PDB-8avm: Mutant of Superoxide Dismutase sodfm2 from Bacteroides fragilis

ID or keywords:

Entry

Database: PDB / ID: 8avm

Title

Mutant of Superoxide Dismutase sodfm2 from Bacteroides fragilis

Components

Superoxide dismutase [Fe]

Keywords

OXIDOREDUCTASE / Mutant of superoxide dismutase SodFM2 from Bacteroides fragilis

Function / homology

Function and homology information

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

Biological species

Bacteroides fragilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 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	8avm.cif.gz	442 KB	Display	PDBx/mmCIF format
PDB format	pdb8avm.ent.gz	354.5 KB	Display	PDB format
PDBx/mmJSON format	8avm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8avm_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8avm_full_validation.pdf.gz	2.6 MB	Display
Data in XML	8avm_validation.xml.gz	44.5 KB	Display
Data in CIF	8avm_validation.cif.gz	63.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/8avm ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avm	HTTPS FTP

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Related structure data

Related structure data	8avkC 8avlC 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]

hetero molecules

131 kDa, 6 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
43.5 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)

Unit cell

Length a, b, c (Å)	79.430, 117.110, 139.330
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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

#1: Protein	Superoxide dismutase [Fe] Mass: 21696.432 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides fragilis (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.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.49 Å³/Da / Density % sol: 50.58 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 10 mM zinc chloride, 100 mM sodium acetate pH 5.0 and 20% w/v polyethylene glycol 6000.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89842 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.89842 Å / Relative weight: 1
Reflection	Resolution: 2→69 Å / Num. obs: 88446 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.158 / R_pim(I) all: 0.064 / R_rim(I) all: 0.17 / Net I/σ(I): 11
Reflection shell	Resolution: 2→2.04 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4451 / CC_1/2: 0.444 / % possible all: 97.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1UES

1ues

Resolution: 2→69 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / SU B: 5.251 / SU ML: 0.135 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2289	4329	4.899 %
R_work	0.1927	84036	-
all	0.194	-	-
obs	-	88365	99.986 %

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: 38.986 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.031 Å²	-0 Å²	-0 Å²
2-	-	-0.86 Å²	0 Å²
3-	-	-	0.891 Å²

Refinement step

Cycle: LAST / Resolution: 2→69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9216	0	6	513	9735

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	9480
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	8442
X-RAY DIFFRACTION	r_angle_refined_deg	1.546	1.647	12894
X-RAY DIFFRACTION	r_angle_other_deg	0.532	1.568	19716
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.248	5	1146
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.113	5	30
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.492	10	1524
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.642	10	468
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1344
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	10770
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1902
X-RAY DIFFRACTION	r_nbd_refined	0.226	0.2	2275
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	7769
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	4697
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	5032
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	486
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.062	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.061	0.2	7
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.283	0.2	30
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	96
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.273	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	4.046	3.955	4602
X-RAY DIFFRACTION	r_mcbond_other	4.045	3.955	4602
X-RAY DIFFRACTION	r_mcangle_it	4.838	5.915	5742
X-RAY DIFFRACTION	r_mcangle_other	4.837	5.915	5743
X-RAY DIFFRACTION	r_scbond_it	5.1	4.258	4878
X-RAY DIFFRACTION	r_scbond_other	5.099	4.259	4879
X-RAY DIFFRACTION	r_scangle_it	6.839	6.203	7152
X-RAY DIFFRACTION	r_scangle_other	6.838	6.204	7153
X-RAY DIFFRACTION	r_lrange_it	7.818	54.27	11397
X-RAY DIFFRACTION	r_lrange_other	7.815	53.298	11331
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.064	0.05	6531
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.062	0.05	6552
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.055	0.05	6536
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.043	0.05	6591
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.056	0.05	6559
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.069	0.05	6534
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.067	0.05	6500
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.064	0.05	6548
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.063	0.05	6566
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.059	0.05	6593
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.065	0.05	6558
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.066	0.05	6538
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.058	0.05	6554
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.06	0.05	6524
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.053	0.05	6598

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	0.06356	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06356	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06204	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06204	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.05468	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.05468	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.04301	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.04301	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05556	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05556	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06853	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06853	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06677	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06677	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.06445	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.06445	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.06287	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.06287	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.05864	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.05864	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.0653	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.0653	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.06591	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.06591	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.0585	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.0585	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06042	0.05009
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06042	0.05009
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05304	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05304	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 (%)
2-2.052	0.35	308	0.349	6153	X-RAY DIFFRACTION	100
2.052-2.108	0.359	330	0.312	5932	X-RAY DIFFRACTION	100
2.108-2.169	0.304	255	0.284	5892	X-RAY DIFFRACTION	100
2.169-2.236	0.296	323	0.259	5610	X-RAY DIFFRACTION	100
2.236-2.309	0.275	272	0.23	5502	X-RAY DIFFRACTION	100
2.309-2.39	0.266	300	0.222	5313	X-RAY DIFFRACTION	100
2.39-2.48	0.265	255	0.221	5151	X-RAY DIFFRACTION	100
2.48-2.581	0.26	240	0.21	4966	X-RAY DIFFRACTION	100
2.581-2.696	0.256	262	0.206	4710	X-RAY DIFFRACTION	100
2.696-2.827	0.258	230	0.197	4571	X-RAY DIFFRACTION	100
2.827-2.98	0.265	218	0.198	4346	X-RAY DIFFRACTION	100
2.98-3.16	0.256	215	0.194	4115	X-RAY DIFFRACTION	100
3.16-3.378	0.246	193	0.206	3854	X-RAY DIFFRACTION	100
3.378-3.648	0.237	197	0.212	3629	X-RAY DIFFRACTION	100
3.648-3.995	0.214	167	0.185	3342	X-RAY DIFFRACTION	100
3.995-4.465	0.186	160	0.147	3035	X-RAY DIFFRACTION	100
4.465-5.152	0.151	126	0.129	2715	X-RAY DIFFRACTION	100
5.152-6.301	0.179	112	0.14	2309	X-RAY DIFFRACTION	100
6.301-8.874	0.138	102	0.121	1828	X-RAY DIFFRACTION	100

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