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- PDB-3zyv: Crystal structure of the mouse liver Aldehyde Oxidase 3 (mAOX3) -

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Basic information

Entry
Database: PDB / ID: 3zyv
TitleCrystal structure of the mouse liver Aldehyde Oxidase 3 (mAOX3)
ComponentsAOX3
KeywordsOXIDOREDUCTASE / MOLYBDENUM COFACTOR
Function / homology
Function and homology information


aldehyde oxidase activity => GO:0004031 / : / : / xenobiotic metabolic process => GO:0006805 / Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding ...aldehyde oxidase activity => GO:0004031 / : / : / xenobiotic metabolic process => GO:0006805 / Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / xanthine catabolic process / xanthine dehydrogenase activity / molybdenum ion binding / molybdopterin cofactor binding / FAD binding / 2 iron, 2 sulfur cluster binding / NAD binding / flavin adenine dinucleotide binding / electron transfer activity / iron ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Aldehyde oxidase / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily ...Aldehyde oxidase / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / CO dehydrogenase flavoprotein, C-terminal domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / [2Fe-2S]-binding 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 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Aldehyde Oxidoreductase; domain 3 / 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. / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / FAD-binding, type PCMH-like superfamily / Enolase-like; domain 1 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / Aldehyde oxidase 3 / Aldehyde oxidase 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.545 Å
AuthorsTrincao, J. / Coelho, C. / Mahro, M. / Rodrigues, D. / Terao, M. / Garattini, E. / Leimkuehler, S. / Romao, M.J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The First Mammalian Aldehyde Oxidase Crystal Structure: Insights Into Substrate Specificity.
Authors: Coelho, C. / Mahro, M. / Trincao, J. / Carvalho, A.T.P. / Ramos, M.J. / Terao, M. / Garattini, E. / Leimkuhler, S. / Romao, M.J.
History
DepositionAug 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Apr 24, 2013Group: Structure summary
Revision 1.3Dec 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: AOX3
B: AOX3
C: AOX3
D: AOX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,23228
Polymers588,3654
Non-polymers6,86624
Water11,710650
1
A: AOX3
B: AOX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,61614
Polymers294,1832
Non-polymers3,43312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-125.7 kcal/mol
Surface area86650 Å2
MethodPISA
2
C: AOX3
D: AOX3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,61614
Polymers294,1832
Non-polymers3,43312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-126.2 kcal/mol
Surface area87160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.880, 135.270, 147.370
Angle α, β, γ (deg.)78.16, 77.72, 89.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:558)
211CHAIN B AND (RESSEQ 1:558)
311CHAIN C AND (RESSEQ 1:558)
411CHAIN D AND (RESSEQ 1:558)
112CHAIN A AND (RESSEQ 559:1334)
212CHAIN B AND (RESSEQ 559:1334)
312CHAIN C AND (RESSEQ 559:1334)
412CHAIN D AND (RESSEQ 559:1334)

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
AOX3 / ALDEHYDE OXIDASE / AOH1


Mass: 147091.359 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Organ: LIVER / Strain: CD1
References: UniProt: Q8VI15, UniProt: G3X982*PLUS, aldehyde oxidase

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Non-polymers , 6 types, 674 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#4: 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
#5: Chemical
ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO2S
#6: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.89 Å3/Da / Density % sol: 57.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.54→49.91 Å / Num. obs: 164929 / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.8 Å2
Reflection shellResolution: 2.54→2.57 Å

