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

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Basic information

Entry
Database: PDB / ID: 8cff
TitleCrystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenite
Components(Arsenite oxidase subunit ...) x 2
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 / 2 iron, 2 sulfur cluster binding / metal ion binding / membrane
Similarity search - Function
Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain ...Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / 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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
ARSENITE / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / ISOPROPYL ALCOHOL / Chem-MGD / MOLYBDENUM ATOM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Arsenite oxidase subunit AioB / Arsenite oxidase subunit AioA
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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 3, 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 1.3Oct 23, 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: Arsenite oxidase subunit AioB
C: Arsenite oxidase subunit AioA
D: Arsenite oxidase subunit AioB
E: Arsenite oxidase subunit AioA
F: Arsenite oxidase subunit AioB
G: Arsenite oxidase subunit AioA
H: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)437,55274
Polymers425,7328
Non-polymers11,82066
Water66,3493683
1
A: Arsenite oxidase subunit AioA
B: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55420
Polymers106,4332
Non-polymers3,12118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-54 kcal/mol
Surface area31840 Å2
MethodPISA
2
C: Arsenite oxidase subunit AioA
D: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,37519
Polymers106,4332
Non-polymers2,94217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-70 kcal/mol
Surface area31960 Å2
MethodPISA
3
E: Arsenite oxidase subunit AioA
F: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,25117
Polymers106,4332
Non-polymers2,81815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-72 kcal/mol
Surface area31840 Å2
MethodPISA
4
G: Arsenite oxidase subunit AioA
H: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,37118
Polymers106,4332
Non-polymers2,93816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-70 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.306, 108.982, 116.892
Angle α, β, γ (deg.)97.50, 90.21, 96.06
Int Tables number1
Space group name H-MP1

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Components

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Arsenite oxidase subunit ... , 2 types, 8 molecules ACEGBDFH

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


Mass: 92129.836 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
Arsenite oxidase subunit AioB / AOII / Arsenite oxidase Rieske subunit


Mass: 14303.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: aioB, aoxA, asoB / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIF3, arsenate reductase (azurin)

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Non-polymers , 11 types, 3749 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-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-AST / ARSENITE


Mass: 122.920 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AsO3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3683 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10% v/v PEG 4000, 0.1 M sodium citrate pH 5.5 and 10% v/v isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.57→65.62 Å / Num. obs: 452928 / % possible obs: 74.5 % / Redundancy: 3.5 % / CC1/2: 0.989 / Net I/σ(I): 5.6
Reflection shellResolution: 1.57→1.69 Å / Num. unique obs: 22648 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→65.62 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.938 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20439 -5 %RANDOM
Rwork0.16792 ---
obs0.16974 22648 73.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.07 Å20.01 Å2
2---0.02 Å20.13 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.57→65.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29875 0 644 3683 34202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01331611
X-RAY DIFFRACTIONr_bond_other_d0.0020.01528997
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.66342934
X-RAY DIFFRACTIONr_angle_other_deg1.5061.58266774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64153903
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26722.3091685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.678155055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.42215206
X-RAY DIFFRACTIONr_chiral_restr0.0950.24036
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0236344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027484
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_it0.5090.94215468
X-RAY DIFFRACTIONr_mcbond_other0.5090.94215467
X-RAY DIFFRACTIONr_mcangle_it0.7861.4119380
X-RAY DIFFRACTIONr_mcangle_other0.7861.4119381
X-RAY DIFFRACTIONr_scbond_it0.861.04216143
X-RAY DIFFRACTIONr_scbond_other0.861.04216139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3291.51823507
X-RAY DIFFRACTIONr_long_range_B_refined2.88411.95637045
X-RAY DIFFRACTIONr_long_range_B_other2.79211.54636333
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.606 Å
RfactorNum. reflection% reflection
Rfree0.255 200 -
Rwork0.235 3844 -
obs--52.3 %
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)
10.39280.01510.06270.2608-0.02230.23290.01680.0401-0.0267-0.0211-0.008-0.00320.0270.0121-0.00880.0057-0.00060.00120.0179-0.01260.009210.7542-6.736-10.7814
20.29530.02940.00070.62210.27871.27180.0056-0.0702-0.01140.0714-0.01090.0120.0025-0.04890.00540.0111-0.00110.0040.0318-0.01370.02275.593616.446417.9743
30.39260.0191-0.07170.2563-0.01080.24010.02030.04580.0522-0.0176-0.00220.0067-0.0382-0.0123-0.0180.0101-0.00110.0060.01380.00170.009710.7069-51.9163-61.1876
40.15990.00450.01160.7732-0.43630.89850.0076-0.0639-0.03890.0562-0.015-0.02910.01090.02880.00740.00890.0001-0.0050.0466-0.00450.03315.7324-81.9026-39.6614
50.3875-0.01970.0670.2554-0.0120.2210.0144-0.0419-0.05060.0202-0.0010.00620.0407-0.0068-0.01330.0104-0.0047-0.00080.0144-0.00010.009843.8912-11.973627.1987
60.12830.0667-0.07440.8574-0.55151.01810.00480.05370.0294-0.0625-0.0321-0.035-0.01130.04220.02720.0132-0.00250.00880.0497-0.00430.032449.200917.99775.4645
70.4106-0.0017-0.07750.2733-0.0190.25010.0196-0.03970.03470.0218-0.0065-0.0029-0.03340.0154-0.01310.0078-0.00770.00550.0155-0.0120.009567.7774-57.1851-23.2685
80.34730.0764-0.02340.61450.24771.36730.02120.0756-0.0025-0.0823-0.01690.0187-0.0107-0.0483-0.00430.01980.0025-0.0030.037-0.01610.02162.5391-80.2451-52.2373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 825
2X-RAY DIFFRACTION2B0 - 133
3X-RAY DIFFRACTION3C4 - 825
4X-RAY DIFFRACTION4D0 - 133
5X-RAY DIFFRACTION5E4 - 825
6X-RAY DIFFRACTION6F0 - 133
7X-RAY DIFFRACTION7G4 - 825
8X-RAY DIFFRACTION8H0 - 133

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