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- PDB-1dpd: CRYSTALLOGRAPHIC AND ENZYMATIC INVESTIGATIONS ON THE ROLE OF SER5... -

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Basic information

Entry
Database: PDB / ID: 1dpd
TitleCRYSTALLOGRAPHIC AND ENZYMATIC INVESTIGATIONS ON THE ROLE OF SER558, HIS610 AND ASN614 IN THE CATALYTIC MECHANISM OF AZOTOBACTER VINELANDII DIHYDROLIPOAMIDE ACETYLTRANSFERASE (E2P)
ComponentsDIHYDROLIPOYL-TRANSACETYLASE
KeywordsDIHYDROLIPOAMIDE ACETYLTRANSFERASE
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate dehydrogenase complex / glycolytic process
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. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain ...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
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsHendle, J. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystallographic and enzymatic investigations on the role of Ser558, His610, and Asn614 in the catalytic mechanism of Azotobacter vinelandii dihydrolipoamide acetyltransferase (E2p).
Authors: Hendle, J. / Mattevi, A. / Westphal, A.H. / Spee, J. / de Kok, A. / Teplyakov, A. / Hol, W.G.
#1: 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.
#2: 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.
#3: 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.J.
History
DepositionFeb 3, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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
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 THREE-FOLD RELATED SUBUNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROLIPOYL-TRANSACETYLASE


Theoretical massNumber of molelcules
Total (without water)26,2261
Polymers26,2261
Non-polymers00
Water91951
1
A: DIHYDROLIPOYL-TRANSACETYLASE
x 24


Theoretical massNumber of molelcules
Total (without water)629,41624
Polymers629,41624
Non-polymers00
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 area112170 Å2
ΔGint-877 kcal/mol
Surface area214600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)224.669, 224.669, 224.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Atom site foot note1: CIS PROLINE - PRO 575

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Components

#1: Protein DIHYDROLIPOYL-TRANSACETYLASE


Mass: 26225.682 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.68 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMHEPES1drop
30.02 %azide1drop
412-16 %ammonium sulfate1drop
512-16 %ammonium sulfate1reservoir
650 mMHEPES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Nov 17, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.95 %
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 13826 / % possible obs: 99.8 % / Num. measured all: 191748 / Rmerge(I) obs: 0.108

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.184 -
obs0.184 13826
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 0 51 1862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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

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