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- PDB-2ix5: Short chain specific acyl-CoA oxidase from Arabidopsis thaliana, ... -

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Basic information

Entry
Database: PDB / ID: 2ix5
TitleShort chain specific acyl-CoA oxidase from Arabidopsis thaliana, ACX4 in complex with acetoacetyl-CoA
ComponentsACYL-COENZYME A OXIDASE 4, PEROXISOMAL
KeywordsOXIDOREDUCTASE / FAD / ACX4 / FLAVIN / PEROXISOME / GLYOXYSOME / FATTY ACID METABOLISM / LIPID METABOLISM / ACYL-COA OXIDASE / ELECTRON TRANSFER / FLAVOPROTEIN / BETA-OXIDATION
Function / homology
Function and homology information


acyl-CoA oxidase / glyoxysome / acyl-CoA oxidase activity / salicylic acid binding / short-chain fatty acid metabolic process / acyl-CoA dehydrogenase activity / embryo development ending in seed dormancy / fatty acid beta-oxidation / peroxisome / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Acyl-coenzyme A oxidase 4-like / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal ...Acyl-coenzyme A oxidase 4-like / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETOACETYL-COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase 4, peroxisomal
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMackenzie, J. / Pedersen, L. / Arent, S. / Henriksen, A.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Controlling Electron Transfer in Acyl-Coa Oxidases and Dehydrogenases: A Structural View.
Authors: Mackenzie, J. / Pedersen, L. / Arent, S. / Henriksen, A.
#1: Journal: Acta Crystallogr., Sect.D / Year: 2004
Title: Expression, Purification and Crystallization of Two Peroxisomal Acyl-Coa Oxidases from Arabidopsis Thaliana
Authors: Pedersen, L. / Henriksen, A.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Arabidopsis Mutants in Short- and Medium-Chain Acyl-Coa Oxidase Activities Accumulate Acyl-Coas and Reveal that Fatty Acid Beta-Oxidation is Essential for Embryo Development
Authors: Rylott, E.L. / Rogers, C.A. / Gilday, A.D. / Edgell, T. / Larson, T.R. / Graham, I.A.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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
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: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
B: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
C: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
D: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,97212
Polymers190,4234
Non-polymers6,5498
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.747, 144.747, 149.208
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
ACYL-COENZYME A OXIDASE 4, PEROXISOMAL / ACYL-COA OXIDASE / AOX 4 / SHORT- CHAIN ACYL-COA OXIDASE / SAOX / ATCX4 / G6P / ATG6


Mass: 47605.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Description: ARABIDOPSIS BIOLOGICAL RESOURCE CENTER / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96329, acyl-CoA oxidase
#2: Chemical
ChemComp-CAA / ACETOACETYL-COENZYME A / Acetoacetyl-CoA


Mass: 851.607 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H40N7O18P3S
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.51
Details: 10% PEG8000, 0.1 M CACODYLATE PH 6.5, 0.001 M ACETOACETYL-COA, 2% BENZAMIDINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.082
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.082 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 142184 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 56.98 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.3
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JQI

1jqi


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 24.7 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES WITH NO SIGNIFICANT ELECTRON DENSITY HAVE BEEN OMITTED FROM THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2525 5.1 %RANDOM
Rwork0.186 ---
obs0.189 47195 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.06 Å20 Å2
2---0.13 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12656 0 404 164 13224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1662.00118208
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.71451660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5724.545506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76152190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1691556
X-RAY DIFFRACTIONr_chiral_restr0.0770.22042
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.29750
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.29295
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0810.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2921.58441
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.502213254
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71835978
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2354.54952
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
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 176
Rwork0.308 3395
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)
10.78190.1801-0.1130.8884-0.14821.1073-0.08210.04140.4169-0.02980.02170.2096-0.6161-0.18040.06040.20360.1131-0.1054-0.0636-0.05360.127325.5491-10.5924-7.4301
20.71820.0087-0.16020.19210.33281.8086-0.06370.07730.1081-0.05840.0572-0.0762-0.27820.18020.0065-0.0531-0.0501-0.0373-0.16310.0122-0.068851.933-29.7885-14.3409
30.85370.11260.34920.33780.1251.5721-0.0134-0.15890.03660.19680.0263-0.0654-0.0020.0399-0.0129-0.05130.0175-0.0249-0.1506-0.0412-0.052948.0686-40.616425.2011
40.52250.38350.26441.24660.0560.7049-0.0094-0.24390.10540.1789-0.0310.2618-0.0033-0.3250.0404-0.0680.01310.03680.0423-0.0632-0.0115.7576-42.332817.0967
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 431
2X-RAY DIFFRACTION2B17 - 431
3X-RAY DIFFRACTION3C17 - 431
4X-RAY DIFFRACTION4D17 - 431

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