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Yorodumi- PDB-5teq: C20S C293G MUTANT N-TERMINAL HUMAN ATP CITRATE LYASE BOUND TO CITRATE -
+Open data
-Basic information
Entry | Database: PDB / ID: 5teq | ||||||
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Title | C20S C293G MUTANT N-TERMINAL HUMAN ATP CITRATE LYASE BOUND TO CITRATE | ||||||
Components | ATP-citrate synthase | ||||||
Keywords | TRANSFERASE / ATP-grasp fold / citrate binding | ||||||
Function / homology | Function and homology information ATP citrate synthase / ATP citrate synthase activity / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process ...ATP citrate synthase / ATP citrate synthase activity / Fatty acyl-CoA biosynthesis / citrate metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA biosynthetic process / oxaloacetate metabolic process / coenzyme A metabolic process / lipid biosynthetic process / cholesterol biosynthetic process / tricarboxylic acid cycle / fatty acid biosynthetic process / azurophil granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Hu, J. / Fraser, M.E. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Binding of hydroxycitrate to human ATP-citrate lyase. Authors: Hu, J. / Komakula, A. / Fraser, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5teq.cif.gz | 548.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5teq.ent.gz | 454 KB | Display | PDB format |
PDBx/mmJSON format | 5teq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/5teq ftp://data.pdbj.org/pub/pdb/validation_reports/te/5teq | HTTPS FTP |
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-Related structure data
Related structure data | 5tdeC 5tdfC 5tdmC 5tdzC 5te1C 5tesC 5tetC C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 90611.508 Da / Num. of mol.: 2 / Mutation: C20S, C293G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACLY / Production host: Escherichia coli (E. coli) / References: UniProt: P53396, ATP citrate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.52 Å3/Da / Density % sol: 51.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12.5% P3350, 100-200 mM MES pH 7, 125 mM ammonium citrate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97951 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.08 Å / Num. obs: 79319 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 10.6 |
-Processing
Software | Name: PHENIX / Version: (1.10_2152: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.3→41.458 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→41.458 Å
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Refine LS restraints |
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LS refinement shell |
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