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- PDB-2wu9: Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 2wu9
TitleCrystal structure of peroxisomal KAT2 from Arabidopsis thaliana
Components3-KETOACYL-COA THIOLASE 2, PEROXISOMALThiolase
KeywordsTRANSFERASE / CYSTEINE OXIDATION / FATTY ACID METABOLISM / OXYLIPIN BIOSYNTHESIS / PLANT LIPID METABOLISM / FATTY ACID BIOSYNTHESIS / ACYLTRANSFERASE / LIPID METABOLISM / BETA OXIDATION / LIPID SYNTHESIS
Function / homology
Function and homology information


glyoxysome organization / glyoxysome / positive regulation of abscisic acid-activated signaling pathway / acetyl-CoA C-acyltransferase / jasmonic acid biosynthetic process / acetyl-CoA C-acyltransferase activity / oxylipin biosynthetic process / plant-type vacuole / fatty acid beta-oxidation / response to wounding ...glyoxysome organization / glyoxysome / positive regulation of abscisic acid-activated signaling pathway / acetyl-CoA C-acyltransferase / jasmonic acid biosynthetic process / acetyl-CoA C-acyltransferase activity / oxylipin biosynthetic process / plant-type vacuole / fatty acid beta-oxidation / response to wounding / peroxisome / nucleolus / endoplasmic reticulum / mitochondrion
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
3-ketoacyl-CoA thiolase 2, peroxisomal
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-KETOACYL-COA THIOLASE 2, PEROXISOMAL
B: 3-KETOACYL-COA THIOLASE 2, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,75911
Polymers93,2002
Non-polymers5599
Water20,3751131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint8.3 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.831, 86.670, 72.750
Angle α, β, γ (deg.)90.00, 106.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.09777, 0.9612, -0.2579), (0.9623, 0.02524, -0.2707), (-0.2537, -0.2747, -0.927)
Vector: -3.191, 18.4, 58.38)

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Components

#1: Protein 3-KETOACYL-COA THIOLASE 2, PEROXISOMAL / Thiolase / BETA-KETOTHIOLASE 2 / ACETYL-COA ACYLTRANSFERASE 2 / PEROXISOMAL 3-OXOACYL-COA THIOLASE 2 / ...BETA-KETOTHIOLASE 2 / ACETYL-COA ACYLTRANSFERASE 2 / PEROXISOMAL 3-OXOACYL-COA THIOLASE 2 / PEROXISOME DEFECTIVE PROTEIN 1\ / 3-KETOACYL-COA THIOLASE


Mass: 46600.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 36-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Organelle: PEROXISOME / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PET46 EK/LIC / Variant (production host): ROSETTAGAMI2(DE3) / References: UniProt: Q56WD9, acetyl-CoA C-acyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1131 / Source method: isolated from a natural source / Formula: H2O

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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: 2.04 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP. AT-KAT2 AT 11.8 MG/ML IN 20MM TRIS(HCL) PH9.0, 150MM NACL, 2MM EDTA, 5% (V/V) GLYCEROL, 2MM DTT, 2MM C12-COA AGAINST A WELL SOLUTION CONTAINING 20% (W/V) PEG 3350, 0.2M ...Details: HANGING DROP. AT-KAT2 AT 11.8 MG/ML IN 20MM TRIS(HCL) PH9.0, 150MM NACL, 2MM EDTA, 5% (V/V) GLYCEROL, 2MM DTT, 2MM C12-COA AGAINST A WELL SOLUTION CONTAINING 20% (W/V) PEG 3350, 0.2M LI(CH3COO)2, 0.002% ETHYLENE GLYCOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→34.6 Å / Num. obs: 112318 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 9.59 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 81.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.5_2)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WUA

2wua


Resolution: 1.5→34.6 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 5431 5 %
Rwork0.15 --
obs0.151 108434 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.39 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 14.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.1549 Å2-0 Å20.5309 Å2
2---0.4626 Å20 Å2
3----0.3538 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5892 0 36 1131 7059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066296
X-RAY DIFFRACTIONf_angle_d1.0888547
X-RAY DIFFRACTIONf_dihedral_angle_d14.1082337
X-RAY DIFFRACTIONf_chiral_restr0.074981
X-RAY DIFFRACTIONf_plane_restr0.0051145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.21951320.20942375X-RAY DIFFRACTION64
1.517-1.53490.24031340.21392504X-RAY DIFFRACTION69
1.5349-1.55360.22871440.20732750X-RAY DIFFRACTION75
1.5536-1.57330.24191800.20022953X-RAY DIFFRACTION82
1.5733-1.5940.21361730.18733200X-RAY DIFFRACTION88
1.594-1.61580.20271640.17673380X-RAY DIFFRACTION93
1.6158-1.63890.19761750.16783457X-RAY DIFFRACTION95
1.6389-1.66340.2081910.15663439X-RAY DIFFRACTION94
1.6634-1.68940.17891770.15033494X-RAY DIFFRACTION95
1.6894-1.71710.17511680.15023418X-RAY DIFFRACTION95
1.7171-1.74670.17011870.15623490X-RAY DIFFRACTION96
1.7467-1.77840.18081470.14913518X-RAY DIFFRACTION95
1.7784-1.81260.19241940.14363495X-RAY DIFFRACTION97
1.8126-1.84960.16791780.14283560X-RAY DIFFRACTION97
1.8496-1.88980.17011990.14483546X-RAY DIFFRACTION97
1.8898-1.93380.18392050.13843513X-RAY DIFFRACTION97
1.9338-1.98210.16741860.12833592X-RAY DIFFRACTION98
1.9821-2.03570.14622150.13383589X-RAY DIFFRACTION98
2.0357-2.09560.17021770.13243620X-RAY DIFFRACTION99
2.0956-2.16330.15691830.12923620X-RAY DIFFRACTION99
2.1633-2.24060.17581960.12843595X-RAY DIFFRACTION99
2.2406-2.33030.16111860.13083616X-RAY DIFFRACTION99
2.3303-2.43630.16991740.14123653X-RAY DIFFRACTION99
2.4363-2.56470.18471890.14153624X-RAY DIFFRACTION99
2.5647-2.72530.16981910.14713634X-RAY DIFFRACTION99
2.7253-2.93560.17221990.14513630X-RAY DIFFRACTION99
2.9356-3.23090.18492010.14473638X-RAY DIFFRACTION100
3.2309-3.69790.15551750.13153681X-RAY DIFFRACTION100
3.6979-4.65720.1441920.12323703X-RAY DIFFRACTION100
4.6572-34.6110.15462190.15083716X-RAY DIFFRACTION100

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