[English] 日本語
Yorodumi
- PDB-4eyw: Crystal structure of rat carnitine palmitoyltransferase 2 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eyw
TitleCrystal structure of rat carnitine palmitoyltransferase 2 in complex with 1-[(R)-2-(3,4-Dihydro-1H-isoquinoline-2-carbonyl)-piperidin-1-yl]-2-phenoxy-ethanone
ComponentsCarnitine O-palmitoyltransferase 2, mitochondrial
KeywordsTransferase/Transferase Inhibitor / ACYLTRANSFERASE / MITOCHONDRIAL PROTEIN / Transferase-Transferase Inhibitor complex
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 / acyltransferase activity / fatty acid beta-oxidation / 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 / 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 ...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-L0R / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.885 Å
AuthorsRudolph, M.G. / Benz, J. / Burger, D. / Thoma, R. / Rufer, A. / Joseph, C.
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
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,3876
Polymers143,0662
Non-polymers1,3224
Water21,4201189
1
A: Carnitine O-palmitoyltransferase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1943
Polymers71,5331
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carnitine O-palmitoyltransferase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1943
Polymers71,5331
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.144, 148.144, 192.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Carnitine O-palmitoyltransferase 2, mitochondrial / Carnitine palmitoyltransferase II / CPT II


Mass: 71532.891 Da / Num. of mol.: 2 / Fragment: UNP residues 27-658
Source method: isolated from a genetically manipulated source
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-L0R / 1-[(2R)-2-(3,4-dihydroisoquinolin-2(1H)-ylcarbonyl)piperidin-1-yl]-2-phenoxyethanone


Mass: 378.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N2O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.6 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.972 / Wavelength: 0.972 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.88→45.983 Å / Num. obs: 170100 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 14.42
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.59 / Rsym value: 0.739 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1032)refinement
DENZOdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE MODEL

Resolution: 1.885→45.983 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 8492 4.99 %random
Rwork0.1727 ---
obs0.1739 170055 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.885→45.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10031 0 94 1189 11314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710567
X-RAY DIFFRACTIONf_angle_d1.03314348
X-RAY DIFFRACTIONf_dihedral_angle_d13.6743937
X-RAY DIFFRACTIONf_chiral_restr0.0751553
X-RAY DIFFRACTIONf_plane_restr0.0051868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.885-1.90650.28572450.26744773X-RAY DIFFRACTION89
1.9065-1.92890.27992630.23635193X-RAY DIFFRACTION97
1.9289-1.95240.26762830.22825265X-RAY DIFFRACTION98
1.9524-1.97710.25772980.21895344X-RAY DIFFRACTION100
1.9771-2.00320.24992520.21275385X-RAY DIFFRACTION100
2.0032-2.03060.25712690.20315374X-RAY DIFFRACTION100
2.0306-2.05960.25013110.19535330X-RAY DIFFRACTION100
2.0596-2.09040.22432780.18485382X-RAY DIFFRACTION100
2.0904-2.1230.21932740.18375362X-RAY DIFFRACTION100
2.123-2.15780.22562900.18455338X-RAY DIFFRACTION100
2.1578-2.1950.2063090.17895331X-RAY DIFFRACTION100
2.195-2.23490.23312950.17845397X-RAY DIFFRACTION100
2.2349-2.27790.2162910.18265376X-RAY DIFFRACTION100
2.2779-2.32440.22072730.18275364X-RAY DIFFRACTION100
2.3244-2.3750.19852550.18015435X-RAY DIFFRACTION100
2.375-2.43020.21112790.1775398X-RAY DIFFRACTION100
2.4302-2.4910.20922810.18265393X-RAY DIFFRACTION100
2.491-2.55830.22662770.17495433X-RAY DIFFRACTION100
2.5583-2.63360.20413020.17555376X-RAY DIFFRACTION100
2.6336-2.71860.19392630.16925424X-RAY DIFFRACTION100
2.7186-2.81570.19132580.17385438X-RAY DIFFRACTION100
2.8157-2.92850.20192690.17595440X-RAY DIFFRACTION100
2.9285-3.06170.21293090.18075414X-RAY DIFFRACTION100
3.0617-3.22310.20162970.17465464X-RAY DIFFRACTION100
3.2231-3.4250.17282870.16615456X-RAY DIFFRACTION100
3.425-3.68930.18222900.15395468X-RAY DIFFRACTION100
3.6893-4.06040.15263030.14375473X-RAY DIFFRACTION100
4.0604-4.64740.17172860.1435549X-RAY DIFFRACTION100
4.6474-5.85340.16433090.1525560X-RAY DIFFRACTION100
5.8534-45.9830.18192960.18625628X-RAY DIFFRACTION96

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more