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- PDB-5nqd: Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A -

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Basic information

Entry
Database: PDB / ID: 5nqd
TitleArsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A
Components
  • AroA
  • Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
KeywordsOXIDOREDUCTASE / Arsenite oxidase / DMSOR family / Rieske protein
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 / oxidoreductase activity / metal ion binding / membrane
Similarity search - Function
Phosphorylase Kinase; domain 1 - #200 / 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 / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain ...Phosphorylase Kinase; domain 1 - #200 / 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 / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / 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 / Phosphorylase Kinase; domain 1 / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / OXYGEN ATOM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster / AroA
Similarity search - Component
Biological speciesRhizobium sp. NT-26 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSantos-Silva, T. / Romao, M. / Vieira, M. / Marques, A.T.
Funding support Portugal, 4items
OrganizationGrant numberCountry
FCTPTDC/BBB-BEP/1185/2014 Portugal
FCTUID/Multi/04378/2013 Portugal
FCTPTDC/QEQ-MED/1902/2014 Portugal
PT2020POCI-01-0145-FEDER-007728 Portugal
CitationJournal: To Be Published
Title: Arsenite oxidase AioAB from Rhizobium sp. str. NT-26 mutant AioBF108A
Authors: Santos-Silva, T. / Romao, M. / Vieira, M. / Marques, A.T.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / pdbx_struct_conn_angle / reflns / struct_ref / struct_ref_seq
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 / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_nonpoly.name / _reflns.pdbx_Rpim_I_all / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AroA
B: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
C: AroA
D: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
E: AroA
F: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
G: AroA
H: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,74756
Polymers428,7798
Non-polymers10,96748
Water26,4461468
1
A: AroA
B: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
E: AroA
F: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,49226
Polymers214,3904
Non-polymers5,10222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24360 Å2
ΔGint-253 kcal/mol
Surface area56630 Å2
MethodPISA
2
C: AroA
D: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
G: AroA
H: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,25530
Polymers214,3904
Non-polymers5,86526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26360 Å2
ΔGint-259 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.408, 148.665, 232.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-2250-

HOH

21G-2444-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
AroA / Arsenite oxidase large subunit AioA [3Fe-4S] cluster / Mo-molybdopterin cofactor-binding active site


Mass: 93179.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aroA, aioA, NT26_p10030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VAL8, arsenate reductase (azurin)
#2: Protein
Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster


Mass: 14015.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. NT-26 (bacteria) / Gene: aioB, NT26_p10029 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NMC5, arsenate reductase (azurin)

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Non-polymers , 12 types, 1516 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
#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
#6: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / 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-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#13: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1468 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Hepes sodium pH 7-8, 2 % PEG 400, 2 M ammonium sulphate.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.55 Å / Num. obs: 247069 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 13.8 % / CC1/2: 0.988 / Rpim(I) all: 0.098 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 12160 / CC1/2: 0.59 / Rpim(I) all: 0.524 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4aay

4aay


Resolution: 2.2→49.55 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.261 / SU ML: 0.149 / SU R Cruickshank DPI: 0.2125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.18
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2167 12218 4.9 %RANDOM
Rwork0.1723 ---
obs0.1745 234764 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 26.045 Å2 / Biso min: 7.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.2→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30136 0 591 1468 32195
Biso mean--27.4 25.37 -
Num. residues----3900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01931423
X-RAY DIFFRACTIONr_bond_other_d0.0020.0228821
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.96242656
X-RAY DIFFRACTIONr_angle_other_deg1.046366237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08853892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.924.3981528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.893154928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.48415208
X-RAY DIFFRACTIONr_chiral_restr0.1020.24493
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02136320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027424
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 851 -
Rwork0.272 17311 -
all-18162 -
obs--99.99 %

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