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- PDB-2fw3: Crystal structure of rat carnitine palmitoyltransferase 2 in comp... -

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Basic information

Entry
Database: PDB / ID: 2fw3
TitleCrystal structure of rat carnitine palmitoyltransferase 2 in complex with antidiabetic drug ST1326
ComponentsCarnitine O-palmitoyltransferase II, mitochondrial
KeywordsTRANSFERASE / central six-stranded beta-sheet
Function / homology
Function and homology information


carnitine O-palmitoyltransferase / carnitine O-palmitoyltransferase activity / Carnitine metabolism / carnitine O-octanoyltransferase activity / carnitine metabolic process / long-chain fatty acid metabolic process / response to fatty acid / fatty acid beta-oxidation / acyltransferase activity / long-chain fatty acid transport ...carnitine O-palmitoyltransferase / carnitine O-palmitoyltransferase activity / Carnitine metabolism / carnitine O-octanoyltransferase activity / carnitine metabolic process / long-chain fatty acid metabolic process / response to fatty acid / fatty acid beta-oxidation / acyltransferase activity / long-chain fatty acid transport / positive regulation of cold-induced thermogenesis / mitochondrial inner membrane / in utero embryonic development / mitochondrion
Similarity search - Function
Monooxygenase - #180 / 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 ...Monooxygenase - #180 / 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 / Monooxygenase / Chloramphenicol acetyltransferase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BUI / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRufer, A.C. / Thoma, R. / Benz, J. / Stihle, M. / Gsell, B. / De Roo, E. / Banner, D.W. / Mueller, F. / Chomienne, O. / Hennig, M.
CitationJournal: Structure / Year: 2006
Title: The crystal structure of carnitine palmitoyltransferase 2 and implications for diabetes treatment
Authors: Rufer, A.C. / Thoma, R. / Benz, J. / Stihle, M. / Gsell, B. / De Roo, E. / Banner, D.W. / Mueller, F. / Chomienne, O. / Hennig, M.
History
DepositionFeb 1, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carnitine O-palmitoyltransferase II, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9662
Polymers73,5661
Non-polymers4001
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.800, 96.200, 124.300
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 Carnitine O-palmitoyltransferase II, mitochondrial / / CPT II


Mass: 73566.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P18886, carnitine O-palmitoyltransferase
#2: Chemical ChemComp-BUI / (3R)-3-{[(TETRADECYLAMINO)CARBONYL]AMINO}-4-(TRIMETHYLAMMONIO)BUTANOATE / ST1326 / (R)-N-TETRADECYLCARBAMOYL-AMINOCARNITINE


Mass: 399.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H45N3O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 294 K / Method: microbatch / Details: 25% (v/v) PEG 1500, microbatch, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2005
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator (19.65m, focusing sagittal-horizontal), bendable mirror (20.50m focusing meridional-vertical)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.5→76.03 Å / Num. all: 35312 / Num. obs: 33845 / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.71
Reflection shellResolution: 2.5→2.63 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.19 / % possible all: 91.97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.883 / SU B: 14.946 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29647 1764 5.1 %RANDOM
Rwork0.24124 ---
obs0.24412 32831 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.988 Å2
Baniso -1Baniso -2Baniso -3
1-6.8 Å20 Å20 Å2
2---0.97 Å20 Å2
3----5.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4963 0 28 152 5143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225116
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9556935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79123.887247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88215844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9041531
X-RAY DIFFRACTIONr_chiral_restr0.10.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023930
X-RAY DIFFRACTIONr_nbd_refined0.2280.22413
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.25
X-RAY DIFFRACTIONr_mcbond_it0.6451.53182
X-RAY DIFFRACTIONr_mcangle_it1.15725027
X-RAY DIFFRACTIONr_scbond_it1.57132165
X-RAY DIFFRACTIONr_scangle_it2.4974.51908
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 121 -
Rwork0.409 2232 -
obs--91.2 %

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