PDB-9twc: Legionella monocytogenes SodA wt

ID or keywords:

Entry

Database: PDB / ID: 9twc

Title

Legionella monocytogenes SodA wt

Components

Superoxide dismutase

Keywords

OXIDOREDUCTASE / superoxide dismutase / SOD / redox / metalloenzyme / protein evolution

Function / homology

Function and homology information

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

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Mackenzie, E.S. / Basle, A. / Wldron, K.J.

Funding support

United Kingdom, 1items

Citation

Journal: Mol.Biol.Evol. / Year: 2026
Title: An enzyme's metal preference evolves through redox modulation driven by the cofactor's secondary coordination sphere.
Authors: Mackenzie, E.S. / Sendra, K.M. / Basle, A. / Mazgaj, R. / Kehl-Fie, T.E. / Waldron, K.J.

History

Deposition	Jan 14, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 11, 2026	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2026	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9twc.cif.gz	452.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9twc.ent.gz	363.9 KB	Display	PDB format
PDBx/mmJSON format	9twc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/9twc ftp://data.pdbj.org/pub/pdb/validation_reports/tw/9twc	HTTPS FTP

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Related structure data

Related structure data	9tw9C 9twaC 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 (11)

Deposited unit

A: Superoxide dismutase

B: Superoxide dismutase

C: Superoxide dismutase

D: Superoxide dismutase

E: Superoxide dismutase

G: Superoxide dismutase

hetero molecules

130 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

G: Superoxide dismutase

hetero molecules

defined by author
21.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.190, 105.580, 162.580
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: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 193 / Label seq-ID: 1 - 193

NCS ensembles :

ID	Details (eV)
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 Mass: 21679.203 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F4F5, superoxide dismutase
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.22 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M MES/imidazole pH 6.5, 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each additive alcohol: 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2022

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2→67.48 Å / Num. obs: 121479 / % possible obs: 100 % / Redundancy: 13.1 % / CC_1/2: 0.997 / Net I/σ(I): 10

Reflection shell

Resolution (Å)	Redundancy (%)	Num. unique obs	CC_1/2	Diffraction-ID
10.95-67.47	11.2	121479	0.996	1
2-2.03	13.3	5956	0.443	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0326	refinement
Aimless		data scaling
PHASER		phasing
Coot		model building
BUCCANEER		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→67.472 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.92 / SU B: 4.849 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2273	6036	4.972 %
R_work	0.194	115355	-
all	0.196	-	-
obs	-	121391	99.987 %

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: 42.896 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.941 Å²	-0 Å²	-0 Å²
2-	-	-1.537 Å²	0 Å²
3-	-	-	3.478 Å²

Refinement step

Cycle: LAST / Resolution: 2→67.472 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9228	0	6	585	9819

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	9564
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	8515
X-RAY DIFFRACTION	r_angle_refined_deg	1.353	1.637	13050
X-RAY DIFFRACTION	r_angle_other_deg	0.482	1.56	19658
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.24	5	1152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.289	26.25	96
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.531	10.273	1428
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.5	10	378
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	1338
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	11094
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2299
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	2078
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	7391
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	4728
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	4933
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	463
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.01	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.273	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.134	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	3.426	4.347	4626
X-RAY DIFFRACTION	r_mcbond_other	3.424	4.347	4626
X-RAY DIFFRACTION	r_mcangle_it	4.433	6.508	5772
X-RAY DIFFRACTION	r_mcangle_other	4.432	6.509	5773
X-RAY DIFFRACTION	r_scbond_it	4.767	4.654	4938
X-RAY DIFFRACTION	r_scbond_other	4.767	4.655	4939
X-RAY DIFFRACTION	r_scangle_it	6.974	6.795	7278
X-RAY DIFFRACTION	r_scangle_other	6.973	6.796	7279
X-RAY DIFFRACTION	r_lrange_it	8.186	56.74	11400
X-RAY DIFFRACTION	r_lrange_other	8.185	56.745	11401
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.04	0.05	6613
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.043	0.05	6588
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.047	0.05	6573
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.041	0.05	6597
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.056	0.05	6546
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.038	0.05	6610
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.045	0.05	6576
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.035	0.05	6610
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.05	0.05	6570
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.045	0.05	6583
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.036	0.05	6623
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.045	0.05	6584
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.041	0.05	6596
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.058	0.05	6572
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.051	0.05	6567

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	0.0405	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.0405	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.04303	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.04303	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04662	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.04662	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0413	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0413	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.05582	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.05582	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.03769	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.03769	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.0453	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.0453	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.03461	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.03461	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.05033	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.05033	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.04451	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.04451	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.03576	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.03576	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.04524	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.04524	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.04078	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.04078	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.05824	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.05824	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05117	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05117	0.0501

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
2-2.052	0.377	449	0.36	8400	0.361	8850	0.868	0.876	99.9887	0.355
2.052-2.108	0.357	395	0.33	8269	0.331	8664	0.882	0.9	100	0.32
2.108-2.169	0.329	455	0.297	7966	0.299	8421	0.915	0.925	100	0.28
2.169-2.236	0.281	368	0.272	7797	0.273	8166	0.94	0.944	99.9878	0.249
2.236-2.309	0.264	389	0.243	7568	0.244	7958	0.949	0.952	99.9874	0.219
2.309-2.39	0.277	357	0.226	7354	0.229	7712	0.95	0.966	99.987	0.197
2.39-2.48	0.228	399	0.2	7018	0.202	7417	0.965	0.974	100	0.173
2.48-2.581	0.237	371	0.195	6773	0.198	7144	0.965	0.976	100	0.167
2.581-2.696	0.249	337	0.198	6535	0.2	6873	0.966	0.977	99.9855	0.173
2.696-2.827	0.224	337	0.187	6235	0.189	6572	0.969	0.979	100	0.165
2.827-2.98	0.228	318	0.193	5958	0.195	6276	0.969	0.977	100	0.175
2.98-3.16	0.227	283	0.199	5660	0.201	5944	0.966	0.975	99.9832	0.186
3.16-3.378	0.246	289	0.221	5301	0.223	5590	0.965	0.972	100	0.214
3.378-3.648	0.233	266	0.218	4957	0.219	5223	0.971	0.975	100	0.216
3.648-3.995	0.207	235	0.182	4588	0.184	4823	0.977	0.983	100	0.187
3.995-4.464	0.189	227	0.152	4148	0.154	4375	0.982	0.988	100	0.167
4.464-5.151	0.161	218	0.14	3678	0.141	3896	0.988	0.992	100	0.162
5.151-6.3	0.193	141	0.154	3180	0.156	3322	0.985	0.99	99.9699	0.173
6.3-8.871	0.159	116	0.133	2512	0.134	2629	0.986	0.99	99.962	0.155
8.871-67.472	0.248	85	0.146	1459	0.152	1548	0.899	0.973	99.7416	0.179

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