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- PDB-2c7y: plant enzyme -

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Basic information

Entry
Database: PDB / ID: 2c7y
Titleplant enzyme
Components3-KETOACYL-COA THIOLASE 2
KeywordsTRANSFERASE / FATTY ACID METABOLISM / OXYLIPIN SYNTHESIS / LIPID SYNTHESIS / ACYLTRANSFERASE
Function / homology
Function and homology information


glyoxysome organization / glyoxysome / positive regulation of abscisic acid-activated signaling pathway / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / jasmonic acid biosynthetic process / 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 / acetyl-CoA C-acyltransferase activity / jasmonic acid biosynthetic process / 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, C-terminal / Thiolase, C-terminal domain / Thiolase ...: / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / 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
3-ketoacyl-CoA thiolase 2, peroxisomal / 3-ketoacyl-CoA thiolase 2, peroxisomal
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSundaramoorthy, R. / Micossi, E. / Alphey, M.S. / Germain, V. / Bryce, J.H. / Smith, S.M. / Leonard, G.A. / Hunter, W.N.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of a Plant 3-Ketoacyl-Coa Thiolase Reveals the Potential for Redox Control of Peroxisomal Fatty Acid Beta-Oxidation.
Authors: Sundaramoorthy, R. / Micossi, E. / Alphey, M.S. / Germain, V. / Bryce, J.H. / Smith, S.M. / Leonard, G.A. / Hunter, W.N.
History
DepositionNov 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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
B: 3-KETOACYL-COA THIOLASE 2


Theoretical massNumber of molelcules
Total (without water)84,5312
Polymers84,5312
Non-polymers00
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.154, 94.461, 111.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A38 - 441
2114B39 - 441

NCS oper: (Code: given
Matrix: (-0.9967, 0.0097, 0.08014), (-0.006039, -0.9989, 0.0458), (0.0805, 0.04517, 0.9957)
Vector: 34.56, 94.39, -3.661)

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Components

#1: Protein 3-KETOACYL-COA THIOLASE 2 / 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


Mass: 42265.398 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9S7M3, UniProt: Q56WD9*PLUS, acetyl-CoA C-acyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.7
Details: 25% POLYETHYLENE GLYCOL 4000, 0.1M TRIS-HCL PH 8.5, 300MM MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.2 Å / Num. obs: 44287 / % possible obs: 96.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.2 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFW

1afw


Resolution: 2.1→29.21 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.624 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REGIONS WITH NO DIFFERENCE DENSITY HAVE BEEN LEFT OUT. NON DEFINED SIDE CHAINS ARE MODELLED WITH ZERO OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2200 5.1 %RANDOM
Rwork0.201 ---
obs0.204 41208 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 0 511 6274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9717909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7915787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28124.045220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33215956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8211540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024376
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22877
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23991
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2412
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5131.54005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86226218
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42732019
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3144.51690
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2822 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.320.5
2Bmedium positional0.320.5
1Amedium thermal0.552
2Bmedium thermal0.552
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 128
Rwork0.284 2194
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5961-0.553-0.53671.62380.09071.4149-0.03110.11730.0612-0.24130.02350.01740.24050.00150.00770.01120.0321-0.0037-0.10130.0002-0.109925.66133.0996.14
26.84870.908-1.10564.96531.31353.41170.06790.4121.1157-0.59770.1638-0.3039-0.19980.3688-0.2317-0.00490.06630.11240.02830.05530.110445.42141.992-0.652
31.6869-0.3384-0.45341.59370.24221.5355-0.132-0.22560.1250.03480.124-0.14530.21910.20260.008-0.07510.07110.0022-0.0731-0.0165-0.1232.27835.73718.462
41.5543-0.57790.17891.2307-0.32671.0345-0.03290.1077-0.1115-0.17520.03670.0767-0.0147-0.0055-0.0038-0.0825-0.0053-0.0141-0.12440.0007-0.116410.461.6915.668
52.6435-1.2432-0.45863.655-0.26340.47260.06610.3529-0.8493-0.6941-0.02590.61160.1941-0.0418-0.0402-0.01380.0049-0.1024-0.0058-0.01740.1955-10.5452.3361.442
61.7147-0.20670.12331.6726-0.121.5478-0.0992-0.2371-0.19950.07040.15950.1946-0.0372-0.1418-0.0603-0.13920.04190.0023-0.06770.053-0.11894.43559.63819.197
70.5098-0.4754-0.07530.6852-0.03990.6104-0.06950.0002-0.0102-0.02340.06020.010.06140.01920.0093-0.0066-0.0158-0.0167-0.007-0.0064-0.092717.27949.21311.755
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 259
2X-RAY DIFFRACTION2A260 - 292
3X-RAY DIFFRACTION3A293 - 440
4X-RAY DIFFRACTION4B39 - 259
5X-RAY DIFFRACTION5B260 - 292
6X-RAY DIFFRACTION6B293 - 441
7X-RAY DIFFRACTION7A2001 - 2228
8X-RAY DIFFRACTION7B2001 - 2283

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