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

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Basic information

Entry
Database: PDB / ID: 7ddw
TitleCrystal structure of a mutant Staphylococcus equorum manganese superoxide dismutase S126C
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / superoxide dismutase / Staphylococcus equorum / disulfide bond
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: 1.88 Å
AuthorsRetnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Meidianto, V.F. / Hartanto, A. / Artarini, A. / Ismaya, W.T.
Citation
Journal: J.Struct.Biol. / Year: 2021
Title: The role of S126 in the Staphylococcus equorum MnSOD activity and stability.
Authors: Retnoningrum, D.S. / Yoshida, H. / Razani, M.D. / Muliadi, R. / Meidianto, V.F. / 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
DepositionOct 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 21, 2021Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)141,43812
Polymers141,1096
Non-polymers3306
Water17,889993
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1464
Polymers47,0362
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-16.8 kcal/mol
Surface area17440 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1464
Polymers47,0362
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-16.9 kcal/mol
Surface area17510 Å2
MethodPISA
3
E: Superoxide dismutase
F: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1464
Polymers47,0362
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15.9 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.287, 131.732, 80.188
Angle α, β, γ (deg.)90.000, 110.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

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 - 1972 - 197
21ALAALABB2 - 1972 - 197
12LYSLYSAA2 - 1992 - 199
22LYSLYSCC2 - 1992 - 199
13LYSLYSAA2 - 1992 - 199
23LYSLYSDD2 - 1992 - 199
14LYSLYSAA2 - 1992 - 199
24LYSLYSEE2 - 1992 - 199
15LYSLYSAA2 - 1992 - 199
25LYSLYSFF2 - 1992 - 199
16ALAALABB2 - 1972 - 197
26ALAALACC2 - 1972 - 197
17ALAALABB2 - 1972 - 197
27ALAALADD2 - 1972 - 197
18ALAALABB2 - 1972 - 197
28ALAALAEE2 - 1972 - 197
19ALAALABB2 - 1972 - 197
29ALAALAFF2 - 1972 - 197
110LYSLYSCC2 - 1992 - 199
210LYSLYSDD2 - 1992 - 199
111LYSLYSCC2 - 1992 - 199
211LYSLYSEE2 - 1992 - 199
112LYSLYSCC2 - 1992 - 199
212LYSLYSFF2 - 1992 - 199
113LYSLYSDD2 - 1992 - 199
213LYSLYSEE2 - 1992 - 199
114LYSLYSDD2 - 1992 - 199
214LYSLYSFF2 - 1992 - 199
115LYSLYSEE2 - 1992 - 199
215LYSLYSFF2 - 1992 - 199

