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- PDB-1ik6: 3D structure of the E1beta subunit of pyruvate dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 1ik6
Title3D structure of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum
Componentspyruvate dehydrogenase
KeywordsOXIDOREDUCTASE / e1beta / pyruvate dehydrogenase / tetramer / gxxxg
Function / homology
Function and homology information


2-oxoacid oxidoreductase (ferredoxin) / 2-oxobutyrate synthase activity / pyruvate synthase activity / branched-chain amino acid catabolic process / response to nutrient
Similarity search - Function
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 ...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
2-oxoacid oxidoreductase (ferredoxin)
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKleiger, G. / Perry, J. / Eisenberg, D.
CitationJournal: Biochemistry / Year: 2001
Title: 3D structure and significance of the GPhiXXG helix packing motif in tetramers of the E1beta subunit of pyruvate dehydrogenase from the archeon Pyrobaculum aerophilum.
Authors: Kleiger, G. / Perry, J. / Eisenberg, D.
History
DepositionMay 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE There is an N-terminal his tag that was NOT cleaved. However, it is not ordered so the ...SEQUENCE There is an N-terminal his tag that was NOT cleaved. However, it is not ordered so the author was not able to model it.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pyruvate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)39,9331
Polymers39,9331
Non-polymers00
Water2,414134
1
A: pyruvate dehydrogenase

A: pyruvate dehydrogenase

A: pyruvate dehydrogenase

A: pyruvate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)159,7314
Polymers159,7314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)65.241, 84.543, 131.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -x,-y,z followed by -x,y,-z

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Components

#1: Protein pyruvate dehydrogenase


Mass: 39932.840 Da / Num. of mol.: 1 / Fragment: E1beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Plasmid: pET30Ek/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZUR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 400, Calcium Chloride, Sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
127 mg/mlprotein1drop
20.2 M1reservoirCaCl2
30.1 Msodium HEPES1reservoirpH7.5
428 %(w/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24820 / Num. obs: 22189 / % possible obs: 89.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 22
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.257 / % possible all: 96
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1QS0 Beta-chain

1qs0


Resolution: 2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflectionSelection details
Rfree0.255 2235 Random
Rwork0.212 --
all-22189 -
obs-22189 -
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 0 134 2231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2→2.02 Å /
RfactorNum. reflection
Rfree0.321 46
Rwork0.251 -
obs-381
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.6
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.321 / Rfactor Rwork: 0.251

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