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- PDB-7w6w: Crystal structure of a mutant Staphylococcus equorum manganese su... -

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Basic information

Entry
Database: PDB / ID: 7w6w
TitleCrystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase L169W
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / superoxide dismutase / Staphylococcus equorum
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
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 / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily
Similarity search - Domain/homology
AZIDE ION / : / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus equorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRetnoningrum, D.S. / Yoshida, H. / Artarini, A.A. / Ismaya, W.T.
Funding supportIndonesia, 1items
OrganizationGrant numberCountry
Other government079/E4.1/AK.04.PT/2021Indonesia
Citation
Journal: Appl.Biochem.Biotechnol. / Year: 2023
Title: Introducing Intermolecular Interaction to Strengthen the Stability of MnSOD Dimer.
Authors: Retnoningrum, D.S. / Yoshida, H. / Pajatiwi, I. / Muliadi, R. / Utami, R.A. / Artarini, A. / Ismaya, W.T.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus.
Authors: Retnoningrum, D.S. / Yoshida, H. / Arumsari, S. / Kamitori, S. / Ismaya, W.T.
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Feb 8, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jul 12, 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 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,60410
Polymers94,3004
Non-polymers3046
Water3,765209
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3025
Polymers47,1502
Non-polymers1523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area17410 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3025
Polymers47,1502
Non-polymers1523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.245, 136.527, 55.506
Angle α, β, γ (deg.)90.000, 100.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase /


Mass: 23575.078 Da / Num. of mol.: 4 / Mutation: D13R,L169W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus equorum (bacteria) / Gene: AST02_02815 / Plasmid: pJExpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E5TT85, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, PEG 1000, PEG 3350, L-Na-Glutamate, Alanine, Glycine, Lysine, Serine, HEPES, MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→45.51 Å / Num. obs: 58954 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.032 / Rrim(I) all: 0.058 / Net I/σ(I): 14.4 / Num. measured all: 193383 / Scaling rejects: 128
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.94-1.993.20.5271282140290.7280.3490.6342.299.8
9.1-45.513.40.02519585770.9980.0160.0345.595.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5x2j

5x2j


Resolution: 1.94→42.59 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.164 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 2825 4.8 %RANDOM
Rwork0.2015 ---
obs0.2041 56093 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.17 Å2 / Biso mean: 37.639 Å2 / Biso min: 17.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.05 Å2
2---0.15 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.94→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 10 209 6595
Biso mean--35.22 35.06 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0136564
X-RAY DIFFRACTIONr_bond_other_d00.0175700
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6348954
X-RAY DIFFRACTIONr_angle_other_deg1.3731.57413296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48925368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.77151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0591516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021336
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 195 -
Rwork0.284 4205 -
all-4400 -
obs--99.77 %

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