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Yorodumi- PDB-3tjm: Crystal Structure of the Human Fatty Acid Synthase Thioesterase D... -
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-Basic information
Entry | Database: PDB / ID: 3tjm | ||||||
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Title | Crystal Structure of the Human Fatty Acid Synthase Thioesterase Domain with an Activate Site-Specific Polyunsaturated Fatty Acyl Adduct | ||||||
Components | Fatty acid synthase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / thioesterase domain / fatty acid synthesis / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / fatty acyl-[ACP] hydrolase activity / ether lipid biosynthetic process / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / glandular epithelial cell development ...fatty-acid synthase system / (3R)-3-hydroxybutanoyl-[acyl-carrier-protein] hydratase activity / fatty acyl-[ACP] hydrolase activity / ether lipid biosynthetic process / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / glandular epithelial cell development / : / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / Fatty acyl-CoA biosynthesis / oleoyl-[acyl-carrier-protein] hydrolase / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / modulation by host of viral process / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / ChREBP activates metabolic gene expression / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding / monocyte differentiation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / fatty acid biosynthetic process / osteoblast differentiation / melanosome / cadherin binding / inflammatory response / Golgi apparatus / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | ||||||
Authors | Zhang, W. / Zheng, F. / Florante, A.Q. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Crystal structure of FAS thioesterase domain with polyunsaturated fatty acyl adduct and inhibition by dihomo-gamma-linolenic acid. Authors: Zhang, W. / Chakravarty, B. / Zheng, F. / Gu, Z. / Wu, H. / Mao, J. / Wakil, S.J. / Quiocho, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tjm.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tjm.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tjm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/3tjm ftp://data.pdbj.org/pub/pdb/validation_reports/tj/3tjm | HTTPS FTP |
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-Related structure data
Related structure data | 1xktS 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
#1: Protein | Mass: 30971.041 Da / Num. of mol.: 1 / Fragment: UNP residues 2218-2500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAS, FASN / Plasmid: ProEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P49327, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3- ...References: UniProt: P49327, fatty-acid synthase system, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, 3-oxoacyl-[acyl-carrier-protein] reductase, EC: 4.2.1.61, EC: 1.3.1.10, oleoyl-[acyl-carrier-protein] hydrolase |
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#2: Chemical | ChemComp-7FA / |
#3: 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: 1.95 Å3/Da / Density % sol: 37.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: 18-23% PEG 3350, 0.1M Bis-Tris buffer, pH 5.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→23.56 Å / Num. all: 39110 / Num. obs: 38459 / % possible obs: 98.3341 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XKT Resolution: 1.48→23.56 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.564 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 23.067 Å2
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Refinement step | Cycle: LAST / Resolution: 1.48→23.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.48→1.518 Å / Total num. of bins used: 20
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