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- PDB-6qv8: Staphylococcus aureus superoxide dismutase SodM double mutant -

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Basic information

Entry
Database: PDB / ID: 6qv8
TitleStaphylococcus aureus superoxide dismutase SodM double mutant
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / CAMBIALISTIC / STAPHYLOCOCCUS AUREUS / METALLOENZYME
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / 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 [Mn/Fe] 2 / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBasle, A. / Barwinska-Sendra, A. / Waldron, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilDTP United Kingdom
Wellcome Trust098675/Z/12/Z United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: An evolutionary path to altered cofactor specificity in a metalloenzyme.
Authors: Barwinska-Sendra, A. / Garcia, Y.M. / Sendra, K.M. / Basle, A. / Mackenzie, E.S. / Tarrant, E. / Card, P. / Tabares, L.C. / Bicep, C. / Un, S. / Kehl-Fie, T.E. / Waldron, K.J.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)46,0654
Polymers45,9562
Non-polymers1102
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-11 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.210, 144.210, 49.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Superoxide dismutase


Mass: 22977.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: sodA, sodM, BN1321_40056, BTN44_00625, CSC83_08500, CV021_03995, EP54_06740, EQ90_09180, ERS072840_00559, HMPREF3211_00238, M1K003_0636, NCTC10654_00163, NCTC10702_00282, NCTC11940_00074, ...Gene: sodA, sodM, BN1321_40056, BTN44_00625, CSC83_08500, CV021_03995, EP54_06740, EQ90_09180, ERS072840_00559, HMPREF3211_00238, M1K003_0636, NCTC10654_00163, NCTC10702_00282, NCTC11940_00074, NCTC13131_06218, NCTC13196_01115, NCTC5664_00801, RK64_01130, SAMEA1466939_02412, SAMEA1708674_03236
Production host: Escherichia coli (E. coli)
References: UniProt: W8UU58, UniProt: Q2G261*PLUS, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 30 mM MgCl2, 30 mM CaCl2, 39.1 mM Bicine, 60.9 mM Trizma pH 8.5, 20 % PEG 550 MME and 10 % PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.5→47.2 Å / Num. obs: 93785 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.999 / Net I/σ(I): 18.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 51823 / CC1/2: 0.659 / % possible all: 100

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Processing

Software
NameClassification
GDAdata collection
xia2data reduction
XDSdata reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EX4

6ex4


Resolution: 1.5→47.2 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.844 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 5090 5.1 %RANDOM
Rwork0.13844 ---
obs0.14013 94477 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.266 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20.87 Å20 Å2
2--1.74 Å2-0 Å2
3----5.65 Å2
Refinement stepCycle: 1 / Resolution: 1.5→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 2 321 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133348
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172947
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6434561
X-RAY DIFFRACTIONr_angle_other_deg1.5691.5786879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0424.696181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66115556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.487158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7322.8011590
X-RAY DIFFRACTIONr_mcbond_other2.7242.7991589
X-RAY DIFFRACTIONr_mcangle_it3.2354.2211986
X-RAY DIFFRACTIONr_mcangle_other3.2354.2221987
X-RAY DIFFRACTIONr_scbond_it4.6793.1921758
X-RAY DIFFRACTIONr_scbond_other4.6793.1921758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2624.6142571
X-RAY DIFFRACTIONr_long_range_B_refined4.78233.1373902
X-RAY DIFFRACTIONr_long_range_B_other4.72332.8463855
X-RAY DIFFRACTIONr_rigid_bond_restr4.16236295
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 369 -
Rwork0.277 6967 -
obs--99.77 %

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