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- PDB-1t7q: Crystal structure of the F565A mutant of murine carnitine acetylt... -

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Basic information

Entry
Database: PDB / ID: 1t7q
TitleCrystal structure of the F565A mutant of murine carnitine acetyltransferase in complex with carnitine and CoA
ComponentsCarnitine acetyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / medium-chain fatty acid metabolic process ...carnitine O-acetyltransferase / carnitine O-acetyltransferase activity / Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / acyl-CoA oxidase activity / carnitine O-octanoyltransferase activity / carnitine metabolic process, CoA-linked / fatty acid beta-oxidation using acyl-CoA oxidase / short-chain fatty acid metabolic process / medium-chain fatty acid metabolic process / Peroxisomal protein import / fatty acid metabolic process / peroxisome / mitochondrial inner membrane / endoplasmic reticulum / mitochondrion
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
CARNITINE / COENZYME A / Carnitine O-acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHsiao, Y.-S. / Jogl, G. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural and biochemical studies of the substrate selectivity of carnitine acetyltransferase
Authors: Hsiao, Y.-S. / Jogl, G. / Tong, L.
History
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carnitine acetyltransferase
B: Carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0268
Polymers140,0422
Non-polymers1,9846
Water20,6811148
1
A: Carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0134
Polymers70,0211
Non-polymers9923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carnitine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0134
Polymers70,0211
Non-polymers9923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.130, 89.630, 123.050
Angle α, β, γ (deg.)90.00, 129.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carnitine acetyltransferase / CRAT


Mass: 70021.102 Da / Num. of mol.: 2 / Mutation: F565A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P47934, carnitine O-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-152 / CARNITINE / (3-CARBOXY-2-(R)-HYDROXY-PROPYL)-TRIMETHYL-AMMONIUM


Mass: 162.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1148 / 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: 51.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris, 100 mM NaCl, 15% PEG 3350, 2.3 mM carnitine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 128000 / Num. obs: 119268 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.385 / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.17 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 389355.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 8915 7.5 %RANDOM
Rwork0.191 ---
all0.2 128000 --
obs0.191 119268 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6313 Å2 / ksol: 0.336176 e/Å3
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å2-0.36 Å2
2---1.16 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9548 0 126 1148 10822
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 1240 7.5 %
Rwork0.277 15404 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CAR.PARAMCAR.TOP
X-RAY DIFFRACTION4COA.PARAMCOA.TOP
X-RAY DIFFRACTION5EDO.PARAMEDO.TOP

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