+Open data
-Basic information
Entry | Database: PDB / ID: 5tdz | ||||||
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Title | TEV Cleaved Human ATP Citrate Lyase Bound to Tartrate and ADP | ||||||
Components | (ATP-citrate synthase) x 2 | ||||||
Keywords | TRANSFERASE / TEV cleaved / ATP-grasp fold / Tartrate 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 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 | 5tdz.cif.gz | 297.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tdz.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/5tdz ftp://data.pdbj.org/pub/pdb/validation_reports/td/5tdz | HTTPS FTP |
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-Related structure data
Related structure data | 5tdeC 5tdfC 5tdmC 5te1C 5teqC 5tesC 5tetC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 47836.633 Da / Num. of mol.: 1 / Fragment: unp residues 1-425 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 |
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#2: Protein | Mass: 35421.570 Da / Num. of mol.: 1 / Fragment: unp residues 488-810 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 |
-Non-polymers , 9 types, 516 molecules
#3: Chemical | ChemComp-TLA / | ||||||
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#4: Chemical | ChemComp-ADP / | ||||||
#5: Chemical | ChemComp-MG / | ||||||
#6: Chemical | ChemComp-PO4 / | ||||||
#7: Chemical | ChemComp-ADN / | ||||||
#8: Chemical | #9: Chemical | #10: Chemical | ChemComp-TRS / | #11: Water | ChemComp-HOH / | |
-Details
Sequence details | THE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED TO HAVE TEV PROTEASE CLEAVAGE SITES ...THE AMINO-TERMINAL PORTION OF HUMAN ACLY WAS REDESIGNED |
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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: 2.76 Å3/Da / Density % sol: 55.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 13% P3350, 100 mM TrisHCl pH 8.8, 100 mM ammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.00003 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.38 Å / Num. obs: 61452 / % possible obs: 97.6 % / Redundancy: 3.7 % / Net I/σ(I): 12 |
-Processing
Software | Name: PHENIX / Version: (1.10_2152: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→48.38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.84 / 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→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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