PDB-8r3a: NT-26 Arsenite oxidase B F108C-G123C

ID or keywords:

Entry

Database: PDB / ID: 8r3a

Title

NT-26 Arsenite oxidase B F108C-G123C

Components

AroA
Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

Keywords

OXIDOREDUCTASE / arsenite oxidase / Rieske [2Fe-2S] centre

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

Biological species

Pseudorhizobium banfieldiae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.894 Å

Authors

Engrola, F. / Santos-Silva, T. / Correia, M.A.S. / Romao, M.J.

Funding support

Portugal, 1items

Citation

Journal: To Be Published
Title: NT-26 Arsenite oxidase B F108C-G123C
Authors: Engrola, F. / Santos-Silva, T.

History

Deposition	Nov 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8r3a.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8r3a.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	8r3a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8r3a_validation.pdf.gz	10.6 MB	Display	wwPDB validaton report
Full document	8r3a_full_validation.pdf.gz	10.6 MB	Display
Data in XML	8r3a_validation.xml.gz	194.7 KB	Display
Data in CIF	8r3a_validation.cif.gz	261.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/8r3a ftp://data.pdbj.org/pub/pdb/validation_reports/r3/8r3a	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#144 - Dec 2011 Complex I similarity (6) #137 - May 2011 Cytochrome bc1 similarity (5) #111 - Mar 2009 Hydrogenase similarity (5) #36 - Dec 2002 Cytochrome c similarity (5) #80 - Aug 2006 AAA+ Proteases similarity (1) #220 - Apr 2018 Dehalogenases similarity (2) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (2) #117 - Sep 2009 Xanthine Oxidoreductase similarity (1) #167 - Nov 2013 SNARE Proteins similarity (1) #82 - Oct 2006 Cytochrome p450 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#144 - Dec 2011
Complex I
similarity (6)
#137 - May 2011
Cytochrome bc1
similarity (5)
#111 - Mar 2009
Hydrogenase
similarity (5)
#36 - Dec 2002
Cytochrome c
similarity (5)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#220 - Apr 2018
Dehalogenases
similarity (2)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (2)
#117 - Sep 2009
Xanthine Oxidoreductase
similarity (1)
#167 - Nov 2013
SNARE Proteins
similarity (1)
#82 - Oct 2006
Cytochrome p450
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (2)

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

460 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AroA

B: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

hetero molecules

defined by software
Evidence: gel filtration
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: AroA

D: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

hetero molecules

defined by software
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: AroA

F: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

hetero molecules

defined by software
116 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: AroA

H: Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster

hetero molecules

defined by software
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.607, 148.928, 231.901
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	18
Space group name H-M	P22₁2₁

Components on special symmetry positions

ID	Model	Components
1	1	C-1097- HOH
2	1	G-1355- HOH
3	1	G-1545- HOH
4	1	G-1565- HOH
5	1	G-1592- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
2	1	1	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
3	2	2	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
4	2	2	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
5	3	3	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
6	3	3	ALA	ALA	TYR	TYR	A	2 - 842	2 - 842
7	4	4	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
8	4	4	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
9	5	5	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
10	5	5	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
11	6	6	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
12	6	6	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
13	7	7	ALA	ALA	SER	SER	A - I	2 - 901	2
14	7	7	ALA	ALA	SER	SER	A - I	2 - 901	2
15	8	8	ALA	ALA	SER	SER	A - I	2 - 901	2
16	8	8	ALA	ALA	SER	SER	A - I	2 - 901	2
17	9	9	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
18	9	9	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
19	10	10	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
20	10	10	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
21	11	11	ALA	ALA	SER	SER	A - I	2 - 901	2
22	11	11	ALA	ALA	SER	SER	A - I	2 - 901	2
23	12	12	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175
24	12	12	GLN	GLN	GLY	GLY	A	43 - 175	43 - 175

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein	AroA Mass: 93381.633 Da / Num. of mol.: 4 / Mutation: F108C-G123C 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	Arsenite oxidase small subunit AioB Rieske [2Fe-2S] cluster Mass: 18340.561 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aioB / Production host: Escherichia coli (E. coli) / References: UniProt: L0NMC5

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Non-polymers , 13 types, 2641 molecules

#3: Chemical	ChemComp-SER / SERINE Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₇NO₃
#4: 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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: 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
#9: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#10: 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
#11: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#12: Chemical	ChemComp-O / OXYGEN ATOM Mass: 15.999 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#13: 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
#14: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#15: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2569 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.74 Å³/Da / Density % sol: 55.04 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 2M ammonium sulphate, 0.1 M Hepes pH 7.5 and 2% (v/v) polyethylene glycol (PEG) 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 1.89→49.32 Å / Num. obs: 384388 / % possible obs: 99.4 % / Redundancy: 2 % / CC_1/2: 0.998 / Net I/σ(I): 13.98
Reflection shell	Resolution: 1.89→2.01 Å / Num. unique obs: 60388 / CC_1/2: 0.636

