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- PDB-8y17: Crystal structure of a mutant Staphylococcus equorum manganese su... -

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Basic information

Entry
Database: PDB / ID: 8y17
TitleCrystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C
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
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
: / Superoxide dismutase
Similarity search - Component
Biological speciesStaphylococcus equorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPutri, N.A. / Fadillah, M.D. / Yoshida, H. / Retnoningrum, D.S. / Artarini, A.A. / Utami, R.A. / Ismaya, W.T.
Funding supportIndonesia, 1items
OrganizationGrant numberCountry
Program Penelitian, Pengabdian kepada Masyarakat dan Inovasi ITB (P3MI-ITB) Grant Scheme 202356/IT1/C10/SK-KU/2023Indonesia
Citation
Journal: To Be Published
Title: Crystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase T89C and N187C
Authors: Putri, N.A. / Fadillah, M.D. / Yoshida, H. / Retnoningrum, D.S. / Artarini, A.A. / Utami, R.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 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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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)94,1928
Polymers93,9724
Non-polymers2204
Water1,06359
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0964
Polymers46,9862
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0964
Polymers46,9862
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.920, 135.820, 76.380
Angle α, β, γ (deg.)90.000, 102.740, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 1

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 1982 - 198
21ALAALABB2 - 1982 - 198
12ALAALAAA2 - 1982 - 198
22ALAALACC2 - 1982 - 198
13ALAALAAA2 - 1982 - 198
23ALAALADD2 - 1982 - 198
14LYSLYSBB2 - 1992 - 199
24LYSLYSCC2 - 1992 - 199
15LYSLYSBB2 - 1992 - 199
25LYSLYSDD2 - 1992 - 199
16LYSLYSCC2 - 1992 - 199
26LYSLYSDD2 - 1992 - 199

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.361201, -0.896747, 0.255693), (-0.894526, 0.255773, -0.366611), (0.263357, -0.361144, -0.894549)30.55154, 14.70754, -24.36447
3given(1), (1), (1)
4given(0.338363, 0.902837, -0.265323), (-0.909846, 0.241916, -0.33713), (-0.240187, 0.355475, 0.903298)-30.550449, 15.76295, 22.0872
5given(1), (1), (1)
6given(0.635652, -0.446026, 0.630085), (-0.436044, -0.880971, -0.183728), (0.637034, -0.157958, -0.754478)32.67907, 37.563011, -58.32156
7given(1), (1), (1)
8given(0.628117, -0.448954, 0.635538), (-0.449504, -0.876048, -0.174599), (0.635149, -0.176009, -0.752068)33.381451, 38.287102, -57.562019
9given(1), (1), (1)
10given(0.327226, 0.908409, -0.260224), (-0.911191, 0.23039, -0.341542), (-0.250307, 0.348875, 0.903124)-30.063499, 16.135031, 22.730551
11given(1), (1), (1)
12given(0.456095, 0.688649, 0.563684), (0.695454, -0.671017, 0.257062), (0.555267, 0.274772, -0.784971)21.105289, 33.75267, -96.839218

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Components

#1: Protein
Superoxide dismutase


Mass: 23493.107 Da / Num. of mol.: 4 / Mutation: D13R, T89C and N187C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus equorum (bacteria) / Gene: AST02_02815, M4L21_03170 / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.22 Å3/Da / Density % sol: 70.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: DL-malic acid, PEG3350

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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: 2.8→47.81 Å / Num. obs: 37308 / % possible obs: 96.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 51.755 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.123 / Χ2: 0.897 / Net I/σ(I): 10.19 / Num. measured all: 152979 / Scaling rejects: 497
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.874.3380.6182.3312260283528260.820.70699.7
2.87-2.954.3470.4932.8912093279627820.8960.56299.5
2.95-3.044.3330.4463.2911435266226390.8920.50999.1
3.04-3.134.1980.344.1510815259625760.9280.3999.2
3.13-3.234.1030.2575.2810245253624970.9530.29698.5
3.23-3.353.9140.2066.279476245224210.9630.23998.7
3.35-3.474.010.1697.579395239223430.9760.19598
3.47-3.614.2370.1389.179215224521750.9860.15896.9
3.61-3.784.1460.11310.818707217421000.9870.1396.6
3.78-3.964.0220.09212.748003209619900.9890.10694.9
3.96-4.173.9290.08113.977351199118710.9920.09494
4.17-4.433.7920.07115.646678187517610.9930.08293.9
4.43-4.733.9310.06517.156691179717020.9930.07594.7
4.73-5.114.1390.06118.176448164515580.9930.07194.7
5.11-5.64.0460.06517.415693150414070.9910.07593.6
5.6-6.263.8710.06417.45114138513210.990.07595.4
6.26-7.233.910.0618.984500120811510.9920.0795.3
7.23-8.854.180.05122.57413010379880.9950.05995.3
8.85-12.523.9050.04823.9730078107700.9930.05595.1
12.52-47.814.0070.04624.9617234574300.9920.05594.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.81 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.885 / SU B: 15.991 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.55 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2761 1863 5 %RANDOM
Rwork0.234 ---
obs0.2361 35445 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.52 Å2 / Biso mean: 55.533 Å2 / Biso min: 30.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.09 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.8→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 4 59 6443
Biso mean--45.56 44.62 -
Num. residues----793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136560
X-RAY DIFFRACTIONr_bond_other_d00.0175749
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.6348942
X-RAY DIFFRACTIONr_angle_other_deg1.1111.57513417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1525360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.744151055
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3971516
X-RAY DIFFRACTIONr_chiral_restr0.0340.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027395
X-RAY DIFFRACTIONr_gen_planes_other00.021317
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.87

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A15846.25
2A15844.57
3A15845.67
4B15936.15
5B15935.02
6C15933.64
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 140 -
Rwork0.368 2682 -
all-2822 -
obs--99.72 %

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