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- PDB-8ch9: Crystal structure of arsenite oxidase from Alcaligenes faecalis (... -

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Basic information

Entry
Database: PDB / ID: 8ch9
TitleCrystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenic oxyanion
Components(Arsenite oxidase subunit ...) x 3
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
MOLYBDENUM(IV) ION / ARSENATE / FE3-S4 CLUSTER / HEXACYANOFERRATE(3-) / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / DI(HYDROXYETHYL)ETHER / Arsenite oxidase subunit AioB / Arsenite oxidase subunit AioA
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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: To Be Published
Title: Crystal structure of arsenite oxidase from Alcaligenes faecalis (Af Aio) bound to arsenic oxyanion
Authors: Engrola, F. / Correia, M.A.S. / Romao, M.J. / Santos-Silva, T.
History
DepositionFeb 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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)437,46962
Polymers425,7188
Non-polymers11,75054
Water68,5473805
1
A: Arsenite oxidase subunit AioA
B: Arsenite oxidase subunit AioB
G: Arsenite oxidase subunit AioA
H: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,74231
Polymers212,8524
Non-polymers5,89027
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25180 Å2
ΔGint-160 kcal/mol
Surface area56750 Å2
MethodPISA
2
C: Arsenite oxidase subunit AioA
D: Arsenite oxidase subunit AioB
E: Arsenite oxidase subunit AioA
F: Arsenite oxidase subunit AioB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,72631
Polymers212,8664
Non-polymers5,86027
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25310 Å2
ΔGint-162 kcal/mol
Surface area56820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.288, 109.950, 117.424
Angle α, β, γ (deg.)98.33, 89.97, 96.58
Int Tables number1
Space group name H-MP1

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Components

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Arsenite oxidase subunit ... , 3 types, 8 molecules ACEBDFHG

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


Mass: 92129.836 Da / Num. of mol.: 3
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)
#3: Protein Arsenite oxidase subunit AioA / AOI / Arsenite oxidase Mo-pterin subunit


Mass: 92115.805 Da / Num. of mol.: 1
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)

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Non-polymers , 10 types, 3859 molecules

#4: 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
#5: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#6: Chemical
ChemComp-FC6 / HEXACYANOFERRATE(3-) / FERRI(III)HEXACYANIDE


Mass: 211.949 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6FeN6
#7: 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
#8: Chemical
ChemComp-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AsO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3805 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 10% v/v PEG 6000, 0.01 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.43→65.474 Å / Num. obs: 594307 / % possible obs: 75 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 1.43→1.56 Å / Num. unique obs: 29716 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→65.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.391 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19459 29766 5 %RANDOM
Rwork0.16672 ---
obs0.16811 564518 73.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.157 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.43→65.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29850 0 636 3805 34291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01232106
X-RAY DIFFRACTIONr_bond_other_d0.0010.01629338
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.82943776
X-RAY DIFFRACTIONr_angle_other_deg0.7291.76467550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1354024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.0665234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.498105141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1220.24612
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0238955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027649
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_it1.6861.37315784
X-RAY DIFFRACTIONr_mcbond_other1.6861.37315784
X-RAY DIFFRACTIONr_mcangle_it2.2152.46319885
X-RAY DIFFRACTIONr_mcangle_other2.2152.46319886
X-RAY DIFFRACTIONr_scbond_it3.0041.6316322
X-RAY DIFFRACTIONr_scbond_other3.0041.6316323
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3252.85623851
X-RAY DIFFRACTIONr_long_range_B_refined5.22516.6337304
X-RAY DIFFRACTIONr_long_range_B_other5.06814.9736411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.434→1.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 230 -
Rwork0.267 4605 -
obs--8.02 %

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