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- PDB-1ndf: Carnitine Acetyltransferase in Complex with Carnitine -

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Basic information

Entry
Database: PDB / ID: 1ndf
TitleCarnitine Acetyltransferase in Complex with Carnitine
ComponentsCarnitine Acetyltransferase
KeywordsTRANSFERASE / acetyl transfer / CoA / coenzyme A
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 / short-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA oxidase / 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 / short-chain fatty acid metabolic process / fatty acid beta-oxidation using acyl-CoA oxidase / medium-chain fatty acid metabolic process / Peroxisomal protein import / 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-like domain / Chloramphenicol Acetyltransferase / 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-like domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CARNITINE / Carnitine O-acetyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJogl, G. / Tong, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Crystal Structure of Carnitine Acetyltransferase and Implications for the Catalytic Mechanism and Fatty Acid Transport
Authors: Jogl, G. / Tong, L.
History
DepositionDec 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)135,6874
Polymers135,3632
Non-polymers3242
Water19,2761070
1
A: Carnitine Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8442
Polymers67,6811
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carnitine Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8442
Polymers67,6811
Non-polymers1621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.680, 91.670, 122.610
Angle α, β, γ (deg.)90.00, 128.84, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Carnitine Acetyltransferase / E.C.2.3.1.7 / CARNITINE ACETYLASE / CAT / CARNITINE O-ACETYLTRANSFERASE


Mass: 67681.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P47934, carnitine O-acetyltransferase
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / 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: 2.37 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM TRIS, 12%PEG 3350,1mM Carnitine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH8.0
212 %(w/v)PEG33501reservoir
316 mg/mlprotein1drop
40.6 mMcarnitine1drop

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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: Oct 4, 2002
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 105409 / Num. obs: 105409 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.5 Å2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Num. measured all: 347562 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NDB

1ndb


Resolution: 1.9→19.95 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 7946 7.5 %RANDOM
Rwork0.2 ---
obs0.2001 105409 96.7 %-
all-105409 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4827 Å2 / ksol: 0.35557 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-1.44 Å2
2--0.75 Å20 Å2
3----3.15 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9514 0 22 1070 10606
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_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 1267 7.6 %
Rwork0.236 15497 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CAR.PARCAR.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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