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BDJ

3bdj


Resolution: 2.545→49.906 Å / SU ML: 0.87 / σ(F): 1.99 / Phase error: 31.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 8336 5.1 %
Rwork0.2555 --
obs0.257 164929 75.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.667 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.9531 Å2-1.2428 Å22.4169 Å2
2---7.6341 Å21.6178 Å2
3---9.6575 Å2
Refinement stepCycle: LAST / Resolution: 2.545→49.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37305 0 360 650 38315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00838443
X-RAY DIFFRACTIONf_angle_d1.09352426
X-RAY DIFFRACTIONf_dihedral_angle_d16.64913683
X-RAY DIFFRACTIONf_chiral_restr0.0636060
X-RAY DIFFRACTIONf_plane_restr0.0046698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3599X-RAY DIFFRACTIONPOSITIONAL
12B3599X-RAY DIFFRACTIONPOSITIONAL0.029
13C3555X-RAY DIFFRACTIONPOSITIONAL0.027
14D3550X-RAY DIFFRACTIONPOSITIONAL0.027
21A5576X-RAY DIFFRACTIONPOSITIONAL
22B5576X-RAY DIFFRACTIONPOSITIONAL0.028
23C5493X-RAY DIFFRACTIONPOSITIONAL0.027
24D5521X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.545-2.57390.45241360.42032501X-RAY DIFFRACTION36
2.5739-2.60420.42111260.41522572X-RAY DIFFRACTION37
2.6042-2.6360.43221380.38312852X-RAY DIFFRACTION41
2.636-2.66930.42581660.36613116X-RAY DIFFRACTION44
2.6693-2.70440.44111790.35453368X-RAY DIFFRACTION49
2.7044-2.74150.39921980.35163537X-RAY DIFFRACTION51
2.7415-2.78070.36281820.31913743X-RAY DIFFRACTION54
2.7807-2.82220.37942270.31514037X-RAY DIFFRACTION58
2.8222-2.86620.38791960.31714242X-RAY DIFFRACTION61
2.8662-2.91320.37112580.29834446X-RAY DIFFRACTION64
2.9132-2.96350.3462700.2954662X-RAY DIFFRACTION67
2.9635-3.01730.32272560.29284952X-RAY DIFFRACTION70
3.0173-3.07540.32082730.29345085X-RAY DIFFRACTION74
3.0754-3.13810.29942700.28495421X-RAY DIFFRACTION77
3.1381-3.20640.30233200.27385460X-RAY DIFFRACTION80
3.2064-3.28090.33752930.27565774X-RAY DIFFRACTION83
3.2809-3.3630.31133130.26336043X-RAY DIFFRACTION86
3.363-3.45390.29583070.25986153X-RAY DIFFRACTION89
3.4539-3.55550.31093320.27016328X-RAY DIFFRACTION91
3.5555-3.67020.27713560.25036414X-RAY DIFFRACTION92
3.6702-3.80130.26913650.24216506X-RAY DIFFRACTION93
3.8013-3.95350.27423310.23676601X-RAY DIFFRACTION94
3.9535-4.13330.24313660.23536567X-RAY DIFFRACTION95
4.1333-4.35110.25873600.22836578X-RAY DIFFRACTION95
4.3511-4.62360.24843600.21686602X-RAY DIFFRACTION95
4.6236-4.98020.22773590.20656638X-RAY DIFFRACTION95
4.9802-5.48090.25043520.22136626X-RAY DIFFRACTION95
5.4809-6.27260.26983260.24186668X-RAY DIFFRACTION95
6.2726-7.89780.2443620.24466592X-RAY DIFFRACTION95
7.8978-49.9160.26073590.24896509X-RAY DIFFRACTION93
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)
11.08580.07820.20031.0219-0.06990.66010.0937-0.0565-0.15380.2971-0.08070.5302-0.0482-0.18930.0070.1967-0.06480.06220.1645-0.02720.3878-13.942711.3284-13.6669
20.98340.1480.08830.8221-0.27140.50660.0139-0.3966-0.00460.5831-0.01130.4736-0.0003-0.2082-0.05130.4464-0.14250.15370.32750.00940.4274-15.85961.55244.7372
30.1644-0.010.02220.43910.16090.35740.2146-0.1528-0.36350.3427-0.104-0.30560.3525-0.0084-0.02580.294-0.1497-0.11830.14740.11420.32816.9632-17.3826-8.6336
40.4852-0.00190.12130.81140.33210.2773-0.0131-0.3537-0.14430.98690.0338-0.08730.49720.1125-0.00940.2453-0.2024-0.35690.21230.06350.100617.4353-1.18984.489
