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- PDB-2jgd: E. COLI 2-oxoglutarate dehydrogenase (E1o) -

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Basic information

Entry
Database: PDB / ID: 2jgd
TitleE. COLI 2-oxoglutarate dehydrogenase (E1o)
Components(2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT) x 2
KeywordsOXIDOREDUCTASE / 2-OXOGLUTARATE DEHYDROGENASE / FLAVOPROTEIN / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / ADENOSINE MONOPHOSPHATE / E1O / KGDH / OGDH / GLYCOLYSIS / OXALOACETATE
Function / homology
Function and homology information


oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component ...TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 2-oxoglutarate dehydrogenase E1 component
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsFrank, R.A.W. / Price, A.J. / Northrop, F.D. / Perham, R.N. / Luisi, B.F.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the E1 Component of the Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex.
Authors: Frank, R.A.W. / Price, A.J. / Northrop, F.D. / Perham, R.N. / Luisi, B.F.
History
DepositionFeb 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT
B: 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,0754
Polymers210,3802
Non-polymers6942
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)142.493, 142.493, 251.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A84 - 933
2111B84 - 933

NCS oper: (Code: given
Matrix: (0.79032, 0.61229, -0.02206), (0.61231, -0.79059, -0.00665), (-0.02151, -0.00825, -0.99973)
Vector: 15.62862, -44.72879, 50.09098)

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Components

#1: Protein 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT / ALPHA- KETOGLUTARATE DEHYDROGENASE


Mass: 105170.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AFG3, oxoglutarate dehydrogenase (succinyl-transferring)
#2: Protein 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT / ALPHA- KETOGLUTARATE DEHYDROGENASE


Mass: 105209.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AFG3, oxoglutarate dehydrogenase (succinyl-transferring)
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 3.41 Å3/Da / Density % sol: 63.67 %
Description: SELENIUM SITES WERE FOUND WITH MAD DATA IN SHELXD. PHASES WERE DETERMINED WITH SAD DATA IN PHASER
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: SITTING DROP: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6. 1UL 10MG/ML TE1O. RESERVOIR: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6., pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939272
DetectorDetector: CCD / Date: May 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939272 Å / Relative weight: 1
ReflectionResolution: 2.6→70 Å / Num. obs: 80455 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4041 5 %RANDOM
Rwork0.186 ---
obs0.189 76341 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.54 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12563 0 46 735 13344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02112931
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0791.94717527
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.89451611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34823.738618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.587152086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8381593
X-RAY DIFFRACTIONr_chiral_restr0.0910.21906
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.26181
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.28807
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2723
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.3881.58041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.148212864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it15.48434890
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it16.3734.54659
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6112 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.480.05
tight thermal2.130.5
LS refinement shellResolution: 2.6→2.66 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.399 290
Rwork0.308 5422

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