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- PDB-1eae: ATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE ... -

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Basic information

Entry
Database: PDB / ID: 1eae
TitleATOMIC STRUCTURE OF THE CUBIC CORE OF THE PYRUVATE DEHYDROGENASE MULTIENZYME COMPLEX
ComponentsDIHYDROLIPOYL-TRANSACETYLASE
KeywordsDIHYDROLIPOAMIDE ACETYLTRANSFERASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / glycolytic process / cytoplasm
Similarity search - Function
Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like 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. ...Dihydrolipoamide acetyltransferase pyruvate dehydrogenase complex / : / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like 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) / 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
6,8-DIMERCAPTO-OCTANOIC ACID AMIDE / Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsMattevi, A. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystallographic analysis of substrate binding and catalysis in dihydrolipoyl transacetylase (E2p).
Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Teplyakov, A. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of Lipoamide Dehydrogenase from Pseudomonas Fluorescens at 2.8 Angstroms Resolution. Analysis of Redox and Thermostability Properties
Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Van Berkel, W.J. / Hol, W.G.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Crystal Structure of the Catalytic Domain of Dihydrolipoyl Transacetylase (E2P) from Azotobacter Vinelandii at 2.6 Angstroms Resolution
Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Westphal, A.H. / De Kok, A. / Hol, W.G.
#3: Journal: Biochemistry / Year: 1993
Title: Crystallographic Analysis of Substrate Binding and Catalysis in Dihydrolipoyl Transacetylase (E2P)
Authors: Mattevi, A. / Obmolova, G. / Kalk, K.H. / Teplyakov, A. / Hol, W.G.
History
DepositionDec 16, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET A IS ACTUALLY A FOUR-STRANDED SHEET. IT CONTAINS TWO ADDITIONAL STRANDS A 3 ILE 409 PRO ...SHEET SHEET A IS ACTUALLY A FOUR-STRANDED SHEET. IT CONTAINS TWO ADDITIONAL STRANDS A 3 ILE 409 PRO 413 -1 A 4 THR 566 PHE 568 -1 FROM A THREEFOLD-RELATED SUBUNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIHYDROLIPOYL-TRANSACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4492
Polymers26,2421
Non-polymers2071
Water54030
1
A: DIHYDROLIPOYL-TRANSACETYLASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)634,77948
Polymers629,80224
Non-polymers4,97724
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 area126860 Å2
ΔGint-878 kcal/mol
Surface area212330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)225.540, 225.540, 225.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Atom site foot note1: RESIDUE 575 IS A CIS PROLINE.

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Components

#1: Protein DIHYDROLIPOYL-TRANSACETYLASE


Mass: 26241.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria)
References: UniProt: P10802, dihydrolipoyllysine-residue acetyltransferase
#2: Chemical ChemComp-LPM / 6,8-DIMERCAPTO-OCTANOIC ACID AMIDE


Mass: 207.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NOS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHESE COORDINATES ARE FOR THE BINARY COMPLEX WITH DIHYDROLIPOAMIDE (RESIDUE 639). FOR A MORE ...THESE COORDINATES ARE FOR THE BINARY COMPLEX WITH DIHYDROLIPOAMIDE (RESIDUE 639). FOR A MORE DETAILED DESCRIPTION SEE REFERENCE 3.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ODP2_AZOVI SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLU 458 LYS 458

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 72.97 %
Crystal grow
*PLUS
pH: 7 / Method: unknown / Details: used macroseeding
Components of the solutions
*PLUS
Conc.: 16 %sat / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 10148 / Rmerge(I) obs: 0.053

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 10344
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 12 30 1858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection all: 10344 / σ(F): 0 / Rfactor all: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6

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