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- PDB-4ep9: CRYSTAL STRUCTURE OF RAT CARNITINE PALMITOYLTRANSFERASE 2 IN COMP... -

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Basic information

Entry
Database: PDB / ID: 4ep9
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-0RD / PALMITIC ACID / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 1.3Sep 13, 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_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

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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)74,3233
Polymers73,5661
Non-polymers7572
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.500, 67.500, 308.930
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-0RD / 4-[({1-[(5-chloro-2-methoxyphenyl)sulfonyl]-4-methyl-2,3-dihydro-1H-indol-6-yl}carbonyl)amino]benzoic acid


Mass: 500.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21ClN2O6S
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hampton Index #76 0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 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: 0.97955 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 13, 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: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.03→19.7 Å / Num. all: 47020 / % possible obs: 98.4 % / Observed criterion σ(I): 3.42
Reflection shellResolution: 2.03→2.15 Å / % possible all: 91.4

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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: 2.03→19.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 4.311 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24287 2380 5.1 %RANDOM
Rwork0.17845 ---
obs0.18165 44732 98.58 %-
all-47761 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.734 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.03→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 50 407 5433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225154
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.966990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58623.887247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74715846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0441531
X-RAY DIFFRACTIONr_chiral_restr0.0890.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023966
X-RAY DIFFRACTIONr_nbd_refined0.2020.22527
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2448
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.218
X-RAY DIFFRACTIONr_mcbond_it2.48823216
X-RAY DIFFRACTIONr_mcangle_it3.41535043
X-RAY DIFFRACTIONr_scbond_it5.39842217
X-RAY DIFFRACTIONr_scangle_it7.29161947
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 157 -
Rwork0.213 2698 -
obs--82.85 %

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