50.78650.25220.23820.58260.2270.60090.00540.0339-0.0025-0.1633-0.0972-0.02770.013-0.0880.07950.22030.0259-0.02640.1164-0.05950.1288-3.0665-19.3525-62.5782
60.61760.0025-0.14560.5881-0.06720.7547-00.1573-0.03-0.29470.0155-0.2771-0.0893-0.0392-0.02580.0110.04250.12450.0394-0.02550.174620.7807-2.9067-63.5417
70.25780.19050.03590.25360.03830.28550.03970.15560.0024-0.1949-0.0573-0.21640.00340.1618-0.02390.09330.06610.24010.1813-0.07160.376829.4908-8.197-64.0182
81.3018-0.14090.10661.0398-0.24640.73540.10580.0239-0.2833-0.2749-0.00350.02190.1121-0.0976-0.05910.2590.0443-0.02080.13430.01560.3554-2.692579.5113-56.3865
90.90630.1102-0.14780.4320.02780.49430.05180.27910.113-0.4483-0.0531-0.1353-0.20760.1696-0.02980.54560.05770.07040.2770.08630.534510.650874.8547-74.1145
100.45750.0424-0.07970.6956-0.2071.54570.1050.0418-0.2776-0.3105-0.17610.1710.7740.2026-0.00090.39380.0813-0.0920.1459-0.00640.5307-7.686447.6032-54.7717
110.3590.15580.0830.9914-0.28530.96180.06580.2788-0.1059-0.79110.11250.39360.4008-0.1624-0.10580.5412-0.0028-0.29210.33110.01770.6565-25.102858.3653-74.0117
120.516-0.1402-0.30930.8232-0.03420.32010.16470.1880.0493-0.4532-0.05740.32430.1109-0.1729-0.07170.4748-0.0194-0.2720.3297-0.00170.6254-27.347868.939-69.7668
131.68330.1390.01381.14640.00820.8020.2193-0.24290.11580.2897-0.19970.3171-0.08060.07780.0180.2396-0.0767-0.00550.17410.06540.4044-14.289946.3406-15.4325
141.42490.2210.20441.3362-0.19030.93080.0308-0.15630.1810.5712-0.1630.1423-0.25860.26970.16150.4394-0.179-0.07670.47720.16170.4465.536153.403-6.7067
150.93370.2745-0.07410.8129-0.09250.65760.0318-0.6265-0.17140.6631-0.10470.1262-0.33040.18770.03690.8303-0.19550.06390.63880.1260.6042-12.301152.778114.8708
160.58350.15790.04820.6562-0.2190.52590.0967-0.27230.19860.334-0.07070.633-0.1553-0.031-0.08010.3822-0.08270.20640.2262-0.04150.8924-32.722274.1575-13.1862
170.53350.1651-0.14990.6152-0.1740.43990.0813-0.09750.02670.1554-0.03080.49690.0096-0.09460.06550.186-0.11570.18420.21960.05671.0275-42.254356.7831-18.0756
180.538-0.1557-0.05230.433-0.06350.80480.1016-0.27410.22420.4512-0.25080.3981-0.06560.07490.09430.5399-0.17860.25720.58780.13260.879-39.255959.73473.7946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 7:324)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 325:651)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 652:846)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 847:1334)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 7:382)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 383:1117)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 1118:1334)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 7:167)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 168:588)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 589:702)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 703:1036)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 1037:1334)
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 7:211)
14X-RAY DIFFRACTION14CHAIN D AND (RESSEQ 212:311)
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 312:578)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 579:967)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 968:1236)
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 1237:1334)

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