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- PDB-1gjx: Solution structure of the lipoyl domain of the chimeric dihydroli... -

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Basic information

Entry
Database: PDB / ID: 1gjx
TitleSolution structure of the lipoyl domain of the chimeric dihydrolipoyl dehydrogenase P64K from Neisseria meningitidis
ComponentsPYRUVATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / LIPOYL DOMAIN / DIHYDROLIPOYL DEHYDROGENASE / MULTIENZYME COMPLEX / NEISSERIA MENINGITIDIS / POST-TRANSLATIONAL MODIFICATION
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / cell redox homeostasis / flavin adenine dinucleotide binding
Similarity search - Function
Dihydrolipoamide dehydrogenase / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme ...Dihydrolipoamide dehydrogenase / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTozawa, K. / Broadhurst, R.W. / Raine, A.R.C. / Fuller, C. / Alvarez, A. / Guillen, G. / Padron, G. / Perham, R.N.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Solution Structure of the Lipoyl Domain of the Chimeric Dihydrolipoyl Dehydrogenase P64K from Neisseria Meningitidis
Authors: Tozawa, K. / Broadhurst, R.W. / Raine, A.R. / Fuller, C. / Alvarez, A. / Guillen, G. / Padron, G. / Perham, R.N.
History
DepositionAug 3, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: 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

Downloads & links

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Assembly

Deposited unit
A: PYRUVATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)8,3291
Polymers8,3291
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)18 / 40NO VIOLATIONS, LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PYRUVATE DEHYDROGENASE / LIPOAMIDE DEHYDROGENASE / E3 COMPONENT


Mass: 8329.452 Da / Num. of mol.: 1 / Fragment: LIPOYL DOMAIN RESIDUES 2-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Plasmid: PM-143 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q9JZ09, dihydrolipoyl dehydrogenase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131HNCA
141HN (CO)CA
15115N NOESY-HSQC
16115N-TOCSY-HSQC
171(H)CCH-TOCSY
18113C-NOESY-HSQC
NMR detailsText: STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED LIPOYL DOMAIN

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Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Azarastructure solution
ANSIGstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO VIOLATIONS, LOWEST ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 18

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