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- PDB-2wua: Structure of the peroxisomal 3-ketoacyl-CoA thiolase from Sunflower -

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Basic information

Entry
Database: PDB / ID: 2wua
TitleStructure of the peroxisomal 3-ketoacyl-CoA thiolase from Sunflower
ComponentsACETOACETYL COA THIOLASE
KeywordsTRANSFERASE / BETA OXIDATION / PLANT LIPID METABOLISM / ACYLTRANSFERASE / CYSTEINE OXIDATION
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / 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
Acetoacetyl CoA thiolase
Similarity search - Component
Biological speciesHELIANTHUS ANNUUS (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPye, V.E. / Christensen, C.E. / Dyer, J.H. / Arent, S. / Henriksen, A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Peroxisomal Plant 3-Ketoacyl-Coa Thiolases Structure and Activity are Regulated by a Sensitive Redox Switch
Authors: Pye, V.E. / Christensen, C.E. / Dyer, J.H. / Arent, S. / Henriksen, A.
History
DepositionOct 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETOACETYL COA THIOLASE
B: ACETOACETYL COA THIOLASE


Theoretical massNumber of molelcules
Total (without water)92,0612
Polymers92,0612
Non-polymers00
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-26.2 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.596, 100.692, 105.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.09777, 0.9612, -0.2579), (0.9623, 0.02524, -0.2707), (-0.2537, -0.2747, -0.9275)
Vector: -3.191, 18.49, 58.38)

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Components

#1: Protein ACETOACETYL COA THIOLASE / 3-KETOACYL-COA THIOLASE


Mass: 46030.730 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-449 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELIANTHUS ANNUUS (common sunflower) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6W6X6, acetyl-CoA C-acyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ALA 223 TO THR ENGINEERED RESIDUE IN CHAIN B, ALA 223 TO THR

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP. HAKAT AT 10 MG/ML IN 20MM TRIS(HCL) PH9.0, 150MM NACL, 2MM EDTA, 5% (V/V) GLYCEROL, 2MM DTT MIXED WITH WELL SOLUTION: 20% (W/V) PEG 3350, 0.2M LI(CH3COO)2, 0.01M TAURINE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→78.6 Å / Num. obs: 77995 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 28.31 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.6 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C7Y

2c7y


Resolution: 1.8→50.346 Å / SU ML: 0.23 / σ(F): 1.37 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 3875 5 %
Rwork0.1856 --
obs0.1872 77233 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.649 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 33.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.8496 Å2-0 Å20 Å2
2---0.1614 Å2-0 Å2
3---1.011 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5734 0 0 709 6443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065980
X-RAY DIFFRACTIONf_angle_d1.028117
X-RAY DIFFRACTIONf_dihedral_angle_d13.6642217
X-RAY DIFFRACTIONf_chiral_restr0.068941
X-RAY DIFFRACTIONf_plane_restr0.0041077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8220.28631120.24432291X-RAY DIFFRACTION88
1.822-1.8450.28511210.23532400X-RAY DIFFRACTION92
1.845-1.86930.29241320.23142531X-RAY DIFFRACTION97
1.8693-1.89490.27741440.22912546X-RAY DIFFRACTION98
1.8949-1.9220.26781320.22532631X-RAY DIFFRACTION100
1.922-1.95070.23021600.21072590X-RAY DIFFRACTION100
1.9507-1.98110.2271320.19982598X-RAY DIFFRACTION100
1.9811-2.01360.23831210.2022682X-RAY DIFFRACTION100
2.0136-2.04840.26461280.2012616X-RAY DIFFRACTION100
2.0484-2.08560.23381440.20112619X-RAY DIFFRACTION100
2.0856-2.12570.24221340.18762657X-RAY DIFFRACTION100
2.1257-2.16910.21761430.19222580X-RAY DIFFRACTION100
2.1691-2.21630.26061260.18592623X-RAY DIFFRACTION100
2.2163-2.26780.22881520.18772630X-RAY DIFFRACTION100
2.2678-2.32450.22091230.1882660X-RAY DIFFRACTION100
2.3245-2.38740.23581430.18752633X-RAY DIFFRACTION100
2.3874-2.45760.21341400.19132645X-RAY DIFFRACTION100
2.4576-2.5370.2694860.19262684X-RAY DIFFRACTION100
2.537-2.62760.24882040.1942567X-RAY DIFFRACTION100
2.6276-2.73280.295790.19582777X-RAY DIFFRACTION100
2.7328-2.85720.23151830.19222619X-RAY DIFFRACTION100
2.8572-3.00780.22381560.19032635X-RAY DIFFRACTION100
3.0078-3.19620.25321510.1892651X-RAY DIFFRACTION100
3.1962-3.4430.19932180.182594X-RAY DIFFRACTION100
3.443-3.78930.19611020.16422714X-RAY DIFFRACTION100
3.7893-4.33740.161650.14122680X-RAY DIFFRACTION100
4.3374-5.46360.16471610.13542710X-RAY DIFFRACTION100
5.4636-50.36580.19561530.2012795X-RAY DIFFRACTION98

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