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.894→49.32 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.092 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1854	16000	5.004 %
R_work	0.1523	365109	-
all	0.154	-	-
obs	-	300000	99.431 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 28.817 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.007 Å²	-0 Å²	-0 Å²
2-	-	0.002 Å²	-0 Å²
3-	-	-	0.005 Å²

Refinement step

Cycle: LAST / Resolution: 1.894→49.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30162	0	767	2569	33498

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	32162
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	29471
X-RAY DIFFRACTION	r_angle_refined_deg	2.046	1.824	43641
X-RAY DIFFRACTION	r_angle_other_deg	0.698	1.761	67836
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.968	5	4016
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.967	5	244
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.163	5	16
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.512	10	5071
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.425	10	1546
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	4577
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	39029
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7571
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	6424
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.197	0.2	28738
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	15844
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	16984
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	2247
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.047	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.099	0.2	19
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.231	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.186	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.13	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	3.144	2.627	15911
X-RAY DIFFRACTION	r_mcbond_other	3.144	2.627	15911
X-RAY DIFFRACTION	r_mcangle_it	3.739	4.702	19978
X-RAY DIFFRACTION	r_mcangle_other	3.74	4.702	19979
X-RAY DIFFRACTION	r_scbond_it	4.941	3.015	16251
X-RAY DIFFRACTION	r_scbond_other	4.941	3.016	16252
X-RAY DIFFRACTION	r_scangle_it	6.785	5.318	23631
X-RAY DIFFRACTION	r_scangle_other	6.785	5.318	23632
X-RAY DIFFRACTION	r_lrange_it	7.305	24.828	36606
X-RAY DIFFRACTION	r_lrange_other	7.258	24.555	36050
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	29029
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.064	0.05	29055
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.064	0.05	29026
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.032	0.05	4108
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.048	0.05	4068
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.033	0.05	4108
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.055	0.05	29217
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.058	0.05	29105
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.047	0.05	4023
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.031	0.05	4061
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.057	0.05	28965
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.049	0.05	4019

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.0664	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0664	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06394	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06394	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06384	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06384	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0324	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0324	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0484	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0484	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.03326	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.03326	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.05467	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.05467	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.05796	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.05796	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.04674	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.04674	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.03078	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.03078	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.05675	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.05675	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.04858	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.04858	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.894-1.943	0.371	1372	0.357	20000	X-RAY DIFFRACTION	94.3623
1.943-1.996	0.307	1401	0.298	20000	X-RAY DIFFRACTION	99.8915
1.996-2.054	0.286	1275	0.263	25510	X-RAY DIFFRACTION	99.7542
2.054-2.117	0.247	1279	0.214	20000	X-RAY DIFFRACTION	99.9464
2.117-2.187	0.223	1308	0.183	20000	X-RAY DIFFRACTION	99.9448
2.187-2.263	0.203	1157	0.168	23345	X-RAY DIFFRACTION	99.947
2.263-2.348	0.197	1197	0.154	20000	X-RAY DIFFRACTION	99.9493
2.348-2.444	0.185	1210	0.146	20000	X-RAY DIFFRACTION	99.93
2.444-2.552	0.18	1074	0.138	20000	X-RAY DIFFRACTION	99.7435
2.552-2.677	0.181	1078	0.136	19817	X-RAY DIFFRACTION	99.6709
2.677-2.821	0.184	1024	0.138	18911	X-RAY DIFFRACTION	99.99
2.821-2.991	0.179	916	0.138	17993	X-RAY DIFFRACTION	99.9841
2.991-3.197	0.184	869	0.143	16895	X-RAY DIFFRACTION	99.9437
3.197-3.452	0.172	910	0.137	15671	X-RAY DIFFRACTION	99.8855
3.452-3.78	0.157	764	0.126	14464	X-RAY DIFFRACTION	99.4189
3.78-4.223	0.143	693	0.11	13134	X-RAY DIFFRACTION	99.7259
4.223-4.87	0.124	550	0.107	11771	X-RAY DIFFRACTION	99.9432
4.87-5.95	0.167	579	0.136	9921	X-RAY DIFFRACTION	99.9714
5.95-8.354	0.154	351	0.14	7801	X-RAY DIFFRACTION	98.8361
8.354-49.32	0.182	224	0.165	4609	X-RAY DIFFRACTION	99.7935

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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Non-polymers , 13 types, 2641 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Open data

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Protein , 2 types, 8 molecules ACEGBDFH

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Non-polymers , 13 types, 2641 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi