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- PDB-1b5s: DIHYDROLIPOYL TRANSACETYLASE (E.C.2.3.1.12) CATALYTIC DOMAIN (RES... -

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Basic information

Entry
Database: PDB / ID: 1b5s
TitleDIHYDROLIPOYL TRANSACETYLASE (E.C.2.3.1.12) CATALYTIC DOMAIN (RESIDUES 184-425) FROM BACILLUS STEAROTHERMOPHILUS
ComponentsDIHYDROLIPOAMIDE ACETYLTRANSFERASEDihydrolipoyl transacetylase
KeywordsACYLTRANSFERASE / DIHYDROLIPOYL TRANSACETYLASE / PYRUVATE DEHYDROGENASE / E2P / DIHYDROLIPOYL ACETYLTRANSFERASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / glycolytic process / cytoplasm
Similarity search - Function
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. ...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
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 Å
AuthorsIzard, T. / Aevarsson, A. / Allen, M.D. / Westphal, A.H. / Perham, R.N. / De Kok, A. / Hol, W.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Principles of quasi-equivalence and Euclidean geometry govern the assembly of cubic and dodecahedral cores of pyruvate dehydrogenase complexes.
Authors: Izard, T. / Aevarsson, A. / Allen, M.D. / Westphal, A.H. / Perham, R.N. / de Kok, A. / Hol, W.G.
History
DepositionJan 10, 1999Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Other
Revision 1.4Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
B: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
C: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
D: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
E: DIHYDROLIPOAMIDE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)132,1845
Polymers132,1845
Non-polymers00
Water0
1
A: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
B: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
C: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
D: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
E: DIHYDROLIPOAMIDE ACETYLTRANSFERASE
x 12


Theoretical massNumber of molelcules
Total (without water)1,586,20760
Polymers1,586,20760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation82_555-y,z,-x1
Unit cell
Length a, b, c (Å)534.400, 534.400, 534.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.501974, 0.8088, 0.306374), (-0.806941, 0.3105, 0.502429), (0.311236, -0.499432, 0.808517)0.1691, -0.3217, -0.0525
2given(-0.308651, 0.502944, 0.80733), (-0.499448, -0.808042, 0.312443), (0.809498, -0.306783, 0.500598)0.1773, -0.3268, -0.055
3given(-0.31174, -0.498006, 0.809202), (0.500546, -0.809961, -0.305641), (0.807634, 0.309762, 0.501772)0.1763, -0.3215, -0.0571
4given(0.497079, -0.810701, 0.309314), (0.811098, 0.30748, -0.49757), (0.308272, 0.498216, 0.810401)0.1764, -0.3218, -0.058

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Components

#1: Protein
DIHYDROLIPOAMIDE ACETYLTRANSFERASE / Dihydrolipoyl transacetylase / DIHYDROLIPOYL TRANSACETYLASE


Mass: 26436.783 Da / Num. of mol.: 5 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria)
References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growpH: 7 / Details: pH 7
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMTris-HCl1drop
320 %MPD1reservoir
4100 mMTris-HCl1reservoir
55 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 4.4→50 Å / Num. obs: 34381 / % possible obs: 63.4 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 4.4→4.68 Å / Rmerge(I) obs: 0.387 / % possible all: 34.9
Reflection
*PLUS
Num. measured all: 219513

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAA

1eaa


Highest resolution: 4.4 Å / Details: NOT YET FULLY REFINED.
Refinement stepCycle: LAST / Highest resolution: 4.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 0 0 5980

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