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

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Basic information

Entry
Database: PDB / ID: 1ead
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
OXIDIZED COENZYME A / 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)27,0252
Polymers26,2421
Non-polymers7841
Water81145
1
A: DIHYDROLIPOYL-TRANSACETYLASE
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)648,60748
Polymers629,80224
Non-polymers18,80524
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 area148420 Å2
ΔGint-900 kcal/mol
Surface area205560 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-CAO / OXIDIZED COENZYME A


Mass: 783.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHESE COORDINATES ARE FOR THE BINARY COMPLEX WITH COA (RESIDUE 638). THE ELECTRON DENSITY SUGGESTS ...THESE COORDINATES ARE FOR THE BINARY COMPLEX WITH COA (RESIDUE 638). THE ELECTRON DENSITY SUGGESTS THAT THE REACTIVE SULPHUR (I.E. PS1) OF COA IS OXIDIZED TO SULPHENIC ACID (EXTRA OXYGEN PO1). 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: 2.6 Å / Lowest resolution: 10 Å / Num. obs: 13596 / Rmerge(I) obs: 0.052

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→10 Å / Rfactor Rwork: 0.2 / Rfactor obs: 0.2 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1816 0 49 45 1910
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
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: 2.6 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor all: 0.2 / Rfactor Rwork: 0.2
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_deg26.3

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