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- PDB-6q6q: Human aldehyde oxidase SNP G1269R -

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Basic information

Entry
Database: PDB / ID: 6q6q
TitleHuman aldehyde oxidase SNP G1269R
ComponentsAldehyde oxidase
KeywordsOXIDOREDUCTASE / Single-nucleotide Polymorphism / Moco-free form
Function / homology
Function and homology information


Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / intercellular bridge / FAD binding / xenobiotic metabolic process / lipid metabolic process / 2 iron, 2 sulfur cluster binding ...Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor / aldehyde oxidase / aldehyde oxidase activity / Vitamin B6 activation to pyridoxal phosphate / molybdopterin cofactor binding / intercellular bridge / FAD binding / xenobiotic metabolic process / lipid metabolic process / 2 iron, 2 sulfur cluster binding / NAD binding / flavin adenine dinucleotide binding / microtubule cytoskeleton / nuclear body / iron ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Aldehyde oxidase / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin 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 / 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 / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-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 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / 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 / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / MALONATE ION / Aldehyde oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.10003770671 Å
AuthorsMota, C. / Coelho, C. / Santos-Silva, T. / Romao, M.J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
PTDC/BBB-BEP/1185/2014 Portugal
Citation
Journal: Febs Open Bio / Year: 2019
Title: Human aldehyde oxidase (hAOX1): structure determination of the Moco-free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms.
Authors: Mota, C. / Esmaeeli, M. / Coelho, C. / Santos-Silva, T. / Wolff, M. / Foti, A. / Leimkuhler, S. / Romao, M.J.
#1: Journal: Febs Open Bio / Year: 2019
Title: Human aldehyde oxidase (hAOX1): structure determination of the Moco‐free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms
Authors: Mota, C. / Esmaeeli, M. / Coelho, C. / Santos-Silva, T. / Wolff, M. / Foti, A. / Leimkuhler, S. / Romao, M.J.
#2: Journal: Nat. Chem. Biol. / Year: 2015
Title: Structural insights into xenobiotic and inhibitor binding to human aldehyde oxidase
Authors: Coelho, C. / Foti, A. / Hartmann, T. / Santos-Silva, T. / Leimkuhler, S. / Romao, M.J.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7428
Polymers148,1971
Non-polymers1,5457
Water28816
1
A: Aldehyde oxidase
hetero molecules

A: Aldehyde oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,48416
Polymers296,3932
Non-polymers3,09114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area11540 Å2
ΔGint-71 kcal/mol
Surface area90890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.197, 148.197, 132.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Aldehyde oxidase / Aldehyde oxidase 1 / Azaheterocycle hydroxylase


Mass: 148196.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOX1, AO / Production host: Escherichia coli (E. coli)
References: UniProt: Q06278, aldehyde oxidase, Oxidoreductases; Acting on CH or CH2 groups; With oxygen as acceptor
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG3350, Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.1→49.4 Å / Num. obs: 50950 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 84.2337235282 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.04 / Rrim(I) all: 0.117 / Rsym value: 0.11 / Net I/σ(I): 15.6
Reflection shellResolution: 3.1→3.29 Å / Rmerge(I) obs: 0.921 / Rpim(I) all: 0.331 / Rrim(I) all: 0.981 / Rsym value: 0.921

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UHX

4uhx


Resolution: 3.10003770671→46.8640062404 Å / SU ML: 0.384293005148 / Cross valid method: FREE R-VALUE / σ(F): 0.204487145437 / Phase error: 23.729061676
RfactorNum. reflection% reflection
Rfree0.235662739667 2433 4.77526987242 %
Rwork0.191587822435 --
obs0.19367591884 50950 99.8295354351 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.6965461748 Å2
Refinement stepCycle: LAST / Resolution: 3.10003770671→46.8640062404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10034 0 89 16 10139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073825180205110345
X-RAY DIFFRACTIONf_angle_d0.49598093865913976
X-RAY DIFFRACTIONf_chiral_restr0.04202333537461556
X-RAY DIFFRACTIONf_plane_restr0.003072455942871794
X-RAY DIFFRACTIONf_dihedral_angle_d4.840187910546246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.16330.4004213825491420.3352464260872849X-RAY DIFFRACTION100
3.1633-3.23210.2901437921381460.2935081834522857X-RAY DIFFRACTION100
3.2321-3.30720.3286479378371440.2724831793382888X-RAY DIFFRACTION100
3.3072-3.38990.3096494966541540.2570522688872827X-RAY DIFFRACTION100
3.3899-3.48150.3044972704061530.2479548926492854X-RAY DIFFRACTION100
3.4815-3.5840.2283116346781590.2330871574772823X-RAY DIFFRACTION99.9664767013
3.584-3.69960.2580389087441290.221765328472894X-RAY DIFFRACTION100
3.6996-3.83180.2915856175111190.2019726999792856X-RAY DIFFRACTION99.8657267539
3.8318-3.98510.2481708364031550.1998667240982854X-RAY DIFFRACTION100
3.9851-4.16640.2240796694581640.1974306333342828X-RAY DIFFRACTION99.9331997328
4.1664-4.38590.2604139280931340.1871974374692868X-RAY DIFFRACTION100
4.3859-4.66040.2096226566081510.172281132572861X-RAY DIFFRACTION99.9668104879
4.6604-5.01990.2020471349041540.1601951576852826X-RAY DIFFRACTION99.765651155
5.0199-5.52430.1828665832041300.1670909180652887X-RAY DIFFRACTION99.7025776603
5.5243-6.32210.2181071962741410.1863447077732853X-RAY DIFFRACTION99.7667444185
6.3221-7.95880.2312084334261060.1779565334462867X-RAY DIFFRACTION99.3981945838
7.9588-46.86930.2026925386951520.1427887750712825X-RAY DIFFRACTION98.7723954877

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