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- PDB-2h4t: Crystal structure of rat carnitine palmitoyltransferase II -

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Basic information

Entry
Database: PDB / ID: 2h4t
TitleCrystal structure of rat carnitine palmitoyltransferase II
ComponentsCarnitine O-palmitoyltransferase II, mitochondrial
KeywordsTRANSFERASE / carnitine acyltransferase
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
DODECANE / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHsiao, Y.S. / Jogl, G. / Esser, V. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Crystal structure of rat carnitine palmitoyltransferase II (CPT-II).
Authors: Hsiao, Y.S. / Jogl, G. / Esser, V. / Tong, L.
History
DepositionMay 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: 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 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,4688
Polymers141,4462
Non-polymers1,0226
Water28,8781603
1
A: Carnitine O-palmitoyltransferase II, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2344
Polymers70,7231
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carnitine O-palmitoyltransferase II, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2344
Polymers70,7231
Non-polymers5113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.770, 73.800, 90.560
Angle α, β, γ (deg.)70.65, 73.62, 88.06
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 70722.906 Da / Num. of mol.: 2 / Fragment: Residues 32-656 / Mutation: A547T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cpt2 / Production host: Escherichia coli (E. coli)
References: UniProt: P18886, carnitine O-palmitoyltransferase
#2: Chemical
ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1603 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes, 15% Tacsimate, 16% PEG 5000MME, 1% Benzyldimethyldodecyl ammonium bromide (BAM), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9798
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 14, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 126888 / % possible obs: 90.7 % / Redundancy: 2 % / Biso Wilson estimate: 8.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7986
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.741 / % possible all: 72.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBTHEN SOLVE/RESOLVEphasing
CNS1.1refinement
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.7 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1004088.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 8805 7.5 %RANDOM
Rwork0.189 ---
all0.189 ---
obs0.189 116945 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3659 Å2 / ksol: 0.347011 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-4.69 Å24.87 Å2
2--0.75 Å2-2.81 Å2
3----0.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9959 0 72 1603 11634
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_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.316 713 7.4 %
Rwork0.31 8902 -
obs--70.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION512c.par12c.top

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