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- PDB-1t1u: Structural Insights and Functional Implications of Choline Acetyl... -

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Basic information

Entry
Database: PDB / ID: 1t1u
TitleStructural Insights and Functional Implications of Choline Acetyltransferase
ComponentsCholine O-acetyltransferaseCholine acetyltransferase
KeywordsTRANSFERASE / choline acetyltransferase
Function / homology
Function and homology information


choline O-acetyltransferase / choline O-acetyltransferase activity / Synthesis of PC / acetylcholine biosynthetic process / rhythmic excitation / rhythmic behavior / establishment of synaptic specificity at neuromuscular junction / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline binding ...choline O-acetyltransferase / choline O-acetyltransferase activity / Synthesis of PC / acetylcholine biosynthetic process / rhythmic excitation / rhythmic behavior / establishment of synaptic specificity at neuromuscular junction / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline binding / adult walking behavior / muscle organ development / antral ovarian follicle growth / dendrite development / response to nutrient / neuron differentiation / memory / chemical synaptic transmission / response to ethanol / response to hypoxia / neuron projection / response to xenobiotic stimulus / axon / neuronal cell body / synapse / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGovindasamy, L. / Pedersen, B. / Lian, W. / Kukar, T. / Gu, Y. / Jin, S. / Agbandje-McKenna, M. / Wu, D.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Structural insights and functional implications of choline acetyltransferase
Authors: Govindasamy, L. / Pedersen, B. / Lian, W. / Kukar, T. / Gu, Y. / Jin, S. / Agbandje-McKenna, M. / Wu, D.
History
DepositionApr 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The author states that the database reference sequence used in this structure contains errors.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,9061
Polymers71,9061
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.949, 77.505, 59.209
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: 71905.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Chat / Production host: Escherichia coli (E. coli) / References: UniProt: P32738, choline O-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM MES buffer, 100mM NaCl, PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9504 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9504 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 429316 / Num. obs: 72446 / Biso Wilson estimate: 26.9 Å2 / Rsym value: 0.054 / Net I/σ(I): 10.5
Reflection shellResolution: 1.51→1.55 Å / Mean I/σ(I) obs: 3.2 / Num. unique all: 72446 / Rsym value: 0.337

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NM8

1nm8


Resolution: 1.55→30 Å / Isotropic thermal model: isotropic / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 --random
Rwork0.171 ---
all-429316 --
obs-72446 5 %-
Displacement parametersBiso mean: 23.814 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 0 408 5119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.112
X-RAY DIFFRACTIONc_angle_deg3.266

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