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- PDB-6qv9: Staphylococcus aureus superoxide dismutase SodA double mutant -

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Basic information

Entry
Database: PDB / ID: 6qv9
TitleStaphylococcus aureus superoxide dismutase SodA double mutant
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / CAMBIALISTIC / STAPHYLOCOCCUS AUREUS / METALLOENZYME
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Mn] 1 / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)45,7674
Polymers45,6572
Non-polymers1102
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-11 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.250, 68.150, 57.290
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Superoxide dismutase


Mass: 22828.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: sodA, sodA_1, BN1321_260190, BTN44_04405, CSC83_01345, CSC87_02560, CV021_16580, EP54_01115, EQ90_12445, ERS072840_00871, HMPREF3211_01704, M1K003_1305, NCTC10654_01617, NCTC11940_01488, ...Gene: sodA, sodA_1, BN1321_260190, BTN44_04405, CSC83_01345, CSC87_02560, CV021_16580, EP54_01115, EQ90_12445, ERS072840_00871, HMPREF3211_01704, M1K003_1305, NCTC10654_01617, NCTC11940_01488, NCTC13131_01937, NCTC13196_02481, RK64_08340, SAMEA1466939_00978, SAMEA1708674_02019
Production host: Escherichia coli (E. coli)
References: UniProt: W8TT57, UniProt: P0A0J3*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.: 133 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM MgCl2, 100 mM Bis-Tris pH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.55 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: 1.55 Å / Relative weight: 1
ReflectionResolution: 1.8→43.46 Å / Num. obs: 36588 / % possible obs: 99.4 % / Redundancy: 6 % / CC1/2: 0.995 / Net I/σ(I): 10.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2068 / CC1/2: 0.73 / % possible all: 96.4

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Processing

Software
NameClassification
GDAdata collection
xia2data reduction
XDSdata scaling
Aimlessdata scaling
MOLREPphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EX3

6ex3


Resolution: 1.8→35.77 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.473 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20685 1735 4.8 %RANDOM
Rwork0.17076 ---
obs0.17252 34541 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-1.65 Å2
2---0.73 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.8→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 2 133 3333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133290
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172892
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6364482
X-RAY DIFFRACTIONr_angle_other_deg1.4751.5746744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03824.835182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70615530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.422158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023700
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
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_it1.922.0891574
X-RAY DIFFRACTIONr_mcbond_other1.9152.0881573
X-RAY DIFFRACTIONr_mcangle_it2.8433.1241964
X-RAY DIFFRACTIONr_mcangle_other2.8423.1251965
X-RAY DIFFRACTIONr_scbond_it3.2492.4191716
X-RAY DIFFRACTIONr_scbond_other3.2482.4191717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2323.4722519
X-RAY DIFFRACTIONr_long_range_B_refined5.96323.9493772
X-RAY DIFFRACTIONr_long_range_B_other5.96123.9053756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 120 -
Rwork0.191 2469 -
obs--96.89 %

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