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- PDB-9h1n: Dihydrolipoamide Acetyltransferase (E2) PSBD in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 9h1n
TitleDihydrolipoamide Acetyltransferase (E2) PSBD in complex with the Pyruvate Dehydrogenase (E1) binding domain from E. coli
Components
  • Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
  • Pyruvate dehydrogenase E1 component
KeywordsPROTEIN BINDING / Complex / pyruvate dehydrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


stress response to acid chemical / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate decarboxylation to acetyl-CoA / lipoic acid binding / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding ...stress response to acid chemical / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate decarboxylation to acetyl-CoA / lipoic acid binding / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / : / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal ...Pyruvate dehydrogenase E1 component, N-terminal / Pyruvate dehydrogenase E1 component, middle domain / : / Pyruvate dehydrogenase E1 component middle domain / Pyruvate dehydrogenase E1 component / Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / : / Transketolase-like TK C-terminal domain / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / 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) / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Pyruvate dehydrogenase E1 component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsBothe, S.N. / Racunica, D. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: A cooperative binding mechanism steers the recruitment of peripheral subunits in the E. coli pyruvate dehydrogenase complex
Authors: Bothe, S.N. / Racunica, D. / Zajec Hudnik, T. / Zdanowicz, R. / Bothe, A. / Giese, C. / Glockshuber, R.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)18,4773
Polymers18,4773
Non-polymers00
Water2,198122
1
C: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

C: Pyruvate dehydrogenase E1 component
B: Pyruvate dehydrogenase E1 component
A: Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)36,9536
Polymers36,9536
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)87.262, 87.262, 42.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-115-

HOH

21B-120-

HOH

31B-129-

HOH

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Components

#1: Protein/peptide Pyruvate dehydrogenase E1 component / PDH E1 component


Mass: 5633.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: isolated binding domain of E1 (residues 1-50) / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceE, b0114, JW0110 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AFG8, pyruvate dehydrogenase (acetyl-transferring)
#2: Protein Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoyllysine-residue acetyltransferase (E2) component of pyruvate dehydrogenase complex


Mass: 7210.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aceF, b0115, JW0111 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P06959, dihydrolipoyllysine-residue acetyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 56% Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.54→39.02 Å / Num. obs: 24525 / % possible obs: 99.87 % / Redundancy: 2 % / Biso Wilson estimate: 32.63 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.01196 / Rpim(I) all: 0.01196 / Rrim(I) all: 0.01691 / Net I/σ(I): 19.07
Reflection shellResolution: 1.54→1.6 Å / Rmerge(I) obs: 0.6179 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2383 / CC1/2: 0.546 / CC star: 0.84 / Rpim(I) all: 0.6179 / Rrim(I) all: 0.8738 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→39.02 Å / SU ML: 0.2238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 1215 4.95 %
Rwork0.204 23307 -
obs0.2052 24522 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.99 Å2
Refinement stepCycle: LAST / Resolution: 1.54→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 122 1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211239
X-RAY DIFFRACTIONf_angle_d1.23561679
X-RAY DIFFRACTIONf_chiral_restr0.0789185
X-RAY DIFFRACTIONf_plane_restr0.0114227
X-RAY DIFFRACTIONf_dihedral_angle_d4.1904179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.610.38031130.38242526X-RAY DIFFRACTION99.1
1.61-1.680.32451410.30992545X-RAY DIFFRACTION99.96
1.68-1.770.30771160.2612578X-RAY DIFFRACTION99.96
1.77-1.880.30141360.25332533X-RAY DIFFRACTION100
1.88-2.020.30421510.2432562X-RAY DIFFRACTION100
2.02-2.230.22531560.20962542X-RAY DIFFRACTION100
2.23-2.550.25651320.20722602X-RAY DIFFRACTION100
2.55-3.210.24061370.21132639X-RAY DIFFRACTION100
3.21-39.020.18291330.17892780X-RAY DIFFRACTION99.86

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