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- PDB-2cyu: NMR structure of a downhill folding protein -

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Basic information

Entry
Database: PDB / ID: 2cyu
TitleNMR structure of a downhill folding protein
Components2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX
KeywordsTRANSFERASE / helix bundle / downhill folding protein
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / cytosol
Similarity search - Function
Dihydrolipoamide succinyltransferase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...Dihydrolipoamide succinyltransferase / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsMunoz, V. / Sadqi, M.
CitationJournal: Nature / Year: 2006
Title: Atom-by-atom analysis of global downhill protein folding.
Authors: Sadqi, M. / Fushman, D. / Munoz, V.
History
DepositionJul 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 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: 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX


Theoretical massNumber of molelcules
Total (without water)4,4001
Polymers4,4001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 2-OXOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX / Dihydrolipoyllysine-residue succinyltransferase component of 2- oxoglutarate dehydrogenase complex


Mass: 4400.073 Da / Num. of mol.: 1 / Fragment: E3-BINDING DOMAIN / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in E coli.
References: UniProt: P0AFG7, dihydrolipoyllysine-residue succinyltransferase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D COSY
1212D TOCSY
1312D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 90% H2O, 10% D2O, trace amounts of DSS for NMR calibration
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 5.3 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipesgi6xF. Delagioprocessing
NMRView5.0.4Bruce A. Johnsondata analysis
XPLOR-NIH2.11refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE FIRST THREE RESIDUES OF OUR PROTEIN VARIANT ARE NOT STRUCTURED (NO DISTANCE RESTRAINTS). ACCORDINGLY, THE COORDINATES FOR THE N-TERMINAL NAPHTHYLALANINE ARE NOT SHOWN
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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