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- PDB-8rtl: Af Aio C65F-C80G -

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Basic information

Entry
Database: PDB / ID: 8rtl
TitleAf Aio C65F-C80G
Components(Arsenite oxidase subunit ...) x 5
KeywordsOXIDOREDUCTASE / arsenite oxidase / cysteine mutation
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 / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / OXYGEN ATOM / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / 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: 1.89 Å
AuthorsEngrola, F. / Romao, M.J. / Correia, M. / Santos-Silva, T.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: To Be Published
Title: Alcaligenes faecalis Aio B C65F-C80G bound to Sb oxyanion
Authors: Engrola, F. / Romao, M.J. / Correia, M. / Santos-Silva, T.
History
DepositionJan 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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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)438,05175
Polymers425,5948
Non-polymers12,45767
Water34,9671941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.164, 108.797, 117.109
Angle α, β, γ (deg.)97.58, 90.04, 96.18
Int Tables number1
Space group name H-MP1

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Components

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Arsenite oxidase subunit ... , 5 types, 8 molecules ACBDFHEG

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


Mass: 92032.719 Da / Num. of mol.: 2
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: 14301.143 Da / Num. of mol.: 1 / Mutation: C65F-C80G
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 AioB / AOII / Arsenite oxidase Rieske subunit


Mass: 14316.113 Da / Num. of mol.: 3 / Mutation: C65F-C80G
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)
#4: Protein Arsenite oxidase subunit AioA / AOI / Arsenite oxidase Mo-pterin subunit


Mass: 92174.875 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)
#5: Protein Arsenite oxidase subunit AioA / AOI / Arsenite oxidase Mo-pterin subunit


Mass: 92103.797 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 , 14 types, 2008 molecules

#6: 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
#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-F3S / FE3-S4 CLUSTER


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


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#12: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#14: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#16: 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
#17: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#18: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#19: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1941 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97372 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97372 Å / Relative weight: 1
ReflectionResolution: 1.89→116.07 Å / Num. obs: 326409 / % possible obs: 92.9 % / Redundancy: 3.2 % / CC1/2: 0.989 / Net I/σ(I): 6.1
Reflection shellResolution: 1.89→1.92 Å / Num. unique obs: 8617 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→116.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.005 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23514 16419 5 %RANDOM
Rwork0.19994 ---
obs0.20172 309935 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.088 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20.04 Å2-0.65 Å2
2--2.26 Å20.3 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.89→116.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29902 0 703 1941 32546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01231472
X-RAY DIFFRACTIONr_bond_other_d0.0030.01628879
X-RAY DIFFRACTIONr_angle_refined_deg2.121.82742689
X-RAY DIFFRACTIONr_angle_other_deg0.8461.76266514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76453853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6155224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.779104994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.24489
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0237681
X-RAY DIFFRACTIONr_gen_planes_other0.0030.027459
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_it1.7611.42615394
X-RAY DIFFRACTIONr_mcbond_other1.7611.42615394
X-RAY DIFFRACTIONr_mcangle_it2.4732.55719253
X-RAY DIFFRACTIONr_mcangle_other2.4732.55719254
X-RAY DIFFRACTIONr_scbond_it2.5321.66916078
X-RAY DIFFRACTIONr_scbond_other2.5321.66916079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6992.9423405
X-RAY DIFFRACTIONr_long_range_B_refined5.25916.8435936
X-RAY DIFFRACTIONr_long_range_B_other5.2316.3335674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 829 -
Rwork0.325 15714 -
obs--63.66 %
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)
10.6455-0.0427-0.15610.36130.00660.36950.0592-0.09290.11080.0202-0.0093-0.0136-0.06680.04-0.050.0297-0.03230.01350.1488-0.0950.0781-89.615754.8602-37.4246
20.4920.08030.02010.92990.36642.19050.03340.1323-0.0119-0.1037-0.03510.0212-0.0018-0.03330.00170.033-0.0103-0.01820.1827-0.05920.069-94.906331.9537-66.3158
30.64090.0705-0.09750.35080.03880.35850.04430.07220.1349-0.0133-0.00260.0157-0.0626-0.0265-0.04180.0213-0.01180.01010.1473-0.04660.0796-56.493760.0629-75.3462
40.30.02480.0261.3211-0.68051.703-0.0072-0.1404-0.06290.062-0.0366-0.04210.02020.06260.04370.01610.0032-0.01450.2232-0.05420.0851-51.364130.1592-53.8809
50.6308-0.07180.06170.36250.03580.35460.025-0.0662-0.11170.02030.00060.01260.0654-0.0244-0.02560.0297-0.0225-0.01780.1418-0.04960.0721-101.64637.604-102.7923
60.6625-0.05010.07641.4628-0.6751.5545-0.0140.13250.0734-0.0758-0.0158-0.0667-0.03310.05140.02970.0152-0.0203-0.00290.1963-0.05690.0654-96.322237.4328-124.606
70.57230.01680.09880.3686-0.00850.33280.02570.093-0.0683-0.0293-0.0147-0.00680.04770.0126-0.01110.0194-0.0087-0.00420.153-0.08830.0619-44.7217-2.7054-24.7981
80.4785-0.1226-0.0961.15220.54251.79030.0076-0.05560.06620.1314-0.01920.03950.0202-0.06340.01160.0213-0.0085-0.00360.1799-0.06040.0682-49.891120.33943.9989
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 825
2X-RAY DIFFRACTION2B0 - 133
3X-RAY DIFFRACTION3C4 - 825
4X-RAY DIFFRACTION4D-1 - 133
5X-RAY DIFFRACTION5E2 - 825
6X-RAY DIFFRACTION6F-1 - 133
7X-RAY DIFFRACTION7G3 - 825
8X-RAY DIFFRACTION8H-1 - 133

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