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- PDB-2fyo: Crystal structure of rat carnitine palmitoyltransferase 2 in spac... -

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Basic information

Entry
Database: PDB / ID: 2fyo
TitleCrystal structure of rat carnitine palmitoyltransferase 2 in space group P43212
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 shuttle / 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 shuttle / 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 / in utero embryonic development / mitochondrial inner membrane / 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
Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 8, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 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 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carnitine O-palmitoyltransferase II, mitochondrial


Theoretical massNumber of molelcules
Total (without water)74,1291
Polymers74,1291
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.550, 67.550, 307.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Carnitine O-palmitoyltransferase II, mitochondrial / CPT II


Mass: 74128.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P18886, carnitine O-palmitoyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15 M DL-malic acid 20 % (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97853 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 9, 2005
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator (19.65m, focusing sagittal-horizontal) bendable mirror (20.50m focusing meridional-vertical)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→23 Å / Num. all: 49518 / Num. obs: 49466 / Rmerge(I) obs: 0.031 / Net I/σ(I): 28.04
Reflection shellResolution: 2→2.12 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 14.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2→23 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.779 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was measured in MAD mode but only a single (Peak) wavelength was used for solving the structre with molecular replacement. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was measured in MAD mode but only a single (Peak) wavelength was used for solving the structre with molecular replacement. Due to a mistake in beam-line calibration the actual inflection and peak wavellengths were missed.
RfactorNum. reflection% reflectionSelection details
Rfree0.23457 2507 5.1 %RANDOM
Rwork0.17931 ---
obs0.18212 46957 100 %-
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: 21.916 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 0 525 5501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225103
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.956923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94423.887247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7415846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5141531
X-RAY DIFFRACTIONr_chiral_restr0.0780.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023932
X-RAY DIFFRACTIONr_nbd_refined0.2020.22567
X-RAY DIFFRACTIONr_nbtor_refined0.30.23536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2530
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.227
X-RAY DIFFRACTIONr_mcbond_it1.3423214
X-RAY DIFFRACTIONr_mcangle_it1.90135045
X-RAY DIFFRACTIONr_scbond_it3.19142131
X-RAY DIFFRACTIONr_scangle_it4.46861878
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 200 -
Rwork0.185 3347 -
obs--100 %

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