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- PDB-7px0: Drosophila melanogaster Aldehyde Oxidase 1 -

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Basic information

Entry
Database: PDB / ID: 7px0
TitleDrosophila melanogaster Aldehyde Oxidase 1
ComponentsAldehyde oxidase 1
KeywordsOXIDOREDUCTASE / ---
Function / homology
Function and homology information


pyridoxal oxidase / pyridoxal oxidase activity / pyridoxal metabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / peroxisome / oxidoreductase activity / iron ion binding
Similarity search - Function
CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding ...CO dehydrogenase flavoprotein C-terminal domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / Aldehyde oxidase 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVilela-Alves, G. / Mota, C. / Romao, M.J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/1185/2014 Portugal
CitationJournal: To Be Published
Title: Drosophila melanogaster's Aldehyde Oxidase 1: The First Invertebrate AOX structure
Authors: Vilela-Alves, G. / Mota, C. / Romao, M.J.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde oxidase 1
B: Aldehyde oxidase 1
C: Aldehyde oxidase 1
D: Aldehyde oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)565,29840
Polymers557,1104
Non-polymers8,18836
Water44,3712463
1
A: Aldehyde oxidase 1
B: Aldehyde oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,96923
Polymers278,5552
Non-polymers4,41421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14940 Å2
ΔGint-127 kcal/mol
Surface area80450 Å2
MethodPISA
2
C: Aldehyde oxidase 1
D: Aldehyde oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,32917
Polymers278,5552
Non-polymers3,77415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-135 kcal/mol
Surface area80130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.663, 127.914, 152.547
Angle α, β, γ (deg.)90.000, 110.629, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aldehyde oxidase 1 / LD37006p


Mass: 139277.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: AOX1, CT42272, DmAO1, Dmel\CG18522, LPO, lpo, PO, Po, CG18522, Dmel_CG18522
Plasmid: pZM171 / Production host: Escherichia coli (E. coli) / Strain (production host): TP 1000 / References: UniProt: Q9VF53, pyridoxal oxidase

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Non-polymers , 8 types, 2499 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O6PS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2463 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PEG 3350, ammonium citrate, dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→48.66 Å / Num. obs: 257441 / % possible obs: 97.83 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.25 Å2 / CC1/2: 0.986 / Net I/σ(I): 6.3
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 12300 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless1.10.28data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UNC

3unc


Resolution: 2.2→48.66 Å / SU ML: 0.2803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2203 12898 5.01 %RANDOM
Rwork0.1749 244543 --
obs0.1772 257441 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38362 0 448 2463 41273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016139656
X-RAY DIFFRACTIONf_angle_d1.812853751
X-RAY DIFFRACTIONf_chiral_restr0.08955977
X-RAY DIFFRACTIONf_plane_restr0.00816929
X-RAY DIFFRACTIONf_dihedral_angle_d15.035714583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.31963920.29427997X-RAY DIFFRACTION96.01
2.23-2.250.32854120.30737769X-RAY DIFFRACTION93.7
2.25-2.280.31624440.29288135X-RAY DIFFRACTION97.96
2.28-2.310.29054170.27348130X-RAY DIFFRACTION97.84
2.31-2.340.30494290.25418092X-RAY DIFFRACTION97.98
2.34-2.370.3024430.24528180X-RAY DIFFRACTION98.04
2.37-2.40.26743960.23678136X-RAY DIFFRACTION98.16
2.4-2.440.28244290.22928192X-RAY DIFFRACTION98.37
2.44-2.480.27023920.22928145X-RAY DIFFRACTION98.13
2.48-2.520.3024080.22338201X-RAY DIFFRACTION98.18
2.52-2.560.28234500.228137X-RAY DIFFRACTION98.24
2.56-2.610.27414300.21948183X-RAY DIFFRACTION98.32
2.61-2.660.2924180.22298179X-RAY DIFFRACTION98.13
2.66-2.710.25083970.20398003X-RAY DIFFRACTION96.12
2.71-2.770.26284090.18037992X-RAY DIFFRACTION95.86
2.77-2.840.23954460.18098224X-RAY DIFFRACTION98.77
2.84-2.910.25944350.17748223X-RAY DIFFRACTION99.01
2.91-2.990.24374110.17358215X-RAY DIFFRACTION99.01
2.99-3.070.22244580.16678228X-RAY DIFFRACTION98.79
3.07-3.170.22944390.16888185X-RAY DIFFRACTION98.61
3.17-3.290.21694350.16378221X-RAY DIFFRACTION98.76
3.29-3.420.22244050.15818245X-RAY DIFFRACTION98.73
3.42-3.570.20684280.15567907X-RAY DIFFRACTION94.61
3.57-3.760.195030.15028210X-RAY DIFFRACTION98.98
3.76-40.18494420.13978290X-RAY DIFFRACTION99.43
4-4.310.16074350.12838284X-RAY DIFFRACTION99.31
4.31-4.740.15684570.13068279X-RAY DIFFRACTION98.95
4.74-5.420.17534060.13918027X-RAY DIFFRACTION95.57
5.42-6.830.19244650.15958316X-RAY DIFFRACTION99.18
6.83-48.660.17924670.15488218X-RAY DIFFRACTION96.4

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