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Yorodumi- PDB-2fy5: Structures of ligand bound human choline acetyltransferase provid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fy5 | ||||||
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Title | Structures of ligand bound human choline acetyltransferase provide insight into regulation of acetylcholine synthesis | ||||||
Components | Choline O-acetyltransferaseCholine acetyltransferase | ||||||
Keywords | TRANSFERASE / two domain / alpha-beta protein / S-2-(oxopropyl)-coenzyme A | ||||||
Function / homology | Function and homology information choline O-acetyltransferase / choline O-acetyltransferase activity / acetylcholine biosynthetic process / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / phosphatidylcholine biosynthetic process / neurotransmitter transport / Synthesis of PC / neuron projection / synapse ...choline O-acetyltransferase / choline O-acetyltransferase activity / acetylcholine biosynthetic process / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / phosphatidylcholine biosynthetic process / neurotransmitter transport / Synthesis of PC / neuron projection / synapse / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kim, A.R. / Rylett, R.J. / Shilton, B.H. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Substrate binding and catalytic mechanism of human choline acetyltransferase. Authors: Kim, A.R. / Rylett, R.J. / Shilton, B.H. | ||||||
History |
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Remark 999 | SEQUENCE The original sequence SSRKLIRADSVSE (residues 464-476 in SWS entry CLAT_HUMAN) was mutated ...SEQUENCE The original sequence SSRKLIRADSVSE (residues 464-476 in SWS entry CLAT_HUMAN) was mutated to the sequence PELVRSPMVP (residues 346-357 in the coordinates) in order to make the protein crystallize. The other mutations mentioned in SEQADV were made for the same purpose. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fy5.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fy5.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/2fy5 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/2fy5 | HTTPS FTP |
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-Related structure data
Related structure data | 2fy2C 2fy3C 2fy4C 1q6xS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68113.352 Da / Num. of mol.: 1 / Fragment: RESIDUES 120-733 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHAT / Plasmid: pProEXHTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28329, choline O-acetyltransferase |
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#2: Chemical | ChemComp-SOP / [( |
#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: 2.49 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 11-13% PEG 3350, 0.1M Tris-HCl, crystal soaked in 20mM S-(2-oxopropyl)-coenzyme A, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 16, 2005 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Graded multilayer (osmic) / 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→40 Å / Num. all: 21009 / Num. obs: 21009 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Rmerge(I) obs: 0.133 / Χ2: 0.945 / Net I/σ(I): 6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR | Rfactor: 0.717 / Cor.coef. Fo:Fc: 0.3 / Cor.coef. Io to Ic: 0.244
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Q6X Resolution: 2.6→17.99 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 27.2943 Å2 / ksol: 0.312029 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.05 Å2 / Biso mean: 43.5 Å2 / Biso min: 12.32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→17.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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