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- PDB-1qfl: BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH A RE... -

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Basic information

Entry
Database: PDB / ID: 1qfl
TitleBIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH A REACTION INTERMEDIATE.
ComponentsPROTEIN (ACETOACETYL-COA THIOLASE)
KeywordsTRANSFERASE / THIOLASE / COA / TETRAMERIZATION MOTIF / COVALENT INTERMEDIATE / ACETYL-CYSTEINE
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 / Thiolase, N-terminal ...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 / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsModis, Y. / Wierenga, R.K.
Citation
Journal: Structure Fold.Des. / 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.
#1: 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. / Mayer, F. / Peoples, O.P. / Masamune, S. / Sinskey, A. / Walsh, C.T.
History
DepositionApr 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ACETOACETYL-COA THIOLASE)
B: PROTEIN (ACETOACETYL-COA THIOLASE)
C: PROTEIN (ACETOACETYL-COA THIOLASE)
D: PROTEIN (ACETOACETYL-COA THIOLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,83814
Polymers161,1924
Non-polymers3,64710
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19200 Å2
ΔGint-112 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.459, 78.864, 149.745
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.00123, -0.00039), (-0.00123, -1, 0.00048), (-0.00039, 0.00048, 1)42.23032, 0.01166, 0.03425
2given(0.44082, -0.89683, -0.0372), (-0.89746, -0.4411, -0.00065), (-0.01583, 0.03367, -0.99931)13.46427, 19.38684, 68.78861
3given(-0.43795, 0.89801, -0.0423), (0.89885, 0.43826, -0.002), (0.01674, -0.0389, -0.9991)32.14719, -18.56064, 68.12791

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Components

#1: Protein
PROTEIN (ACETOACETYL-COA THIOLASE) / BIOSYNTHETIC THIOLASE


Mass: 40297.949 Da / Num. of mol.: 4 / Fragment: RESIDUES 4-392
Source method: isolated from a genetically manipulated source
Details: CYS89 IS ACETYLATED / Source: (gene. exp.) Zoogloea ramigera (bacteria) / Plasmid: PZTH, BASED ON PTRC99A (PHARMACIA) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Description: ADDITIONAL DATA WERE COLLECTED AT THE ESRF ID14 BEAMLINE IN FEB-1999.
Crystal growpH: 5
Details: 1 M LITHIUM SULPHATE, 0.9 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 5.0 A REACTION INTERMEDIATE WAS TRAPPED BY FLASH-FREEZING THE CRYSTAL AFTER A SHORT SOAK WITH ACETOACETYL-COA SUBSTRATE.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
25 mMacetoacetyl-CoA1drop
31 Mlithium sulfate1reservoir
40.9 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH5.0
61 mMdithiothreitol1reservoir
71 mMEDTA1reservoir
81 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 1, 1998 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 130872 / % possible obs: 93 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.19 Å2 / Rsym value: 8.4 / Net I/σ(I): 7
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 5 / Rsym value: 13 / % possible all: 77

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
XDSV. 1999data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFW

1afw


Resolution: 1.92→50 Å / SU B: 4.32859 / SU ML: 0.12482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17198 / ESU R Free: 0.16273
Details: INITIAL SIMULATED ANNEALING MOLECULAR DYNAMICS REFINEMENT WAS CARRIED OUT WITH CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6438 5 %RANDOM
Rwork0.209 ---
obs-127433 85.5 %-
Displacement parametersBiso mean: 39.84 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 222 718 12204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.018
X-RAY DIFFRACTIONp_angle_d0.0410.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3143
X-RAY DIFFRACTIONp_mcangle_it4.0634
X-RAY DIFFRACTIONp_scbond_it5.8195
X-RAY DIFFRACTIONp_scangle_it6.5956
X-RAY DIFFRACTIONp_plane_restr0.0173
X-RAY DIFFRACTIONp_chiral_restr0.2050.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1970.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor18.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.520
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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