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- PDB-8ccq: Crystal structure of arsenite oxidase from Pseudorhizobium banfie... -

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Basic information

Entry
Database: PDB / ID: 8ccq
TitleCrystal structure of arsenite oxidase from Pseudorhizobium banfieldiae str. NT-26 (NT-26 Aio) bound to antimony trioxide
Components
  • AroA
  • AroB
KeywordsOXIDOREDUCTASE / arsenite oxidase / molybdenum cofactor / MGD / arsenic oxyanion / antimony oxyanion
Function / homology
Function and homology information


arsenate reductase (azurin) / 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 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily ...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 / 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 / TRIETHYLENE GLYCOL / TRIHYDROXYANTIMONITE(III) / AroA / AroB
Similarity search - Component
Biological speciesPseudorhizobium banfieldiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsEngrola, F. / Santos-Silva, T. / Romao, M.J. / Correia, M.A.S.
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
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
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 / _pdbx_validate_planes.type
Revision 1.2Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Sep 6, 2023Group: Atomic model / Data collection / Category: atom_site / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AroA
B: AroB
C: AroA
D: AroB
E: AroA
F: AroB
G: AroA
H: AroB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,31862
Polymers447,0058
Non-polymers12,31354
Water64,2603567
1
A: AroA
B: AroB
E: AroA
F: AroB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,57331
Polymers223,5024
Non-polymers6,07027
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26580 Å2
ΔGint-263 kcal/mol
Surface area55560 Å2
2
C: AroA
D: AroB
G: AroA
H: AroB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,74531
Polymers223,5024
Non-polymers6,24327
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26950 Å2
ΔGint-251 kcal/mol
Surface area55410 Å2
Unit cell
Length a, b, c (Å)141.533, 148.395, 232.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11G-2802-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
AroA


Mass: 93381.633 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aroA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VAL8
#2: Protein
AroB


Mass: 18369.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aroB / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VAL9

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Non-polymers , 11 types, 3621 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.: 8 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-SBO / TRIHYDROXYANTIMONITE(III)


Mass: 172.782 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H3O3Sb / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#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.: 3567 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2 M ammonium sulphate, 0.1 M HEPES sodium salt pH 7.5 and 2% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.89→49.3 Å / Num. obs: 354714 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.997 / Net I/σ(I): 13.1
Reflection shellResolution: 1.89→1.98 Å / Num. unique obs: 17429 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→141.53 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.863 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20039 19519 5 %RANDOM
Rwork0.15487 ---
obs0.15715 368315 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.108 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.89→141.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30164 0 653 3567 34384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01931600
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228996
X-RAY DIFFRACTIONr_angle_refined_deg2.091.96342892
X-RAY DIFFRACTIONr_angle_other_deg1.083366656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96253916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63824.3781544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11154957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.66315212
X-RAY DIFFRACTIONr_chiral_restr0.1210.24508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02136510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027482
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_it2.1542.65715615
X-RAY DIFFRACTIONr_mcbond_other2.1532.65715614
X-RAY DIFFRACTIONr_mcangle_it2.8963.97619512
X-RAY DIFFRACTIONr_mcangle_other2.8973.97619513
X-RAY DIFFRACTIONr_scbond_it3.5242.98515984
X-RAY DIFFRACTIONr_scbond_other3.5242.98515984
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3044.33923337
X-RAY DIFFRACTIONr_long_range_B_refined7.27722.9639917
X-RAY DIFFRACTIONr_long_range_B_other7.02122.24938115
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
Rfree0.341 1451 -
Rwork0.338 26912 -
obs--99.35 %

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