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- PDB-6m30: Crystal structure of a mutant Staphylococcus equorum manganese su... -

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Basic information

Entry
Database: PDB / ID: 6m30
TitleCrystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase N73F
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / superoxide dismutase / Staphylococcus equorum
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 speciesStaphylococcus equorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRetnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Meidianto, V.F. / Hartanto, A. / Artarini, A. / Ismaya, W.T.
Citation
Journal: Curr Enzym Inhib / Year: 2021
Title: Unprecedented Role of The N73-F124 Pair in The Staphylococcus equorum MnSOD Activity.
Authors: Retnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Meidianto, V.F. / Hartanto, 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
DepositionMar 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,54012
Polymers141,2116
Non-polymers3306
Water10,647591
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1804
Polymers47,0702
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-14 kcal/mol
Surface area17380 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1804
Polymers47,0702
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area17450 Å2
MethodPISA
3
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1804
Polymers47,0702
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.123, 132.504, 80.507
Angle α, β, γ (deg.)90.000, 110.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase


Mass: 23535.098 Da / Num. of mol.: 6 / Mutation: D13R, N73F
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.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate, Bis-Tris, Pentaerythritol ethoxylate

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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: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→46.28 Å / Num. obs: 137152 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 8.4 / Num. measured all: 469453 / Scaling rejects: 4
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
1.74-1.773.40.6542271467230.7520.4150.7761.598.3
9.53-46.283.50.02630358570.9980.0160.03130.497.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X2J

5x2j


Resolution: 1.74→44.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.361 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.106
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 6916 5 %RANDOM
Rwork0.1624 ---
obs0.1649 130198 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.34 Å2 / Biso mean: 24.268 Å2 / Biso min: 11.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å20.01 Å2
2---0.5 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.74→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9594 0 6 591 10191
Biso mean--15.04 25.98 -
Num. residues----1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0139882
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178676
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.63513472
X-RAY DIFFRACTIONr_angle_other_deg1.3071.57520232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33451186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63424.836550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.027151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3421526
X-RAY DIFFRACTIONr_chiral_restr0.0560.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211150
X-RAY DIFFRACTIONr_gen_planes_other00.022016
X-RAY DIFFRACTIONr_rigid_bond_restr4.167318558
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 502 -
Rwork0.256 9577 -
all-10079 -
obs--98.3 %

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