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Yorodumi- PDB-3eq6: Crystal structure of human acyl-CoA synthetase medium-chain famil... -
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-Basic information
Entry | Database: PDB / ID: 3eq6 | ||||||
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Title | Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in a ternary complex with products | ||||||
Components | Acyl-coenzyme A synthetase ACSM2A | ||||||
Keywords | LIGASE / Middle-chain acyl-CoA synthetase / xenobiotic/medium-chain fatty acid-CoA ligase / ATP-binding / fatty acid metabolism / lipid metabolism / magnesium / metal-binding / mitochondrion / nucleotide-binding polymorphism / transit peptide / Structural Genomics / SGC / Structural Genomics Consortium | ||||||
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: 2.4 Å | ||||||
Authors | Pilka, E.S. / Kochan, G. / Yue, W.W. / Bhatia, C. / Von delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / 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 | 3eq6.cif.gz | 234.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eq6.ent.gz | 183.3 KB | Display | PDB format |
PDBx/mmJSON format | 3eq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eq6_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3eq6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3eq6_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 3eq6_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eq6 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eq6 | HTTPS FTP |
-Related structure data
Related structure data | 2vzeC 2wd9C 3b7wSC 3c5eC 3dayC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 37 - 569 / Label seq-ID: 30 - 562
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-Components
#1: Protein | Mass: 63334.562 Da / Num. of mol.: 2 / Fragment: UNP residues 32-577 / Mutation: L64P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACSM2A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): high five / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase #2: Chemical | #3: Chemical | #4: 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Mg(form), 15% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING 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: Jul 4, 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: 2.4→24.99 Å / Num. all: 49866 / Num. obs: 47300 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.107 / Rsym value: 0.07 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7167 / Rsym value: 0.323 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B7W Resolution: 2.4→21.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.136 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.394 / ESU R Free: 0.25 / 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: 17.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→21.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 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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