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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rcu
TitleCrystal structure of rat carnitine palmitoyltransferase 2 in complex with r-3-(hexadecanoylamino)-4-(trimethylazaniumyl)butanoate
ComponentsCarnitine O-palmitoyltransferase 2
KeywordsTRANSFERASE / ACYLTRANSFERASE / MITOCHONDRIAL PROTEIN / Acetylation / Fatty acid metabolism / Inner membrane / Lipid metabolism / Membrane / Mitochondrion / Transit peptide / Transport / TRANSFERASE 04-MAI-06 R
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-BUJ / Carnitine O-palmitoyltransferase 2, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsRufer, A.C. / Benz, J. / Chomienne, O. / Thoma, R. / Hennig, M.
CitationJournal: Febs Lett. / Year: 2007
Title: Carnitine palmitoyltransferase 2: analysis of membrane association and complex structure with a substrate analog.
Authors: Rufer, A.C. / Lomize, A. / Benz, J. / Chomienne, O. / Thoma, R. / Hennig, M.
History
DepositionSep 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Sep 25, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 5, 2021Group: Data collection / Structure summary / Category: chem_comp / reflns / reflns_shell
Item: _chem_comp.pdbx_synonyms / _reflns.pdbx_redundancy / _reflns_shell.pdbx_redundancy
Revision 1.6Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carnitine O-palmitoyltransferase 2
B: Carnitine O-palmitoyltransferase 2
A: (3R)-3-(hexadecanoylamino)-4-(trimethylammonio)butanoate
B: (3R)-3-(hexadecanoylamino)-4-(trimethylammonio)butanoate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,2225
Polymers147,1322
Non-polymers1,0903
Water19,3841076
1
A: Carnitine O-palmitoyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2573
Polymers73,5661
Non-polymers6912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carnitine O-palmitoyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9652
Polymers73,5661
Non-polymers3991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.273, 97.750, 312.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsCarnitine palmitoyltransferase is active as monomer. The asymmetric unit of this crystal form contains two molecules of carnitine palmitoyltransferase.

-
Components

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


Mass: 73566.094 Da / Num. of mol.: 2 / Fragment: residues 27-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cpt2, Cpt-2 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21DE3
References: UniProt: P18886, carnitine O-palmitoyltransferase
#2: 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
#3: Chemical
ChemComp-BUJ / (3R)-3-(hexadecanoylamino)-4-(trimethylammonio)butanoate / (3R)-3-(palmitoylamino)-4-(trimethylammonio)butanoate


Mass: 398.623 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / 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: 2.47 Å3/Da / Density % sol: 50.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15 M DL-malic acid pH 7.0, 20% (w/v) PEG 3350 (Index 91, Hampton Research), VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 139208 / Num. obs: 126696 / % possible obs: 91 % / Redundancy: 7.2 % / Biso Wilson estimate: 0.18307 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.034 / Net I/σ(I): 22.26
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 12.71 / Num. unique all: 21752 / Rsym value: 0.078 / % possible all: 95.6

-
Processing

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

2deb


Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.474 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22331 6400 5.1 %RANDOM
Rwork0.17749 ---
obs0.17978 120296 91.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10015 0 76 1076 11167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210341
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.95714016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75551251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34123.855498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.023151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.741564
X-RAY DIFFRACTIONr_chiral_restr0.0870.21534
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027912
X-RAY DIFFRACTIONr_nbd_refined0.1980.25143
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.21025
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.252
X-RAY DIFFRACTIONr_mcbond_it2.1826440
X-RAY DIFFRACTIONr_mcangle_it2.881310141
X-RAY DIFFRACTIONr_scbond_it4.67744375
X-RAY DIFFRACTIONr_scangle_it6.57963875
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 473 -
Rwork0.196 8937 -
obs--92.55 %

+
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