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

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Basic information

Entry
Database: PDB / ID: 7wnl
TitleCrystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase K38R and A121Y
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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
AZIDE ION / BROMIDE ION / : / DI(HYDROXYETHYL)ETHER / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus equorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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
DepositionJan 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: 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

Downloads & links

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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)95,24514
Polymers94,4894
Non-polymers75610
Water21,0051166
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6627
Polymers47,2442
Non-polymers4185
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-7 kcal/mol
Surface area17920 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5827
Polymers47,2442
Non-polymers3385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-7 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.926, 102.624, 179.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-723-

HOH

21D-628-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Superoxide dismutase


Mass: 23622.139 Da / Num. of mol.: 4 / Mutation: D13R, K38R, A121Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus equorum (bacteria) / Gene: AST02_02815 / Plasmid: plasmid / Details (production host): pJExpress414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1E5TT85, superoxide dismutase

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Non-polymers , 6 types, 1176 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1166 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium fluoride, sodium bromide, sodium iodide, imidazole, MES, PEG MME 500, PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.98 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: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.51→45.93 Å / Num. obs: 144687 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.047 / Rrim(I) all: 0.115 / Net I/σ(I): 10.7 / Num. measured all: 873802 / Scaling rejects: 74
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
1.51-1.545.80.7894141171240.7920.3620.869299.9
8.27-45.936.50.04363909850.9980.0180.04630.799.1

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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: 1.51→44.79 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.911 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 7045 4.9 %RANDOM
Rwork0.1714 ---
obs0.1747 137549 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.49 Å2 / Biso mean: 19.993 Å2 / Biso min: 8.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0 Å2
2--0.38 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.51→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6490 0 34 1166 7690
Biso mean--28.33 33.12 -
Num. residues----799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136700
X-RAY DIFFRACTIONr_bond_other_d0.0070.0175830
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.6359126
X-RAY DIFFRACTIONr_angle_other_deg1.3941.57413590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2924.595383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.164151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.711520
X-RAY DIFFRACTIONr_chiral_restr0.0640.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021373
X-RAY DIFFRACTIONr_rigid_bond_restr5.847312528
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 568 -
Rwork0.243 10038 -
all-10606 -
obs--99.94 %

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