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9999, 0.008988, -0.010892), (-0.012385, -0.187607, 0.982166), (0.006784, 0.982203, 0.187699)27.05673, -33.70409, 27.854759
3given(1), (1), (1)
4given(0.999883, 0.014029, 0.006159), (0.011115, -0.387495, -0.921805), (-0.010546, 0.921765, -0.387605)-0.27145, -11.32766, 35.969688
5given(1), (1), (1)
6given(-0.999993, -0.003783, 5.2E-5), (-0.003709, 0.977579, -0.210537), (0.000746, -0.210535, -0.977586)26.932699, 3.40154, 23.72019
7given(1), (1), (1)
8given(0.997199, 0.010822, 0.074009), (-0.057516, -0.52161, 0.851243), (0.047816, -0.853115, -0.519527)-1.09222, -35.26965, 7.93956
9given(1), (1), (1)
10given(-0.99746, -0.001142, -0.07122), (0.049094, -0.735458, -0.675789), (-0.051608, -0.677569, 0.733646)28.09701, -19.242849, -5.14346
11given(1), (1), (1)
12given(-0.999991, -0.002887, 0.003006), (-0.003449, 0.978112, -0.20805), (-0.002339, -0.208059, -0.978114)27.1073, 3.52229, 23.798771
13given(1), (1), (1)
14given(0.999932, -0.010984, -0.003881), (-0.007853, -0.389419, -0.921027), (0.008605, 0.920995, -0.389479)-0.36874, -11.01715, 35.650558
15given(1), (1), (1)
16given(-0.996109, -0.007623, -0.087801), (0.064693, -0.739793, -0.669717), (-0.059849, -0.672791, 0.737408)28.139771, -19.49263, -4.97295
17given(1), (1), (1)
18given(0.996474, 0.00864, 0.083457), (-0.066382, -0.527149, 0.847176), (0.051314, -0.849729, -0.524717)-1.29476, -35.156139, 7.93415
19given(1), (1), (1)
20given(-0.999922, 0.009462, 0.008124), (-0.012079, -0.572899, -0.819537), (-0.003101, -0.819571, 0.572969)27.493839, -16.612431, -8.65963
21given(1), (1), (1)
22given(0.995919, 0.013952, 0.089168), (0.080495, -0.58414, -0.807652), (0.040818, 0.811533, -0.582879)-0.79916, -16.573919, 32.92955
23given(1), (1), (1)
24given(-0.996221, -0.002007, -0.086831), (-0.081001, -0.339327, 0.937175), (-0.031345, 0.940666, 0.337882)28.72031, -34.41111, 23.41312
25given(1), (1), (1)
26given(-0.996917, -0.009405, -0.077897), (-0.070428, -0.330366, 0.941222), (-0.034587, 0.943806, 0.328685)28.168261, -34.376431, 23.56716
27given(1), (1), (1)
28given(0.997217, 0.003294, 0.074481), (0.062737, -0.576798, -0.814474), (0.040278, 0.81688, -0.5754)-1.10613, -16.09099, 32.972599
29given(1), (1), (1)
30given(-0.999953, 0.009222, 0.002948), (0.00806, 0.961627, -0.27424), (-0.005363, -0.274204, -0.961657)27.576731, 3.10491, 22.600771

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Components

#1: Protein
Superoxide dismutase


Mass: 23518.092 Da / Num. of mol.: 6 / Mutation: D13R, S126C
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 993 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Magnesium chloride, Calcium chloride, Imidazole, MES, PEG 550 MME, 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: 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: 1.88→46.25 Å / Num. obs: 106216 / % possible obs: 97.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Net I/σ(I): 10.8 / Num. measured all: 370052 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.910.5081884052160.8510.310.5972.196.3
10.3-46.250.018242967510.0110.02137.997.2

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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: 1.88→42.44 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.182 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 5222 4.9 %RANDOM
Rwork0.1567 ---
obs0.1599 100960 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.42 Å2 / Biso mean: 26.218 Å2 / Biso min: 9.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20.05 Å2
2---0.17 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.88→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9567 0 6 993 10566
Biso mean--19.39 34.79 -
Num. residues----1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178627
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.63513453
X-RAY DIFFRACTIONr_angle_other_deg1.271.57420141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.8035.2981223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02825.065539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.654151557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.021524
X-RAY DIFFRACTIONr_chiral_restr0.0550.21241
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212149
X-RAY DIFFRACTIONr_gen_planes_other00.021979
X-RAY DIFFRACTIONr_rigid_bond_restr9.011318485
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1599TIGHT POSITIONAL0.310.11
1A1599TIGHT POSITIONAL0.330.11
1A1599TIGHT POSITIONAL0.370.11
1A1599TIGHT POSITIONAL0.310.11
1A1599TIGHT POSITIONAL0.360.11
1A1599TIGHT POSITIONAL0.260.11
1A1585TIGHT THERMAL12.421.12
2A1599TIGHT THERMAL9.531.12
3A1599TIGHT THERMAL5.451.12
4A1599TIGHT THERMAL10.431.12
5A1599TIGHT THERMAL12.581.12
6B1585TIGHT THERMAL7.781.12
7B1585TIGHT THERMAL11.661.12
8B1585TIGHT THERMAL12.31.12
9B1585TIGHT THERMAL12.331.12
10C1599TIGHT THERMAL8.431.12
11C1599TIGHT THERMAL10.371.12
12C1599TIGHT THERMAL11.181.12
13D1599TIGHT THERMAL10.061.12
14D1599TIGHT THERMAL11.841.12
15E1599TIGHT THERMAL5.871.12
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 379 -
Rwork0.208 7341 -
all-7720 -
obs--95.96 %

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