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- PDB-2fon: X-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycop... -

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Basic information

Entry
Database: PDB / ID: 2fon
TitleX-ray crystal structure of LeACX1, an acyl-CoA oxidase from Lycopersicon esculentum (tomato)
Componentsperoxisomal acyl-CoA oxidase 1A
KeywordsOXIDOREDUCTASE / peroxisomal beta-oxidation / FAD cofactor
Function / homology
Function and homology information


acyl-CoA oxidase activity / fatty acid beta-oxidation / FAD binding / peroxisome
Similarity search - Function
Acyl-CoA oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / 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 oxidase/dehydrogenase, middle domain ...Acyl-CoA oxidase, C-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase, N-terminal / Acyl-CoA oxidase / Acyl-coenzyme A oxidase N-terminal / 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 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
FLAVIN-ADENINE DINUCLEOTIDE / Acyl-coenzyme A oxidase
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsGaravito, R.M. / Powers, R.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure determination and analysis of acyl-CoA oxidase (ACX1) from tomato.
Authors: Powers, R.A. / Rife, C.L. / Schilmiller, A.L. / Howe, G.A. / Garavito, R.M.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peroxisomal acyl-CoA oxidase 1A
B: peroxisomal acyl-CoA oxidase 1A
C: peroxisomal acyl-CoA oxidase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,9926
Polymers229,6363
Non-polymers2,3573
Water64936
1
A: peroxisomal acyl-CoA oxidase 1A
B: peroxisomal acyl-CoA oxidase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6624
Polymers153,0902
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-86 kcal/mol
Surface area46950 Å2
MethodPISA
2
C: peroxisomal acyl-CoA oxidase 1A
hetero molecules

C: peroxisomal acyl-CoA oxidase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6624
Polymers153,0902
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Unit cell
Length a, b, c (Å)120.200, 240.330, 89.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a homodimer. The asymmetric unit contains the biological assembly (homodimer) and a single monomer for a total of three molecules.

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Components

#1: Protein peroxisomal acyl-CoA oxidase 1A


Mass: 76545.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: ACX1A / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5D8D3, acyl-CoA oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% 2-methyl-2,4-pentanediol, 7% PEG 6000, 100 mM Tris, 1 mM acetyl-CoA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 32-ID11
SYNCHROTRONAPS 32-ID21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 28, 2004
MARRESEARCH2CCDMar 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 64138 / % possible obs: 95.4 % / Redundancy: 6 % / Biso Wilson estimate: 50.87 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.048 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.7-2.7799.80.37447041.0851
2.77-2.8499.90.3147601.1341
2.84-2.9399.90.24947301.091
2.93-3.0299.90.21347151.0841
3.02-3.1399.80.18247311.0461
3.13-3.2599.60.15447641.0081
3.25-3.499.60.12947391.041
3.4-3.5870.40.12833371.0681
3.58-3.870.50.09933861.0131
3.8-4.198.60.07847111.0191
4.1-4.51990.06847800.9931
4.51-5.1699.30.06248211.0071
5.16-6.4999.40.13948551.0691
6.49-3099.70.07851051.0131

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.74→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 24.049 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.578 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3221 5 %RANDOM
Rwork0.212 ---
all0.214 ---
obs-63839 92.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.077 Å2
Baniso -1Baniso -2Baniso -3
1--4.83 Å20 Å20 Å2
2--2.47 Å20 Å2
3---2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.74→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14754 0 159 36 14949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215247
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.95520755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.47223.707642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.783152309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8891590
X-RAY DIFFRACTIONr_chiral_restr0.1250.22309
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211657
X-RAY DIFFRACTIONr_nbd_refined0.2510.27273
X-RAY DIFFRACTIONr_nbtor_refined0.3180.210521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2593
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.211
X-RAY DIFFRACTIONr_mcbond_it0.7361.59896
X-RAY DIFFRACTIONr_mcangle_it1.254215393
X-RAY DIFFRACTIONr_scbond_it2.16336344
X-RAY DIFFRACTIONr_scangle_it3.4484.55362
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.229 3239 -
obs-3397 67.98 %
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)
11.7562-0.6573-1.1761.80840.32694.57710.22330.2374-0.2075-0.1195-0.16920.124-0.3069-0.5479-0.0541-0.1550.1951-0.0213-0.1778-0.003-0.3593-10.634355.2346-38.0319
22.27010.6387-1.2791.3772-0.09524.136-0.0266-0.5034-0.10430.2608-0.0649-0.0228-0.17110.4260.0915-0.1236-0.146-0.0712-0.0030.0004-0.408427.190952.3703-6.7519
35.8981-4.1403-2.11117.98052.03228.01510.32180.35450.5448-0.2273-0.017-0.3139-0.24350.2595-0.30490.40740.11560.18310.50770.10860.4694-38.99612.0999-70.7956
44.1594-0.8937-0.81452.8368-0.48062.64-0.02890.0775-0.28670.3620.08570.6677-0.2848-0.7056-0.0569-0.18790.16020.13750.0051-0.0409-0.2743-22.186953.074-16.8709
53.9110.8537-1.12262.25290.08932.62250.0416-0.4931-0.2316-0.08020.0443-0.3689-0.2270.8272-0.0859-0.2542-0.14420.002-0.05260.0709-0.389438.392349.6521-27.8986
69.4277-1.2810.84672.37310.28995.41050.56330.67110.2946-0.17380.0149-0.1902-0.02550.3401-0.57820.56660.53360.13220.4619-0.17050.373-30.8657-10.3163-68.3251
70.89660.9383-0.92982.6701-0.54232.20390.11180.0339-0.20040.0901-0.07430.5858-0.051-0.4407-0.0375-0.28860.0549-0.0045-0.3374-0.0434-0.1869-2.015833.5403-32.7209
80.5714-0.9029-0.96732.87820.88692.07760.0313-0.4001-0.27820.1356-0.0105-0.32490.01640.3982-0.0208-0.2388-0.012-0.0015-0.21020.1418-0.259416.178131.9523-12.8969
92.5959-1.60792.22521.9255-1.32233.28870.7531.15830.1667-0.4271-0.3418-0.3346-0.02410.5259-0.41130.3140.39040.2590.25410.07190.3506-49.91468.5873-50.0588
102.07430.3498-0.58972.0733-0.30331.782-0.0350.0931-0.6591-0.0231-0.08430.24950.2315-0.24140.1192-0.28650.0445-0.016-0.4215-0.0535-0.16551.810226.0286-33.5246
111.8347-0.617-0.33132.03270.25071.8113-0.0724-0.3281-0.61760.2761-0.02480.06540.28340.13350.0971-0.2474-0.02770.0313-0.27170.181-0.213511.239125.1256-12.4488
122.5286-1.32740.86722.6525-0.85471.40540.38260.44250.3229-0.1874-0.0359-0.1759-0.32210.0308-0.34660.2230.34440.21220.03360.04660.3841-53.50779.9665-42.2972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA29 - 13048 - 149
22BB29 - 13048 - 149
33CC29 - 13048 - 149
44AA131 - 272150 - 291
55BB131 - 272150 - 291
66CC131 - 272150 - 291
77AA273 - 446292 - 465
88BB273 - 446292 - 465
99CC273 - 446292 - 465
1010AA447 - 650466 - 669
1111BB447 - 650466 - 669
1212CC447 - 650466 - 669

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