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- PDB-1jeh: CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1jeh
TitleCRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE
ComponentsDIHYDROLIPOAMIDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / 2-oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex
Function / homology
Function and homology information


Glycine degradation / OGDH complex synthesizes succinyl-CoA from 2-OG / PDH complex synthesizes acetyl-CoA from PYR / : / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / glycine cleavage complex / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity ...Glycine degradation / OGDH complex synthesizes succinyl-CoA from 2-OG / PDH complex synthesizes acetyl-CoA from PYR / : / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / glycine cleavage complex / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / L-valine catabolic process / L-isoleucine catabolic process / L-leucine catabolic process / hydrogen peroxide metabolic process / oxoglutarate dehydrogenase complex / pyruvate decarboxylation to acetyl-CoA / L-serine biosynthetic process / pyruvate dehydrogenase complex / 2-oxoglutarate metabolic process / pyruvate metabolic process / cellular respiration / mitochondrial nucleoid / tricarboxylic acid cycle / flavin adenine dinucleotide binding / mitochondrion
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / 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 / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Dihydrolipoamide dehydrogenase / : / 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 / FAD/NAD-linked reductase, dimerisation 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Dihydrolipoyl dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsToyoda, T. / Suzuki, K. / Sekigushi, T. / Reed, J. / Takenaka, A.
CitationJournal: J.Biochem. / Year: 1998
Title: Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.
Authors: Toyoda, T. / Suzuki, K. / Sekiguchi, T. / Reed, L.J. / Takenaka, A.
History
DepositionJun 18, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.6Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8194
Polymers103,2482
Non-polymers1,5712
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10530 Å2
ΔGint-55 kcal/mol
Surface area34920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.100, 158.700, 67.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DIHYDROLIPOAMIDE DEHYDROGENASE


Mass: 51623.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09624, dihydrolipoyl dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 73 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7 / Details: PEG6000, pH 7.00, MICRODIALYSIS, temperature 298K
Crystal grow
*PLUS
Details: Toyoda, T., (1997) J.Biochem.(Tokyo), 121, 1.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein11
225 mMpotassium phosphate11
35 %(w/v)PEG600012with water

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. obs: 33372 / % possible obs: 80.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.4→2.68 Å / % possible all: 42.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Redundancy: 2.9 % / Num. measured all: 97677

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATAdata reduction
MERLOTphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GRS

3grs


Resolution: 2.4→10 Å / σ(F): 4
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -10 %RANDOM
Rwork0.202 ---
obs0.202 25458 --
Displacement parametersBiso mean: 35.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7184 0 106 73 7363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.532
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
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rfree0.303 10 %
Rwork0.286 -
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.7 Å2
Refine LS restraints
*PLUS
Type: x_improper_angle_d / Dev ideal: 0.763
LS refinement shell
*PLUS
Rfactor Rfree: 0.303 / % reflection Rfree: 10 % / Rfactor Rwork: 0.286

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