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- PDB-1w4g: Peripheral-subunit binding domains from mesophilic, thermophilic,... -

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Basic information

Entry
Database: PDB / ID: 1w4g
TitlePeripheral-subunit binding domains from mesophilic, thermophilic, and hyperthermophilic bacteria fold by ultrafast, apparently two-state folding transitions
ComponentsDIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE
KeywordsTRANSFERASE / PERIPHERAL-SUBUNIT BINDING DOMAIN / ULTRAFAST FOLDING / HOMOLOGUES
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / cytoplasm
Similarity search - Function
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 ...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 acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodSOLUTION NMR
AuthorsFerguson, N. / Sharpe, T.D. / Schartau, P.J. / Allen, M.D. / Johnson, C.M. / Sato, S. / Fersht, A.R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Ultra-Fast Barrier-Limited Folding in the Peripheral Subunit-Binding Domain Family.
Authors: Ferguson, N. / Sharpe, T.D. / Schartau, P.J. / Sato, S. / Allen, M.D. / Johnson, C.M. / Rutherford, T.J. / Fersht, A.R.
History
DepositionJul 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)5,1331
Polymers5,1331
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 / 21NO VIOLATIONS > 0.25A
RepresentativeModel #1

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Components

#1: Protein/peptide DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE / DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Mass: 5132.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 125-169 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase
Compound detailsCHAIN A ENGINEERED MUTATION TYR 138 TRP
Sequence detailsMUTATION Y138W WAS REQUIRED FOR FLUORESCENCE MEASUREMENT

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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 PROTEIN

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Sample preparation

DetailsContents: 95% WATER/5% D2O, 3MM SAMPLE
Sample conditionsIonic strength: 150 mM / pH: 5.5 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
ANSIGstructure solution
Azarastructure solution
CNSstructure solution
RefinementSoftware ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: NO VIOLATIONS > 0.25A / Conformers calculated total number: 21 / Conformers submitted total number: 20

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