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- PDB-2wxc: The folding mechanism of BBL: Plasticity of transition-state stru... -

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Basic information

Entry
Database: PDB / ID: 2wxc
TitleThe folding mechanism of BBL: Plasticity of transition-state structure observed within an ultrafast folding protein family.
ComponentsDIHYDROLIPOYLTRANSSUCCINASE
KeywordsTRANSFERASE / LIPOYL / ACYLTRANSFERASE
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / oxoglutarate dehydrogenase complex / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / tricarboxylic acid cycle / cytosol / cytoplasm
Similarity search - Function
Dihydrolipoamide succinyltransferase / E3-binding domain / Dihydrolipoamide Transferase / 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 ...Dihydrolipoamide succinyltransferase / E3-binding domain / Dihydrolipoamide Transferase / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
: / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / CNS
AuthorsNeuweiler, H. / Sharpe, T.D. / Rutherford, T.J. / Johnson, C.M. / Allen, M.D. / Ferguson, N. / Fersht, A.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The Folding Mechanism of Bbl: Plasticity of Transition-State Structure Observed within an Ultrafast Folding Protein Family.
Authors: Neuweiler, H. / Sharpe, T.D. / Rutherford, T.J. / Johnson, C.M. / Allen, M.D. / Ferguson, N. / Fersht, A.R.
History
DepositionNov 6, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionNov 17, 2009ID: 2WAV
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOYLTRANSSUCCINASE


Theoretical massNumber of molelcules
Total (without water)5,0091
Polymers5,0091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20NO VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein/peptide DIHYDROLIPOYLTRANSSUCCINASE


Mass: 5008.610 Da / Num. of mol.: 1 / Fragment: RESIDUES 109-153 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: B7M5P0, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 125 TO TRP
Sequence detailsHIS-TRP POINT MUTATION WAS INTRODUCED TO ENABLE FOLDING ANALYSIS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MATERIAL AND BU 1H METHODS

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Sample preparation

DetailsContents: 10% WATER/90% D2O
Sample conditionspH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance8002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIG3.3structure solution
RefinementMethod: CNS / Software ordinal: 1
NMR ensembleConformer selection criteria: NO VIOLATIONS / Conformers calculated total number: 20 / Conformers submitted total number: 20

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