[English] 日本語
Yorodumi- PDB-2jif: Structure of human short-branched chain acyl-CoA dehydrogenase (A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jif | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human short-branched chain acyl-CoA dehydrogenase (ACADSB) | ||||||
Components | SHORT/BRANCHED CHAIN SPECIFIC ACYL-COA DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / MITOCHONDRION / TRANSIT PEPTIDE / FATTY ACID METABOLISM / FAD / FLAVOPROTEIN / DISEASE MUTATION / LIPID METABOLISM | ||||||
Function / homology | Function and homology information short-chain 2-methylacyl-CoA dehydrogenase / : / acyl-CoA dehydrogenase activity / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / fatty acid metabolic process / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. ...Pike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Short-Branched Chain Acyl-Coa Dehydrogenase Authors: Pike, A.C.W. / Hozjan, V. / Smee, C. / Niesen, F.H. / Kavanagh, K.L. / Umeano, C. / Turnbull, A.P. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Sundstrom, M. / Oppermann, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jif.cif.gz | 329.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jif.ent.gz | 267.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jif_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2jif_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 2jif_validation.xml.gz | 64.7 KB | Display | |
Data in CIF | 2jif_validation.cif.gz | 92.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jif ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jif | HTTPS FTP |
-Related structure data
Related structure data | 1jqiS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 44474.492 Da / Num. of mol.: 4 / Fragment: RESIDUES 52-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45954, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors |
---|
-Non-polymers , 5 types, 938 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COS / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 66.7 % |
---|---|
Crystal grow | pH: 6.3 Details: 30% PEG6000, 0.15M AMMONIUM CHLORIDE PH6.3, 10% ETHYLENE GLYCOL, pH 6.30 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2→70.36 Å / Num. obs: 175824 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 25.84 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 95.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JQI Resolution: 2→70 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.099 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACETOACETYL COA WAS ADDED TO THE PROTEIN PRIOR TO CRYSTALLIZATION. HOWEVER THE DENSITY IN THE ACTIVE SITE IS MORE CONSISTENT WITH AND HAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ACETOACETYL COA WAS ADDED TO THE PROTEIN PRIOR TO CRYSTALLIZATION. HOWEVER THE DENSITY IN THE ACTIVE SITE IS MORE CONSISTENT WITH AND HAS BEEN MODELLED AS COA PERSULPHIDE. COA PERSULPHIDE PRESUMABLY COPURIFIES WITH THE BACTERIALLY EXPRESSED ENZYME.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 22.76 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→70 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|