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Yorodumi- PDB-2wd9: CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wd9 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH IBUPROFEN | ||||||
Components | ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL | ||||||
Keywords | LIGASE / NUCLEOTIDE-BINDING / FATTY ACID METABOLISM / TRANSIT PEPTIDE / LIPID METABOLISM / NUCLEOTIDE BINDING / MITOCHONDRION / METAL-BINDING / LIGASE ACTIVITY / MEDIUM-CHAIN FATTY ACID / FATTY ACID METABOLIC PROCESS / MAGNESIUM / ATP-BINDING | ||||||
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: 2.6 Å | ||||||
Authors | Yue, W.W. / Kochan, G.T. / Pilka, E.S. / Bhatia, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U. | ||||||
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. / Delft, F.V. / Oppermann, U. / Yue, W.W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wd9.cif.gz | 314.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wd9.ent.gz | 254.2 KB | Display | PDB format |
PDBx/mmJSON format | 2wd9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wd9_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 2wd9_full_validation.pdf.gz | 477.6 KB | Display | |
Data in XML | 2wd9_validation.xml.gz | 55.7 KB | Display | |
Data in CIF | 2wd9_validation.cif.gz | 78.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wd9 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wd9 | HTTPS FTP |
-Related structure data
Related structure data | 2vzeC 3b7wSC 3c5eC 3dayC 3eq6C 3gpcC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
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-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: Ens-ID: 1
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-Components
#1: Protein | Mass: 63206.438 Da / Num. of mol.: 3 / Fragment: RESIDUES 32-576 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q08AH3, medium-chain acyl-CoA ligase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 64 TO PRO ENGINEERED RESIDUE IN CHAIN B, LEU 64 TO PRO ...ENGINEERED | |
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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: 2.43 Å3/Da / Density % sol: 49.39 % / Description: NONE |
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Crystal grow | Details: 0.2M AM ACETATE, 0.1M TRIS PH 8.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 11, 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: 2.6→38.92 Å / Num. obs: 54507 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B7W Resolution: 2.6→38.92 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.882 / SU B: 26.872 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.258 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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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: 13.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→38.92 Å
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Refine LS restraints |
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