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- PDB-1q6x: Crystal structure of rat choline acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 1q6x
TitleCrystal structure of rat choline acetyltransferase
Componentscholine O-acetyltransferaseCholine acetyltransferase
KeywordsTRANSFERASE / alpha beta sandwich / extended loop / two domains
Function / homology
Function and homology information


choline O-acetyltransferase / choline O-acetyltransferase activity / Synthesis of PC / acetylcholine biosynthetic process / rhythmic excitation / establishment of synaptic specificity at neuromuscular junction / rhythmic behavior / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline binding ...choline O-acetyltransferase / choline O-acetyltransferase activity / Synthesis of PC / acetylcholine biosynthetic process / rhythmic excitation / establishment of synaptic specificity at neuromuscular junction / rhythmic behavior / Acetylcholine Neurotransmitter Release Cycle / neuromuscular synaptic transmission / choline binding / adult walking behavior / muscle organ development / antral ovarian follicle growth / dendrite development / response to nutrient / memory / neuron differentiation / 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: 2.5 Å
AuthorsCai, Y. / Rodgers, D.W.
CitationJournal: Embo J. / Year: 2004
Title: Choline acetyltransferase structure reveals distribution of mutations that cause motor disorders.
Authors: Cai, Y. / Cronin, C.N. / Engel, A.G. / Ohno, K. / Hersh, L.B. / Rodgers, D.W.
History
DepositionAug 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHOR MAINTAINS THAT THE SEQUENCE IN THE SEQUENCE DATABASE IS INCORRECT

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: choline O-acetyltransferase
B: choline O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,9964
Polymers144,9502
Non-polymers462
Water6,215345
1
A: choline O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4982
Polymers72,4751
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: choline O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4982
Polymers72,4751
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.701, 78.882, 139.364
Angle α, β, γ (deg.)90.00, 98.38, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a single polypeptide chain, and there are two biological assemblies in the asymmetric unit.

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Components

#1: Protein choline O-acetyltransferase / Choline acetyltransferase


Mass: 72475.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: cholinergic gene locus / Plasmid: pLENTY / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alphaF'IQ / References: UniProt: P32738, choline O-acetyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, (2-(N-Morpholino)ethanesulfonic acid, sodium chloride, 2-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2002 / Details: double crystal focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 62300 / Num. obs: 62219 / Observed criterion σ(F): -4 / Observed criterion σ(I): -4 / Redundancy: 3.8 % / Biso Wilson estimate: 38.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6012 / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NDB

1ndb


Resolution: 2.5→28.94 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Only C-alpha positions could be assigned for residues 356-367 in both chains A and B
RfactorNum. reflection% reflectionSelection details
Rfree0.251 6279 10.1 %RANDOM
Rwork0.223 ---
all0.226 62034 --
obs0.226 62033 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.3927 Å2 / ksol: 0.312752 e/Å3
Displacement parametersBiso mean: 30.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.56 Å20 Å20.24 Å2
2---3.67 Å20 Å2
3----3.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9334 0 2 345 9681
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it10.211.5
X-RAY DIFFRACTIONc_mcangle_it11.212
X-RAY DIFFRACTIONc_scbond_it7.222
X-RAY DIFFRACTIONc_scangle_it6.72.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 1043 10.2 %
Rwork0.288 9232 -
obs-9232 98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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