PDB-8avl: Superoxide dismutase SodFM2 from Bacteroides fragilis

ID or keywords:

Entry

Database: PDB / ID: 8avl

Title

Superoxide dismutase SodFM2 from Bacteroides fragilis

Components

Superoxide dismutase [Fe]

Keywords

OXIDOREDUCTASE / Superoxide dismutase (SOD). Oxidoreductase. Iron. Bacterial. Metalloenzyme.

Function / homology

Function and homology information

superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function

Biological species

Bacteroides fragilis YCH46 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Basle, A. / Barwinska-Sendra, A. / Sendra, K.M. / Waldron, K.

Funding support

United States,

United Kingdom, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01 AI55611	United States
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S006818/1	United Kingdom

Citation

Journal: Nat Ecol Evol / Year: 2023
Title: An ancient metalloenzyme evolves through metal preference modulation.
Authors: Sendra, K.M. / Barwinska-Sendra, A. / Mackenzie, E.S. / Basle, A. / Kehl-Fie, T.E. / Waldron, K.J.

History

Deposition	Aug 26, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 24, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8avl.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb8avl.ent.gz	1002.8 KB	Display	PDB format
PDBx/mmJSON format	8avl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8avl_validation.pdf.gz	4.4 MB	Display	wwPDB validaton report
Full document	8avl_full_validation.pdf.gz	4.4 MB	Display
Data in XML	8avl_validation.xml.gz	68.2 KB	Display
Data in CIF	8avl_validation.cif.gz	100.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/8avl ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avl	HTTPS FTP

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Related structure data

Related structure data	8avkC 8avmC 8avnC 1uesS S: Starting model for refinement C: citing same article (ref.)
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	#94 - Oct 2007 Superoxide Dismutase similarity (10)

Deposited unit

A: Superoxide dismutase [Fe]

B: Superoxide dismutase [Fe]

C: Superoxide dismutase [Fe]

D: Superoxide dismutase [Fe]

E: Superoxide dismutase [Fe]

F: Superoxide dismutase [Fe]

G: Superoxide dismutase [Fe]

H: Superoxide dismutase [Fe]

hetero molecules

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

1

A: Superoxide dismutase [Fe]

B: Superoxide dismutase [Fe]

hetero molecules

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

2

C: Superoxide dismutase [Fe]

D: Superoxide dismutase [Fe]

hetero molecules

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

3

E: Superoxide dismutase [Fe]

F: Superoxide dismutase [Fe]

hetero molecules

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

4

G: Superoxide dismutase [Fe]

hetero molecules

H: Superoxide dismutase [Fe]

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.130, 100.110, 103.600
Angle α, β, γ (deg.)	90.000, 91.800, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 192 / Label seq-ID: 1 - 192

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
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Superoxide dismutase [Fe] Mass: 21696.410 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis YCH46 (bacteria) / Strain: YCH46 / Gene: sodB, sod, BF2527 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53638, superoxide dismutase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1507 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.12 Å³/Da / Density % sol: 42.09 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 200 mM sodium chloride, 100 mM Tris pH 8.5 and 25 % w/v polyethylene glycol 3350.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.89843 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.89843 Å / Relative weight: 1

Reflection

Resolution: 1.6→103.55 Å / Num. obs: 190799 / % possible obs: 100 % / Redundancy: 7 % / CC_1/2: 0.998 / Net I/σ(I): 12

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique obs	CC_1/2	Diffraction-ID
8.76-103.55	6.6	1224	0.99	1
1.6-1.63	7.2	9403	0.548	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
REFMAC	5.8.0352	refinement
Aimless		data scaling
xia2		data reduction
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UES

1ues

Resolution: 1.6→103.549 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.964 / WR_factor R_free: 0.194 / WR_factor R_work: 0.128 / SU B: 5.042 / SU ML: 0.074 / Average fsc free: 0.9657 / Average fsc work: 0.9863 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.092
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2038	9665	5.066 %
R_work	0.1333	181102	-
all	0.137	-	-
obs	-	190767	99.988 %

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: 22.889 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.039 Å²	0 Å²	0.17 Å²
2-	-	-0.099 Å²	-0 Å²
3-	-	-	0.049 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→103.549 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12304	0	16	1507	13827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	12682
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	11290
X-RAY DIFFRACTION	r_angle_refined_deg	1.485	1.645	17243
X-RAY DIFFRACTION	r_angle_other_deg	0.548	1.569	26357
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.15	5	1532
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.945	5	40
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.67	10	2027
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.922	10	633
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	1779
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	14434
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2578
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	2691
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	10394
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	5981
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	6315
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.147	0.2	1018
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	39
X-RAY DIFFRACTION	r_nbd_other	0.174	0.2	210
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.213	0.2	90
X-RAY DIFFRACTION	r_mcbond_it	4.401	2.287	6141
X-RAY DIFFRACTION	r_mcbond_other	4.401	2.287	6141
X-RAY DIFFRACTION	r_mcangle_it	5	3.441	7662
X-RAY DIFFRACTION	r_mcangle_other	5	3.442	7663
X-RAY DIFFRACTION	r_scbond_it	6.435	2.593	6541
X-RAY DIFFRACTION	r_scbond_other	6.435	2.594	6542
X-RAY DIFFRACTION	r_scangle_it	6.874	3.726	9579
X-RAY DIFFRACTION	r_scangle_other	6.873	3.727	9580
X-RAY DIFFRACTION	r_lrange_it	6.397	38.43	15052
X-RAY DIFFRACTION	r_lrange_other	6.285	34.374	14681
X-RAY DIFFRACTION	r_rigid_bond_restr	5.618	3	23972
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.081	0.05	6475
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.075	0.05	6521
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.073	0.05	6510
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.074	0.05	6507
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.067	0.05	6514
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.083	0.05	6469
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.058	0.05	6563
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.087	0.05	6398
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.082	0.05	6412
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.086	0.05	6386
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.083	0.05	6406
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.078	0.05	6438
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.082	0.05	6410
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.077	0.05	6473
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.065	0.05	6524
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.076	0.05	6471
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.086	0.05	6400
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.072	0.05	6457
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.068	0.05	6450
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.066	0.05	6514
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.079	0.05	6423
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.075	0.05	6454
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.079	0.05	6413
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.076	0.05	6407
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.072	0.05	6446
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.082	0.05	6425
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.063	0.05	6478
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.077	0.05	6452

