel, A. / Scrutton, N.S. / Leys, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a1t.cif.gz | 405.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a1t.ent.gz | 325.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1t ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1t | HTTPS FTP |
---|
-Related structure data
Related structure data | 2a1uC 1t9gS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Refine code: 6
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 46648.273 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTRC99C / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P11310, EC: 1.3.99.3 |
---|
-Electron transfer flavoprotein ... , 2 types, 2 molecules RS
#2: Protein | Mass: 35121.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P13804 |
---|---|
#3: Protein | Mass: 27827.611 Da / Num. of mol.: 1 / Mutation: E165A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PK18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P38117 |
-Non-polymers , 3 types, 70 molecules
#4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-AMP / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 5000MME, 50mM sodium thiocyanate, sodium cacodylate 0.1M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 5, 2005 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. all: 171306 / Num. obs: 55260 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 82 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T9G Resolution: 2.8→19.98 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.87 / SU B: 16.374 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.633 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 5650 / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.871 Å / Total num. of bins used: 20
|