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- PDB-4eph: CRYSTAL STRUCTURE OF RAT CARNITINE PALMITOYLTRANSFERASE 2 IN COMP... -

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Basic information

Entry
Database: PDB / ID: 4eph
TitleCRYSTAL STRUCTURE OF RAT CARNITINE PALMITOYLTRANSFERASE 2 IN COMPLEX with CoA-site inhibitor
ComponentsCarnitine O-palmitoyltransferase 2, mitochondrial
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / ACYLTRANSFERASE / MITOCHONDRIAL PROTEIN / CoA / acylcarnitine / mitochondrial inner membrane / lipid transport / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / acyltransferase activity / fatty acid beta-oxidation / 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 / acyltransferase activity / fatty acid beta-oxidation / 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-like domain ...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-like domain / Chloramphenicol Acetyltransferase / Monooxygenase / Chloramphenicol acetyltransferase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0RK / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: FEBS Open Bio / Year: 2013
Title: Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein.
Authors: Perspicace, S. / Rufer, A.C. / Thoma, R. / Mueller, F. / Hennig, M. / Ceccarelli, S. / Schulz-Gasch, T. / Seelig, J.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carnitine O-palmitoyltransferase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3943
Polymers73,5661
Non-polymers8282
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.640, 67.640, 309.370
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 2, mitochondrial / Carnitine palmitoyltransferase II / CPT II


Mass: 73566.094 Da / Num. of mol.: 1 / Fragment: Carnitine O-palmitoyltransferase 2, mitochondrial
Source method: isolated from a genetically manipulated source
Details: pET28a_rCPT-2_27-658 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cpt2, Cpt-2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P18886, carnitine O-palmitoyltransferase
#2: Chemical ChemComp-0RK / 2-chloro-4-[({1-[(5-chloro-2-methoxyphenyl)sulfonyl]-4-methyl-2,3-dihydro-1H-indol-6-yl}carbonyl)amino]benzoic acid


Mass: 535.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20Cl2N2O6S
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE OF THE SULFONAMIDE MOIETY OF LIGAND 0RK IN PDB ENTRY 4EPH FITS THE DENSITY BEST, ...THE STRUCTURE OF THE SULFONAMIDE MOIETY OF LIGAND 0RK IN PDB ENTRY 4EPH FITS THE DENSITY BEST, HOWEVER IT IS NOT IN THE CONFORMATION WITH LOWEST ENERGY AS OBSERVED FOR PDB ENTRY 4EP9

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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: 2.4 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hampton Index #69 0.2 M Ammonium sulfate, 0.1 M Tris 8.5, 25 % (w/v)polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97965 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2005
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR (19.65M, FOCUSING SAGITTAL-HORIZONTAL) BENDABLE MIRROR (20.50 M FOCUSING MERIDIONAL-VERTICAL)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.28→47.31 Å / Num. all: 33839 / % possible obs: 98.8 % / Observed criterion σ(I): 9.31
Reflection shellResolution: 2.28→2.41 Å / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DEB

2deb


Resolution: 2.3→47.31 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.876 / SU B: 6.604 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1670 5 %RANDOM
Rwork0.18573 ---
obs0.18888 31450 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 55 264 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225160
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9627003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43223.887247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50215846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991531
X-RAY DIFFRACTIONr_chiral_restr0.0960.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023962
X-RAY DIFFRACTIONr_nbd_refined0.2060.22371
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2349
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.27
X-RAY DIFFRACTIONr_mcbond_it0.7671.53215
X-RAY DIFFRACTIONr_mcangle_it1.24225043
X-RAY DIFFRACTIONr_scbond_it2.0632224
X-RAY DIFFRACTIONr_scangle_it3.1194.51960
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 99 -
Rwork0.189 2184 -
obs--95.96 %

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