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Yorodumi- PDB-3day: Crystal structure of human acyl-CoA synthetase medium-chain famil... -
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-Basic information
Entry | Database: PDB / ID: 3day | ||||||
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Title | Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with AMP-CPP | ||||||
Components | Acyl-coenzyme A synthetase ACSM2A, mitochondrial precursor | ||||||
Keywords | LIGASE / MIDDLE-CHAIN ACYL-COA SYNTHETASE / XENOBIOTIC/MEDIUM-CHAIN FATTY ACID-COA LIGASE / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-BINDING / FATTY ACID METABOLISM / LIPID METABOLISM / MAGNESIUM / METAL-BINDING / MITOCHONDRION / NUCLEOTIDE-BINDING POLYMORPHISM / TRANSIT PEPTIDE | ||||||
Function / homology | Function and homology information Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process ...Conjugation of salicylate with glycine / fatty acid ligase activity / decanoate-CoA ligase activity / medium-chain acyl-CoA ligase / : / benzoate-CoA ligase / benzoate-CoA ligase activity / medium-chain fatty-acyl-CoA metabolic process / fatty-acyl-CoA synthase activity / acyl-CoA metabolic process / triglyceride homeostasis / Aspirin ADME / fatty acid biosynthetic process / glucose homeostasis / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Pilka, E.S. / Kochan, G.T. / Yue, W.W. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Wikstrom, M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A. Authors: Kochan, G. / Pilka, E.S. / von Delft, F. / Oppermann, U. / Yue, W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3day.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3day.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 3day.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3day_validation.pdf.gz | 771.4 KB | Display | wwPDB validaton report |
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Full document | 3day_full_validation.pdf.gz | 777.1 KB | Display | |
Data in XML | 3day_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 3day_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3day ftp://data.pdbj.org/pub/pdb/validation_reports/da/3day | HTTPS FTP |
-Related structure data
Related structure data | 2vzeC 2wd9C 3b7wC 3c5eSC 3eq6C 3gpcC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 63334.562 Da / Num. of mol.: 1 / Fragment: Residues 32-577 / Mutation: L64P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACSM2A, ACSM2, MACS2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase |
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-Non-polymers , 7 types, 782 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-APC / | #5: Chemical | ChemComp-TRS / | #6: Chemical | ChemComp-UNX / #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 0.20M NaCl, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 17, 2008 / Details: OSMIC |
Radiation | Monochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→32.72 Å / Num. all: 48550 / Num. obs: 45963 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Rsym value: 0.055 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6604 / Rsym value: 0.303 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3C5E Resolution: 1.95→31.51 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.675 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.143 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ADDITIONAL DENSITY IN THE ACTIVE SITE, PROBABLY UNIDENTIFIED ENDOGENOUS SUBSTRATE, WAS MODELLED AS A SET OF UNKNOWN (UNX) ATOMS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.974 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→31.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 23.9408 Å / Origin y: -9.3816 Å / Origin z: -17.9111 Å
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