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- PDB-2ix6: SHORT CHAIN SPECIFIC ACYL-COA OXIDASE FROM ARABIDOPSIS THALIANA, ACX4 -

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Basic information

Entry
Database: PDB / ID: 2ix6
TitleSHORT CHAIN SPECIFIC ACYL-COA OXIDASE FROM ARABIDOPSIS THALIANA, ACX4
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 / short-chain fatty acid metabolic process / salicylic acid binding / 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 / 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-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 / 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, N-terminal domain / Acyl-CoA dehydrogenase, C-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 oxidase/dehydrogenase, middle domain superfamily / 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
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase 4, peroxisomal
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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 / 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: 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
E: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
F: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,96412
Polymers295,2506
Non-polymers4,7136
Water00
1
A: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
C: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
hetero molecules

A: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
C: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,9768
Polymers196,8334
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
MethodPQS
2
B: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
D: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
E: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
F: ACYL-COENZYME A OXIDASE 4, PEROXISOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,9768
Polymers196,8334
Non-polymers3,1424
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)198.600, 198.600, 150.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22B
32C
42D
52E
62F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A17 - 432
2111B17 - 432
3111C17 - 432
4111D17 - 432
5111E17 - 432
6111F17 - 432
1121A800 - 801
2121B800 - 801
3121C800 - 801
4121D800 - 801
5121E800 - 801
6121F800 - 801

NCS ensembles :
ID
1
2

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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: 49208.371 Da / Num. of mol.: 6
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
Sequence detailsA C-TERMINAL HIS-TAG WAS INCLUDED IN THE CLONING PROCEDURE

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7
Details: 0.1 M BIS-TRIS-PROPANE PH 7.0, 6% PEG8000, 8% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.9→30 Å / Num. obs: 27647 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 25.19 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.4
Reflection shellResolution: 3.9→4.1 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IX5

2ix5


Resolution: 3.9→171.5 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.861 / SU B: 93.008 / SU ML: 0.613 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.838 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS HAVE BEEN EXCLUDED FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3015 9.6 %RANDOM
Rwork0.247 ---
obs0.247 28462 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: 55.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.27 Å20 Å2
2--0.55 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 3.9→171.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 318 0 19416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02219866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.881.98726994
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.76152490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63224.609768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.211153342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0011584
X-RAY DIFFRACTIONr_chiral_restr0.0590.23018
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214736
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.29750
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.213947
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2530
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.2104
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0360.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0281.512776
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.043219938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.06238448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0924.57056
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3184tight positional0.010.05
12B3184tight positional0.010.05
13C3184tight positional0.010.05
14D3184tight positional0.010.05
15E3184tight positional0.010.05
16F3184tight positional0.010.05
21A53tight positional0.010.05
22B53tight positional0.010.05
23C53tight positional0.010.05
24D53tight positional0.010.05
25E53tight positional0.010.05
26F53tight positional0.010.05
11A3184tight thermal0.010.5
12B3184tight thermal0.010.5
13C3184tight thermal0.010.5
14D3184tight thermal0.010.5
15E3184tight thermal0.010.5
16F3184tight thermal0.010.5
21A53tight thermal0.020.5
22B53tight thermal0.010.5
23C53tight thermal0.010.5
24D53tight thermal0.010.5
25E53tight thermal0.010.5
26F53tight thermal0.020.5
LS refinement shellResolution: 3.9→4 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 201
Rwork0.246 2099
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)
11.5215-0.39590.68811.0379-0.71293.82410.02420.1859-0.0694-0.1775-0.00530.10820.18610.1697-0.0189-0.54880.00350.0318-0.48410.0777-0.3123.2681-5.57254.9719
21.76870.5389-1.69841.4872-0.41914.8071-0.03780.40360.0789-0.31120.0875-0.05510.0463-0.3085-0.0497-0.3559-0.04970.0695-0.2423-0.0832-0.30587.252236.5819-36.8914
31.7966-0.53110.2442.8779-0.0161.80450.08980.1621-0.32720.004-0.083-0.27930.55180.8303-0.0068-0.45330.24710.06910.13250.1082-0.253353.8644-16.598512.362
42.1187-0.0584-0.44662.46930.69874.1120.0392-0.337-0.07730.39510.0916-0.30140.13910.4431-0.1307-0.2446-0.0318-0.0424-0.2271-0.0422-0.252698.182533.37673.2378
54.06470.0503-0.850.9659-0.32872.0773-0.28220.2874-0.4223-0.25030.21960.15750.5413-0.58620.06260.0232-0.28850.1206-0.1268-0.2159-0.156668.046710.4022-29.118
62.2938-0.07060.03822.76220.07984.39530.0285-0.1666-0.7730.34340.1221-0.65991.14831.1049-0.15060.48340.21650.0264-0.09590.02710.1738100.02730.6734-4.2877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 432
2X-RAY DIFFRACTION2B17 - 432
3X-RAY DIFFRACTION3C17 - 432
4X-RAY DIFFRACTION4D17 - 432
5X-RAY DIFFRACTION5E17 - 432
6X-RAY DIFFRACTION6F17 - 432

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