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- PDB-8avk: Superoxide dismutase SodFM1 from CPR Parkubacteria Wolfebacteria -

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Basic information

Entry
Database: PDB / ID: 8avk
TitleSuperoxide dismutase SodFM1 from CPR Parkubacteria Wolfebacteria
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Superoxide dismutase (SOD). Oxidoreductase. Iron. Bacterial. Metalloenzyme.
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesCandidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBasle, A. / Barwinska-Sendra, A. / Sendra, K.M. / Waldron, K.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: 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 1.2Feb 7, 2024Group: 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

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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)47,0974
Polymers46,9852
Non-polymers1122
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.531, 70.586, 57.788
Angle α, β, γ (deg.)90.000, 100.301, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 203 / Label seq-ID: 2 - 203

Dom-ID
1
2

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

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Components

#1: Protein Superoxide dismutase


Mass: 23492.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Wolfebacteria bacterium GW2011_GWB1_47_1 (bacteria)
Gene: UX70_C0001G0692 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0G1X6V3, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate trihydrate pH 4.5 and 25% w/v polyethylene glycol 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89843 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89843 Å / Relative weight: 1
ReflectionResolution: 2.1→70.59 Å / Num. obs: 21632 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.996 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.16 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1781 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IX9

1ix9


Resolution: 2.1→56.857 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.217 / SU ML: 0.212 / Cross valid method: FREE R-VALUE / ESU R: 0.302 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2563 1048 4.853 %
Rwork0.2089 20546 -
all0.211 --
obs-21594 99.907 %
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: 37.345 Å2
Baniso -1Baniso -2Baniso -3
1--1.993 Å2-0 Å21.639 Å2
2--2.519 Å20 Å2
3----1.052 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 2 11 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123418
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163004
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6574664
X-RAY DIFFRACTIONr_angle_other_deg0.6251.5697012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.656510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40110550
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.35310174
X-RAY DIFFRACTIONr_chiral_restr0.090.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023830
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
X-RAY DIFFRACTIONr_nbd_refined0.2430.2814
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22758
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21722
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21736
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.231
X-RAY DIFFRACTIONr_nbd_other0.2470.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0760.24
X-RAY DIFFRACTIONr_mcbond_it2.6312.7271614
X-RAY DIFFRACTIONr_mcbond_other2.622.7251613
X-RAY DIFFRACTIONr_mcangle_it3.5954.0772014
X-RAY DIFFRACTIONr_mcangle_other3.5954.0782015
X-RAY DIFFRACTIONr_scbond_it3.413.0131804
X-RAY DIFFRACTIONr_scbond_other3.4093.0131805
X-RAY DIFFRACTIONr_scangle_it4.8054.4072650
X-RAY DIFFRACTIONr_scangle_other4.8044.4072651
X-RAY DIFFRACTIONr_lrange_it5.66439.4394038
X-RAY DIFFRACTIONr_lrange_other5.66639.4464038
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.056918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098130.05008
12AX-RAY DIFFRACTIONLocal ncs0.098130.05008
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
2.1-2.1550.355780.33615210.33716040.8930.92399.68830.334
2.155-2.2130.346860.32314620.32515500.9170.92699.8710.319
2.213-2.2780.326820.29714220.29815070.9140.93899.80090.287
2.278-2.3480.31850.26713720.26914600.9370.95399.79450.255
2.348-2.4240.279570.23813630.23914200.9520.9621000.222
2.424-2.5090.275700.22412940.22713660.9570.96999.85360.202
2.509-2.6040.348730.22612590.23213320.9380.9721000.198
2.604-2.710.322520.22812320.23112850.9370.96999.92220.201
2.71-2.830.323500.21711420.22111940.9320.97399.83250.191
2.83-2.9680.317560.23811280.24211850.9450.96899.91560.202
2.968-3.1280.307540.2410640.24311180.9410.9661000.208
3.128-3.3170.308430.22310010.22610450.9490.96999.90430.198
3.317-3.5450.239460.1989530.2019990.9680.9761000.178
3.545-3.8280.179470.1888800.1879270.9840.9821000.173
3.828-4.1920.209350.158160.1538510.9720.9881000.144
4.192-4.6830.188420.157330.1527750.980.991000.148
4.683-5.4010.213300.1436530.1466830.9830.9911000.142
5.401-6.6010.154300.1725550.1715850.9830.9871000.172
6.601-9.2720.197190.154420.1524610.9690.991000.153
9.272-56.8570.224130.2022540.2032670.9920.9841000.203
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2361-0.2915-0.14491.1055-0.39912.10950.0175-0.0688-0.09190.1361-0.00540.07480.0399-0.1075-0.01210.0283-0.00680.00820.06540.01330.0399-11.18745.5013-32.2035
21.1006-0.15010.24291.26790.52231.57990.01040.1606-0.0846-0.1459-0.0228-0.0377-0.0215-0.04150.01250.0182-0.00190.00530.04-0.00110.0277-6.08025.6326-62.0873
Refinement TLS groupSelection: ALL

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