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Yorodumi- PDB-3b7w: Crystal structure of human acyl-CoA synthetase medium-chain famil... -
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-Basic information
Entry | Database: PDB / ID: 3b7w | ||||||
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Title | Crystal structure of human acyl-CoA synthetase medium-chain family member 2A, with L64P mutation | ||||||
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 / 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: 2 Å | ||||||
Authors | Pilka, E.S. / Kochan, G.T. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / 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 | 3b7w.cif.gz | 131.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7w.ent.gz | 99 KB | Display | PDB format |
PDBx/mmJSON format | 3b7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b7w_validation.pdf.gz | 436.6 KB | Display | wwPDB validaton report |
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Full document | 3b7w_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3b7w_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3b7w_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7w ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7w | HTTPS FTP |
-Related structure data
Related structure data | 2vzeC 2wd9C 3c5eC 3dayC 3eq6C 3gpcC 1pg3S S: Starting model for refinement C: citing same article (ref.) |
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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
#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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#2: Chemical | ChemComp-MG / | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 1.4M Na citrate, 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: Sep 25, 2007 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.57 Å / Num. all: 63810 / Num. obs: 60580 / % possible obs: 98.9 % / Observed criterion σ(I): 2.06 / Redundancy: 4.6 % / Rmerge(I) obs: 0.077 / Rsym value: 0.04 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2 / Rsym value: 0.446 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PG3 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.004 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 28.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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