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- PDB-1xmc: C323M mutant structure of mouse carnitine octanoyltransferase -

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Basic information

Entry
Database: PDB / ID: 1xmc
TitleC323M mutant structure of mouse carnitine octanoyltransferase
ComponentsPeroxisomal carnitine O-octanoyltransferase
KeywordsTRANSFERASE / carnitine / octanoyltransferase / hepes / mpd / mutant
Function / homology
Function and homology information


Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine O-octanoyltransferase activity / medium-chain fatty acid metabolic process / carnitine metabolic process / Peroxisomal protein import / coenzyme A metabolic process / fatty acid beta-oxidation / fatty acid transport / fatty acid metabolic process ...Beta-oxidation of pristanoyl-CoA / carnitine O-octanoyltransferase / carnitine O-octanoyltransferase activity / medium-chain fatty acid metabolic process / carnitine metabolic process / Peroxisomal protein import / coenzyme A metabolic process / fatty acid beta-oxidation / fatty acid transport / fatty acid metabolic process / generation of precursor metabolites and energy / peroxisome / response to xenobiotic stimulus / intracellular membrane-bounded organelle / mitochondrion
Similarity search - Function
Choline/Carnitine o-acyltransferase / Carnitine o-acyltransferase, N-terminal / 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 ...Choline/Carnitine o-acyltransferase / Carnitine o-acyltransferase, N-terminal / 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 / Fumarase C; Chain B, domain 1 / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peroxisomal carnitine O-octanoyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJogl, G. / Hsiao, Y.S. / Tong, L.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of mouse carnitine octanoyltransferase and molecular determinants of substrate selectivity.
Authors: Jogl, G. / Hsiao, Y.S. / Tong, L.
History
DepositionOct 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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: Peroxisomal carnitine O-octanoyltransferase
B: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,07511
Polymers140,7712
Non-polymers1,3049
Water9,998555
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A: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7423
Polymers70,3851
Non-polymers3562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peroxisomal carnitine O-octanoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3338
Polymers70,3851
Non-polymers9477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.900, 163.900, 159.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Peroxisomal carnitine O-octanoyltransferase / COT


Mass: 70385.430 Da / Num. of mol.: 2 / Mutation: C323M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crot, Cot / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star
References: UniProt: Q9DC50, carnitine O-octanoyltransferase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100mM Hepes, 62%v/v MPD, pH 7.4, 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: Apr 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 99340 / Num. obs: 99340 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.4 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 90.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→26.75 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 337446.55 / 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
Rfree0.217 7313 7.5 %RANDOM
Rwork0.19 ---
all-99340 --
obs-97083 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4621 Å2 / ksol: 0.373225 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å22.25 Å20 Å2
2--1.8 Å20 Å2
3----3.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9623 0 30 611 10264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 1156 7.6 %
Rwork0.215 14071 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3HEP.PARHEP.TOP
X-RAY DIFFRACTION4MPD.PARMPD.TOP

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