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- PDB-1e2o: CATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1e2o
TitleCATALYTIC DOMAIN FROM DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
ComponentsDIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
KeywordsTRANSFERASE / ACYLTRANSFERASE / KETOGLUTARATE DEHYDROGENASE MULTIENZYME COMPLEX
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle / cytosol / cytoplasm
Similarity search - Function
: / Dihydrolipoamide succinyltransferase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. ...: / Dihydrolipoamide succinyltransferase / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 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) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKnapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of the truncated cubic core component of the Escherichia coli 2-oxoglutarate dehydrogenase multienzyme complex.
Authors: Knapp, J.E. / Mitchell, D.T. / Yazdi, M.A. / Ernst, S.R. / Reed, L.J. / Hackert, M.L.
#1: Journal: Science / Year: 1992
Title: Atomic Structure of the Cubic Core of the Pyruvate Dehydrogenase Multienzyme Complex
Authors: Mattevi, A. / Obmolova, G. / Schulze, E. / Kalk, K.H. / Westphal, A.H. / De Kok, A. / Hol, W.G.
#2: Journal: Eur.J.Biochem. / Year: 1984
Title: Nucleotide Sequence of the Sucb Gene Encoding the Dihydrolipoamide Succinyltransferase of Escherichia Coli K12 and Homology with the Corresponding Acetyltransferase
Authors: Spencer, M.E. / Darlison, M.G. / Stephens, P.E. / Duckenfield, I.K. / Guest, J.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1971
Title: Crystallization and Preliminary Structural Analysis of Dihydrolipoyl Transsuccinylase, the Core of the 2-Oxoglutarate Dehydrogenase Complex
Authors: Derosier, D.J. / Oliver, R.M. / Reed, L.J.
History
DepositionMay 26, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2032
Polymers26,1071
Non-polymers961
Water28816
1
A: DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)628,88448
Polymers626,57824
Non-polymers2,30624
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area86500 Å2
ΔGint-561 kcal/mol
Surface area219200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)222.800, 222.800, 222.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-421-

SO4

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Components

#1: Protein DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE / E2O


Mass: 26107.420 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 172 - 404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SUCB / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 1.2M AMMONIUM SULFATE, 1% ETHANOL, 50 MM POTASSIUM PHOSPHATE, PH 7.0
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
250 mMpotassium phosphate1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
51 mMbenzamidine1drop
61.2 Mammonium sulfate1reservoir
71 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 9906 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Rsym value: 0.046 / Net I/σ(I): 13
Reflection shellResolution: 3→3.16 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.145 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.145

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(ROTAVATAdata scaling
Agrovatadata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAA

1eaa


Resolution: 3→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL AND RESOLUTION-DEPENDENT WEIGHTING SCHEME USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1001 10.3 %RANDOM
Rwork0.205 ---
obs0.205 9696 97.4 %-
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 5 16 1747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 145 9.4 %
Rwork0.261 1397 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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