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- PDB-9twa: Legionella monocytogenes SodA mutant GL to VI -

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Basic information

Entry
Database: PDB / ID: 9twa
TitleLegionella monocytogenes SodA mutant GL to VI
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / superoxide dismutase / SOD / redox / metalloenzyme / protein evolution
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMackenzie, E.S. / Basle, A. / Wldron, K.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: 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
DepositionJan 14, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4804
Polymers45,3682
Non-polymers1122
Water8,269459
1
A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7402
Polymers22,6841
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7402
Polymers22,6841
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.990, 93.380, 94.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 202 / Label seq-ID: 2 - 202

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Superoxide dismutase


Mass: 22684.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: soda, A8L61_06300, AB917_03900, ABZ57_04375, AJL21_03320, ART25_07045, ARY78_04305, B1N52_07385, B1S26_09780, B5K54_05280, BB997_07680, BCZ19_05230, BCZ21_09530, CA369_07515, CAV64_04290, CW845_ ...Gene: soda, A8L61_06300, AB917_03900, ABZ57_04375, AJL21_03320, ART25_07045, ARY78_04305, B1N52_07385, B1S26_09780, B5K54_05280, BB997_07680, BCZ19_05230, BCZ21_09530, CA369_07515, CAV64_04290, CW845_06920, D4920_01675, D4B11_00565, D5N24_03645, D7104_07525, DCK61_09765, DCT16_07745, DQ70_06745, DU018_04420, DYZ80_01535, E1W56_04905, E5F58_09520, EX365_06985, EXZ73_00150, F6436_12875, F6515_04670, FA835_07670, FLQ97_07020, FLR03_13450, FNX40_09325, FV747_03180, G3O21_000994, GHH22_03270, GI949_03855, GJW51_06620, GQG13_08125, GYR60_09845, GYS09_07650, GYX23_06160, GYY14_05675, HQN34_002220, HZJ64_06955, KV70_03880, UI29_08045, Y261_07385
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B8R4R3, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate, 30 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89842 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89842 Å / Relative weight: 1
ReflectionResolution: 1.4→51.99 Å / Num. obs: 91660 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 16.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
7.67-51.9912.19166011
1.4-1.429.444870.5381

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Processing

Software
NameVersionClassification
REFMAC5.8.0326refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.435 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.134 / SU ML: 0.043 / Cross valid method: FREE R-VALUE / ESU R: 0.057 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1913 4561 4.981 %
Rwork0.1761 87013 -
all0.177 --
obs-91574 99.993 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.042 Å2
Baniso -1Baniso -2Baniso -3
1-1.014 Å2-0 Å20 Å2
2---0.086 Å2-0 Å2
3----0.928 Å2
Refinement stepCycle: LAST / Resolution: 1.4→47.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 2 459 3657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123340
X-RAY DIFFRACTIONr_bond_other_d0.0040.0162988
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6364554
X-RAY DIFFRACTIONr_angle_other_deg0.6851.5656894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84724.28642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10610.296507
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.99310140
X-RAY DIFFRACTIONr_chiral_restr0.1250.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
X-RAY DIFFRACTIONr_nbd_refined0.2390.2718
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22706
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21645
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21665
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.217
X-RAY DIFFRACTIONr_nbd_other0.1750.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2510.228
X-RAY DIFFRACTIONr_mcbond_it1.6431.9431627
X-RAY DIFFRACTIONr_mcbond_other1.631.9421627
X-RAY DIFFRACTIONr_mcangle_it2.2132.9092032
X-RAY DIFFRACTIONr_mcangle_other2.2162.9112033
X-RAY DIFFRACTIONr_scbond_it2.772.1461713
X-RAY DIFFRACTIONr_scbond_other2.7692.1491714
X-RAY DIFFRACTIONr_scangle_it4.0483.122522
X-RAY DIFFRACTIONr_scangle_other4.0473.1232523
X-RAY DIFFRACTIONr_lrange_it4.99932.8814021
X-RAY DIFFRACTIONr_lrange_other5.00632.8924022
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.056743
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.078610.05009
12AX-RAY DIFFRACTIONLocal ncs0.078610.05009
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.283080.30563780.30466880.9370.92499.97010.297
1.436-1.4760.2693440.26461770.26465210.9430.9481000.25
1.476-1.5180.2563120.22560190.22763310.9550.9631000.204
1.518-1.5650.2362710.20959210.2161920.9620.971000.185
1.565-1.6160.2183200.19256560.19359760.970.9751000.167
1.616-1.6730.2273460.18854480.19157950.9650.97799.98270.162
1.673-1.7360.2042710.17653230.17755940.9740.981000.152
1.736-1.8070.2052810.1751200.17254010.9720.9821000.147
1.807-1.8870.1872540.1649060.16251600.9780.9841000.141
1.887-1.9790.1882420.16647390.16749820.9780.98399.97990.15
1.979-2.0860.22330.1744920.17147250.9760.9821000.155
2.086-2.2120.1671810.1642830.1644640.9830.9851000.149
2.212-2.3650.1662190.15240060.15342250.9840.9861000.143
2.365-2.5530.1851780.15537660.15739440.9790.9851000.148
2.553-2.7960.1641930.15834470.15836400.9830.9851000.155
2.796-3.1250.2041520.17731580.17833100.9780.9821000.175
3.125-3.6060.2021420.18528010.18629430.9780.9811000.19
3.606-4.410.1531540.15623600.15625140.9860.9851000.171
4.41-6.210.2091010.18818830.18919840.9810.9861000.213
6.21-47.4350.198590.20311310.20211910.9750.98399.9160.231

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