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- PDB-1w3d: NMR structure of the peripheral-subunit binding domain of Bacillu... -

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Basic information

Entry
Database: PDB / ID: 1w3d
TitleNMR structure of the peripheral-subunit binding domain of Bacillus stearothermophilus E2p
ComponentsDIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASEDihydrolipoyl transacetylase
KeywordsTRANSFERASE / PERIPHERAL-SUBUNIT BINDING DOMAIN / DIHYDROLIPOAMIDE ACETYLTRANSFERASE / DIHYDROLIPOAMIDE DEHYDROGENASE / PROTEIN- PROTEIN INTERACTION / PROTEIN STRUCTURE / MULTIENZYME COMPLEX / BACILLUS STEROTHERMOPHILUS / GLYCOLYSIS / ACYLTRANSFERASE / LIPOYL
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / glycolytic process / 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 / 2-oxoacid dehydrogenases 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 speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodSOLUTION NMR
AuthorsAllen, M.D. / Broadhurst, R.W. / Solomon, R.G. / Perham, R.N.
CitationJournal: FEBS J. / Year: 2005
Title: Interaction of the E2 and E3 Components of the Pyruvate Dehydrogenase Multienzyme Complex of Bacillus Stearothermophilus. Use of a Truncated Protein Domain in NMR Spectroscopy
Authors: Allen, M.D. / Broadhurst, R.W. / Solomon, R.G. / Perham, R.N.
History
DepositionJul 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)5,8071
Polymers5,8071
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 VIOLATION > 0.25A
RepresentativeModel #1

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Components

#1: Protein DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF PYRUVATE DEHYDROGENASE / Dihydrolipoyl transacetylase / COMPLEX DIHYDROPOAMIDE ACETYLTRANSFERASE


Mass: 5806.619 Da / Num. of mol.: 1 / Fragment: RESIDUES 118-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase
Compound detailsCATALYTIC ACTIVITY: ACETYL-COA + ENZYME N(6)-(DIHYDROLIPOYL)LYSINE = COA + ENZYME N(6)-(S- ...CATALYTIC ACTIVITY: ACETYL-COA + ENZYME N(6)-(DIHYDROLIPOYL)LYSINE = COA + ENZYME N(6)-(S-ACETYLDIHYDROLIPOYL)LYSINE.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: NONE

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Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 6.5 / Temperature: 298.0 K

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NMR measurement

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

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Processing

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

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