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	0.08064	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08064	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07515	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07515	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07285	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07285	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07398	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07398	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.06652	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.06652	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08274	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08274	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.05762	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.05762	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.08727	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.08727	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.08237	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.08237	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.08584	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.08584	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.08282	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.08282	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07818	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07818	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.08152	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.08152	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.07677	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.07677	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.06487	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.06487	0.0501
16	31	A	X-RAY DIFFRACTION	Local ncs	0.07561	0.05009
16	32	A	X-RAY DIFFRACTION	Local ncs	0.07561	0.05009
17	33	A	X-RAY DIFFRACTION	Local ncs	0.08602	0.05009
17	34	A	X-RAY DIFFRACTION	Local ncs	0.08602	0.05009
18	35	A	X-RAY DIFFRACTION	Local ncs	0.07241	0.05009
18	36	A	X-RAY DIFFRACTION	Local ncs	0.07241	0.05009
19	37	A	X-RAY DIFFRACTION	Local ncs	0.06848	0.05009
19	38	A	X-RAY DIFFRACTION	Local ncs	0.06848	0.05009
20	39	A	X-RAY DIFFRACTION	Local ncs	0.06599	0.0501
20	40	A	X-RAY DIFFRACTION	Local ncs	0.06599	0.0501
21	41	A	X-RAY DIFFRACTION	Local ncs	0.07926	0.05009
21	42	A	X-RAY DIFFRACTION	Local ncs	0.07926	0.05009
22	43	A	X-RAY DIFFRACTION	Local ncs	0.07459	0.0501
22	44	A	X-RAY DIFFRACTION	Local ncs	0.07459	0.0501
23	45	A	X-RAY DIFFRACTION	Local ncs	0.07902	0.05009
23	46	A	X-RAY DIFFRACTION	Local ncs	0.07902	0.05009
24	47	A	X-RAY DIFFRACTION	Local ncs	0.07614	0.05009
24	48	A	X-RAY DIFFRACTION	Local ncs	0.07614	0.05009
25	49	A	X-RAY DIFFRACTION	Local ncs	0.0717	0.05009
25	50	A	X-RAY DIFFRACTION	Local ncs	0.0717	0.05009
26	51	A	X-RAY DIFFRACTION	Local ncs	0.08163	0.05009
26	52	A	X-RAY DIFFRACTION	Local ncs	0.08163	0.05009
27	53	A	X-RAY DIFFRACTION	Local ncs	0.06315	0.05009
27	54	A	X-RAY DIFFRACTION	Local ncs	0.06315	0.05009
28	55	A	X-RAY DIFFRACTION	Local ncs	0.07717	0.05009
28	56	A	X-RAY DIFFRACTION	Local ncs	0.07717	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.6-1.642	0.296	682	0.217	13406	0.22	14088	0.94	0.967	100	0.205
1.642-1.687	0.294	651	0.198	13033	0.202	13684	0.943	0.973	100	0.184
1.687-1.735	0.283	714	0.178	12660	0.183	13374	0.949	0.979	100	0.161
1.735-1.789	0.277	707	0.159	12248	0.165	12956	0.954	0.984	99.9923	0.141
1.789-1.847	0.252	593	0.15	11955	0.155	12548	0.96	0.986	100	0.13
1.847-1.912	0.241	542	0.133	11583	0.138	12127	0.964	0.989	99.9835	0.113
1.912-1.984	0.23	558	0.126	11165	0.131	11724	0.967	0.99	99.9915	0.108
1.984-2.065	0.242	566	0.127	10725	0.133	11292	0.965	0.99	99.9911	0.11
2.065-2.157	0.217	600	0.113	10252	0.119	10854	0.971	0.992	99.9816	0.098
2.157-2.262	0.217	552	0.114	9748	0.119	10302	0.971	0.992	99.9806	0.1
2.262-2.385	0.208	531	0.111	9381	0.116	9912	0.974	0.992	100	0.1
2.385-2.529	0.204	402	0.108	8929	0.112	9331	0.976	0.993	100	0.099
2.529-2.704	0.201	444	0.115	8304	0.12	8748	0.977	0.992	100	0.107
2.704-2.92	0.199	447	0.122	7696	0.126	8143	0.977	0.991	100	0.117
2.92-3.199	0.197	427	0.139	7113	0.142	7541	0.977	0.989	99.9867	0.137
3.199-3.576	0.188	287	0.157	6547	0.158	6838	0.98	0.989	99.9415	0.159
3.576-4.128	0.168	328	0.131	5686	0.133	6017	0.985	0.991	99.9501	0.14
4.128-5.054	0.144	285	0.111	4817	0.113	5102	0.991	0.995	100	0.126
5.054-7.139	0.187	243	0.139	3735	0.142	3978	0.988	0.993	100	0.151
7.139-103.549	0.139	106	0.151	2119	0.15	2230	0.992	0.987	99.7758	0.169

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About Yorodumi

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Yorodumi