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- PDB-2fy2: Structures of ligand bound human choline acetyltransferase provid... -

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Basic information

Entry
Database: PDB / ID: 2fy2
TitleStructures of ligand bound human choline acetyltransferase provide insight into regulation of acetylcholine synthesis
ComponentsCholine O-acetyltransferaseCholine acetyltransferase
KeywordsTRANSFERASE / two domain / alpha-beta protein
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
Choline/Carnitine o-acyltransferase, domain 2 / Acyltransferase ChoActase/COT/CPT / Choline/carnitine acyltransferase domain / Choline/Carnitine o-acyltransferase, domain 2 / Choline/Carnitine o-acyltransferase / Acyltransferases ChoActase / COT / CPT family signature 1. / Acyltransferases ChoActase / COT / CPT family signature 2. / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily ...Choline/Carnitine o-acyltransferase, domain 2 / Acyltransferase ChoActase/COT/CPT / Choline/carnitine acyltransferase domain / Choline/Carnitine o-acyltransferase, domain 2 / Choline/Carnitine o-acyltransferase / Acyltransferases ChoActase / COT / CPT family signature 1. / Acyltransferases ChoActase / COT / CPT family signature 2. / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Choline O-acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKim, A.R. / Rylett, R.J. / Shilton, B.H.
CitationJournal: Biochemistry / Year: 2006
Title: Substrate binding and catalytic mechanism of human choline acetyltransferase.
Authors: Kim, A.R. / Rylett, R.J. / Shilton, B.H.
History
DepositionFeb 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choline O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)68,1131
Polymers68,1131
Non-polymers00
Water9,800544
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.740, 75.750, 165.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Choline O-acetyltransferase / Choline acetyltransferase / CHOACTase / Choline acetylase / ChAT


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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 11-13% PEG 3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 2005 / Details: mirrors
RadiationMonochromator: Graded multilayer (osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 32962 / Num. obs: 32962 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.038 / Χ2: 0.501 / Net I/σ(I): 17.1
Reflection shellResolution: 2.25→2.33 Å / % possible obs: 96.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.093 / Num. unique obs: 3189 / Χ2: 0.62 / % possible all: 96.4

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Phasing

Phasing MRRfactor: 0.717 / Cor.coef. Fo:Fc: 0.3 / Cor.coef. Io to Ic: 0.244
Highest resolutionLowest resolution
Rotation3 Å17.932 Å
Translation3 Å17.932 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q6X

1q6x


Resolution: 2.25→17.91 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3289 10 %random
Rwork0.195 ---
all0.208 33568 --
obs0.208 32854 97.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.9305 Å2 / ksol: 0.34328 e/Å3
Displacement parametersBiso max: 76.82 Å2 / Biso mean: 22.01 Å2 / Biso min: 3.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--2.67 Å20 Å2
3----3.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.12 Å
Luzzati d res high-2.25
Refinement stepCycle: LAST / Resolution: 2.25→17.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 0 544 5128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.928
X-RAY DIFFRACTIONc_improper_angle_d1.146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.25-2.350.2623909.90.19435450.0134133393595.2
2.35-2.470.2640310.10.19936060.0134144400996.7
2.47-2.630.283659.10.20236600.0154151402597
2.63-2.830.24842410.40.18936370.0124162406197.6
2.83-3.110.2443969.70.20336920.0124161408898.2
3.11-3.560.22942010.20.20237070.0114187412798.6
3.56-4.480.20543410.30.17337760.014253421099
4.48-17.910.21745710.40.20739420.014410439999.8

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