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- PDB-1ebd: DIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1ebd
TitleDIHYDROLIPOAMIDE DEHYDROGENASE COMPLEXED WITH THE BINDING DOMAIN OF THE DIHYDROLIPOAMIDE ACETYLASE
Components
  • DIHYDROLIPOAMIDE ACETYLTRANSFERASE
  • DIHYDROLIPOAMIDE DEHYDROGENASE
KeywordsCOMPLEX (OXIDOREDUCTASE/TRANSFERASE) / REDOX-ACTIVE CENTER / GLYCOLYSIS / OXIDOREDUCTASE / COMPLEX (OXIDOREDUCTASE-TRANSFERASE) COMPLEX
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide dehydrogenase / : / : / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site ...E3-binding domain / Dihydrolipoamide Transferase / Dihydrolipoamide dehydrogenase / : / : / 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) / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / 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 / Chloramphenicol acetyltransferase-like domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMande, S.S. / Sarfaty, S. / Allen, M.D. / Perham, R.N. / Hol, W.G.J.
CitationJournal: Structure / Year: 1996
Title: Protein-protein interactions in the pyruvate dehydrogenase multienzyme complex: dihydrolipoamide dehydrogenase complexed with the binding domain of dihydrolipoamide acetyltransferase.
Authors: Mande, S.S. / Sarfaty, S. / Allen, M.D. / Perham, R.N. / Hol, W.G.
History
DepositionFeb 3, 1996Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE DEHYDROGENASE
B: DIHYDROLIPOAMIDE DEHYDROGENASE
C: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6005
Polymers100,0293
Non-polymers1,5712
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.600, 106.600, 204.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.158991, 0.536088, 0.829055), (0.50818, -0.764388, 0.396818), (0.846449, 0.358219, -0.39396)
Vector: 27.5374, 66.9625, -80.4299)

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Components

#1: Protein DIHYDROLIPOAMIDE DEHYDROGENASE / E3BD


Mass: 47795.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P11959, dihydrolipoyl dehydrogenase
#2: Protein/peptide DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Mass: 4438.163 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 130 - 170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P11961
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.27 %
Description: DETAILS OF TWO EXPERIMENTS ARE REPORTED HERE. OVERALL R-MERGE FOR THE DATA SET UP TO 2.6 ANGSTROMS RESOLUTION WAS 0.092 WITH A COMPLETENESS OF 95%.
Crystal grow
*PLUS
pH: 4.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19-10 mg/mlprotein1drop
212 %PEG6001reservoir
3200 mMzinc acetate1reservoir
40.001 mMFAD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 44969 / % possible obs: 95 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Highest resolution: 2.64 Å / Lowest resolution: 2.95 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.6→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.215 -
obs0.215 40754
Refinement stepCycle: LAST / Resolution: 2.6→8 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 0 0
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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