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- PDB-1dm3: ACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1dm3
TitleACETYLATED BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH ACETYL-COA
ComponentsBIOSYNTHETIC THIOLASE ACETYLATED AT CYS89
KeywordsTRANSFERASE / BIOSYNTHETIC THIOLASE / REACTION INTERMEDIATE / ACETYL-COA / BETA-ALPHA FOLD / ACETYL-COA ACETYLTRANSFERASE
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / cytoplasm
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain ...Thiolase, active site / Thiolases active site. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsModis, Y. / Wierenga, R.K.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystallographic analysis of the reaction pathway of Zoogloea ramigera biosynthetic thiolase.
Authors: Modis, Y. / Wierenga, R.K.
#1: Journal: Structure / Year: 1999
Title: A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism
Authors: Modis, Y. / Wierenga, R.K.
#2: Journal: Biochemistry / Year: 1989
Title: Mechanistic studies on beta-ketoacyl thiolase from Zoogloea ramigera: identification of the active-site nucleophile as Cys89, its mutation to Ser89, and kinetic and thermodynamic ...Title: Mechanistic studies on beta-ketoacyl thiolase from Zoogloea ramigera: identification of the active-site nucleophile as Cys89, its mutation to Ser89, and kinetic and thermodynamic characterization of wild-type and mutant enzymes
Authors: Thompson, S. / Mayerl, F. / Peoples, O.P. / Masamune, S. / Sinskey, A.J. / Walsh, C.T.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.classification / _software.name
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89
B: BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89
C: BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89
D: BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,00614
Polymers161,1924
Non-polymers3,81510
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-118 kcal/mol
Surface area47910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.384, 78.846, 149.729
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BIOSYNTHETIC THIOLASE ACETYLATED AT CYS89


Mass: 40297.949 Da / Num. of mol.: 4 / Fragment: ENTIRE THIOLASE, ACETYLATED AT CYS89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoogloea ramigera (bacteria) / Cellular location: CYTOPLASM / Plasmid: PTRC99A / Production host: Escherichia coli (E. coli) / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6
Fragment: ACETYL-COA CHAINS E,F,G AND H ARE NON-COVALENTLY BOUND TO PROTEIN CHAINS A,B,C AND D, RESPECTIVELY
Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.9 M Ammonium sulfate, 1 M lithium sulfate, 0,1 M sodium acetate, 1 mM DTT, 1mM EDTA, 1mM sodium azide, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.9 Mammonium sulfate1reservoir
21 Mlithium sulfate1reservoir
30.1 Msodium acetate1reservoir
41 mMdithiothreitol1reservoir
51 mMsodium azide1reservoir
61 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.057486
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.057486 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 132107 / Num. obs: 126823 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.3
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.22 / Num. unique all: 16710 / % possible all: 94.5
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.22

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
MAR345data collection
XDSdata scaling
RefinementResolution: 2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Weighted sparse matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6346 -Random
Rwork0.214 ---
all-132107 --
obs-126823 96 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 234 804 12302
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_deg2.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS

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