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- PDB-1ni4: HUMAN PYRUVATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1ni4
TitleHUMAN PYRUVATE DEHYDROGENASE
Components(Pyruvate dehydrogenase E1 component: ...) x 2
KeywordsOXIDOREDUCTASE / THIAMIN PYROPHOSPHATE / PYRUVATE / ALPHA-KETO ACID DEHYDROGENASE / PYRUVATE DEHYDROGENASE
Function / homology
Function and homology information


pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / 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 ...pyruvate dehydrogenase (NAD+) activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / 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 / tricarboxylic acid cycle / glucose metabolic process / mitochondrial matrix / nucleolus / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain ...Pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit, subgroup y / Pyruvate dehydrogenase E1 component subunit beta / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial / Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 1.95 Å
AuthorsCiszak, E. / Korotchkina, L.G. / Dominiak, P.M. / Sidhu, S. / Patel, M.S.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase
Authors: Ciszak, E.M. / Korotchkina, L.G. / Dominiak, P.M. / Sidhu, S. / Patel, M.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Molecular cloning and characterization of human pyruvate dehydrogenase beta subunit gene.
Authors: Koike, K. / Urata, Y. / Koike, M.
History
DepositionDec 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate dehydrogenase E1 component: Alpha subunit
B: Pyruvate dehydrogenase E1 component: Beta subunit
C: Pyruvate dehydrogenase E1 component: Alpha subunit
D: Pyruvate dehydrogenase E1 component: Beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,44510
Polymers158,4674
Non-polymers9776
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22240 Å2
ΔGint-149 kcal/mol
Surface area42350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.337, 126.889, 190.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer: two alpha chains and two beta chains. Asymmetric unit contains complete tetrameric asssembly.

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Components

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Pyruvate dehydrogenase E1 component: ... , 2 types, 4 molecules ACBD

#1: Protein Pyruvate dehydrogenase E1 component: Alpha subunit / PDHE1-A type I


Mass: 41277.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P08559, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein Pyruvate dehydrogenase E1 component: Beta subunit / PDHE1-B


Mass: 37956.469 Da / Num. of mol.: 2 / Mutation: V31L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE-9 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41
References: UniProt: P11177, pyruvate dehydrogenase (acetyl-transferring)

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Non-polymers , 4 types, 748 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, sodium thiocyanate, magnesium chloride, thiamin pyrophosphate, sodium azide, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 295 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117 mg/mlprotein1drop
2200 mM1reservoirNaSCN
312 %PEG33501reservoir
410 %(v/v)1,2-propanediol1reservoir
550 mMpotassium phosphate1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97962, 0.97978, 0.96439
DetectorDetector: CCD / Date: Feb 23, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979621
20.979781
30.964391
ReflectionResolution: 1.95→45.2 Å / Num. all: 188753 / Num. obs: 175408 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 2.49 % / Rmerge(I) obs: 0.165
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 95.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD, molecular replacement / Resolution: 1.95→45.17 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 15302 9.6 %RANDOM
Rwork0.202 ---
all0.202 ---
obs0.202 175408 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0859 Å2 / ksol: 0.335138 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2---1.62 Å20 Å2
3----0.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10698 0 56 742 11496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it4.192.5
LS refinement shellResolution: 1.95→2.1 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 1997 9.5 %
Rwork0.321 18963 -
obs--71.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TPP.PARAMTPP.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE_GLY.PARAM
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 45.2 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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