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- PDB-1ivi: Crystal Structure of pig dihydrolipoamide dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1ivi
TitleCrystal Structure of pig dihydrolipoamide dehydrogenase
Componentsdihydrolipoamide dehydrogenase
KeywordsOXIDOREDUCTASE / 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / PYRUVATE DEHYDROGENASE COMPLEX
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 8 Å
AuthorsToyoda, T. / Kobayashi, R. / Sekiguchi, T. / Koike, K. / Koike, M. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray analysis of pig E3, lipoamide dehydrogenase.
Authors: Toyoda, T. / Kobayashi, R. / Sekiguchi, T. / Koike, K. / Koike, M. / Takenaka, A.
History
DepositionMar 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dihydrolipoamide dehydrogenase
D: dihydrolipoamide dehydrogenase
B: dihydrolipoamide dehydrogenase
E: dihydrolipoamide dehydrogenase
C: dihydrolipoamide dehydrogenase


Theoretical massNumber of molelcules
Total (without water)203,4915
Polymers203,4915
Non-polymers00
Water00
1
A: dihydrolipoamide dehydrogenase
D: dihydrolipoamide dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,3962
Polymers81,3962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: dihydrolipoamide dehydrogenase
E: dihydrolipoamide dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,3962
Polymers81,3962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: dihydrolipoamide dehydrogenase

C: dihydrolipoamide dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,3962
Polymers81,3962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)359.300, 359.300, 140.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein
dihydrolipoamide dehydrogenase / Coordinate model: Cα atoms only


Mass: 40698.164 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: dihydrolipoyl dehydrogenase

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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: 6.43 Å3/Da / Density % sol: 80.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMpotassium phosphate1droppH7.0
26.6 mg/mlprotein1drop
30.25 mMFAD1drop
40.75 Mammonium sulfate1drop
550 mMpotassium phosphate1reservoirpH7.0
61.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 8→50 Å / Num. all: 13615 / Num. obs: 5838 / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 8 Å / % possible obs: 98 % / Num. measured all: 13615

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CCP4(SCALA)data scaling
RefinementResolution: 8→50 Å / Rfactor Rwork: 0.378
Details: The coordinates for only the alpha carbons are present in the structure.
Refinement stepCycle: LAST / Resolution: 8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 0 2390
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.379
Solvent computation
*PLUS
Displacement parameters
*PLUS

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