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- PDB-8cgs: Crystal structure of arsenite oxidase from Alcaligenes faecalis (... -

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Basic information

Entry
Database: PDB / ID: 8cgs
TitleCrystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to antimony oxyanion
Components
  • AioB
  • Arsenite oxidase subunit AioA
KeywordsOXIDOREDUCTASE / arsenite oxidase / molybdenum cofactor / MGD / arsenic oxyanion / antimony oxyanion
Function / homology
Function and homology information


arsenate reductase (azurin) / arsenate reductase (azurin) activity / oxidoreductase complex / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / metal ion binding / membrane
Similarity search - Function
Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster / Rieske 3Fe-4S / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / ACETATE ION / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / OXYGEN ATOM / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / tetrakis(oxidanyl)antimony / Arsenite oxidase subunit AioA
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsEngrola, F. / Correia, M.A.S. / Romao, M.J. / Santos-Silva, T.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Arsenite oxidase in complex with antimonite and arsenite oxyanions: Insights into the catalytic mechanism.
Authors: Engrola, F. / Correia, M.A.S. / Watson, C. / Romao, C.C. / Veiros, L.F. / Romao, M.J. / Santos-Silva, T. / Santini, J.M.
History
DepositionFeb 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arsenite oxidase subunit AioA
B: AioB
C: Arsenite oxidase subunit AioA
D: AioB
E: Arsenite oxidase subunit AioA
F: AioB
G: Arsenite oxidase subunit AioA
H: AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)436,50768
Polymers424,8918
Non-polymers11,61660
Water59,8463322
1
A: Arsenite oxidase subunit AioA
B: AioB
C: Arsenite oxidase subunit AioA
D: AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,40935
Polymers212,4464
Non-polymers5,96331
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25710 Å2
ΔGint-204 kcal/mol
Surface area55980 Å2
MethodPISA
2
E: Arsenite oxidase subunit AioA
F: AioB
hetero molecules

G: Arsenite oxidase subunit AioA
H: AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,09833
Polymers212,4464
Non-polymers5,65229
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_654x+1,y,z-11
Buried area25010 Å2
ΔGint-234 kcal/mol
Surface area55940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.378, 109.210, 117.342
Angle α, β, γ (deg.)97.71, 90.06, 96.28
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Arsenite oxidase subunit AioA / AOI / Arsenite oxidase Mo-pterin subunit


Mass: 92032.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aioA, aoxB, asoA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF4, arsenate reductase (azurin)
#2: Protein
AioB


Mass: 14190.044 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Production host: Escherichia coli (E. coli)

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Non-polymers , 16 types, 3382 molecules

#3: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#5: Chemical
ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#10: Chemical
ChemComp-UJI / tetrakis(oxidanyl)antimony / antimony oxyanion


Mass: 189.789 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4O4Sb / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#12: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#13: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#14: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#16: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#17: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15% v/v PEG 4000, 0.1 M sodium citrate pH 5.5 and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.84→48.47 Å / Num. obs: 365490 / % possible obs: 95.3 % / Redundancy: 2 % / CC1/2: 0.993 / Net I/σ(I): 4.2
Reflection shellResolution: 1.84→1.87 Å / Num. unique obs: 17998 / CC1/2: 0.848

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→116.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.471 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18891 18174 5 %RANDOM
Rwork0.15362 ---
obs0.15536 347274 95.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20.42 Å20.04 Å2
2--1.49 Å2-0.47 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.84→116.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29836 0 603 3322 33761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01931340
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228836
X-RAY DIFFRACTIONr_angle_refined_deg1.9541.96342609
X-RAY DIFFRACTIONr_angle_other_deg1.043366336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82953864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70524.1111474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.217155018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.57515206
X-RAY DIFFRACTIONr_chiral_restr0.1090.24482
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02135937
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027465
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3571.82615334
X-RAY DIFFRACTIONr_mcbond_other1.3571.82615331
X-RAY DIFFRACTIONr_mcangle_it1.9162.72919159
X-RAY DIFFRACTIONr_mcangle_other1.9162.72919160
X-RAY DIFFRACTIONr_scbond_it2.3582.06116006
X-RAY DIFFRACTIONr_scbond_other2.3542.0616002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5632.99123388
X-RAY DIFFRACTIONr_long_range_B_refined5.48316.09739343
X-RAY DIFFRACTIONr_long_range_B_other5.48316.09739344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 1391 -
Rwork0.252 25571 -
obs--94.8 %

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