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- PDB-2dnc: Solution Structure of RSGI RUH-054, a lipoyl domain from human 2-... -

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Basic information

Entry
Database: PDB / ID: 2dnc
TitleSolution Structure of RSGI RUH-054, a lipoyl domain from human 2-oxoacid dehydrogenase
ComponentsPyruvate dehydrogenase protein X component
KeywordsTRANSFERASE / Lipoic Acid / Lipoyl domain / 2-oxoacid dehydrogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase complex / : / Pyruvate metabolism / Glyoxylate metabolism and glycine degradation / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / acyltransferase activity / mitochondrial matrix / mitochondrion
Similarity search - Function
Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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 ...Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Pyruvate dehydrogenase protein X component, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRuhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Kurosaki, C. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Solution Structure of RSGI RUH-054, a lipoyl domain from human 2-oxoacid dehydrogenase
Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Hayashi, F. / Kurosaki, C. / Yoshida, M. / Yokoyama, S.
History
DepositionApr 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate dehydrogenase protein X component


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Pyruvate dehydrogenase protein X component / / Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl- ...Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex / Lipoyl-containing pyruvate dehydrogenase complex component X / E3-binding protein / E3BP / proX


Mass: 10148.425 Da / Num. of mol.: 1
Fragment: N-terminal domain of 2-oxoacid dehydrogenases, Lipoyl binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P050613-07 / Production host: Cell free synthesis / References: UniProt: O00330

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.00mM domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 7.0 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
JEOL ECAJEOLECA7002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
Delta NMR4.3.2JEOLcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.04Johnson, B.A.data analysis
KUJIRA0.955Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.data analysis
CYANA1.0.7Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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