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- PDB-6vbs: The C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolu... -

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Basic information

Entry
Database: PDB / ID: 6vbs
TitleThe C2 Crystal form of SodCI Superoxide Dismutase at 1.7 A resolution with 6 molecules in the asymmetric unit.
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXYGEN BINDING / Superoxide Dismutase / virulence factor / peptidoglycan binding
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / periplasmic space / copper ion binding / identical protein binding / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn] / Superoxide dismutase [Cu-Zn] 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSatyshur, K.A. / Forest, K.T. / Newhouse, P.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007215 United States
CitationJournal: To Be Published
Title: Structure and Muropeptide Binding of the Virulence Factor Superoxide Dismutase C1 from Salmonella Typhimurium
Authors: Newhouse, P.W. / Satyshur, K.A. / Slauch, J.M. / Forest, K.T.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,78422
Polymers104,6266
Non-polymers1,15816
Water15,295849
1
A: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1336
Polymers34,8752
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-13 kcal/mol
Surface area13820 Å2
MethodPISA
2
B: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3268
Polymers34,8752
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-42 kcal/mol
Surface area14030 Å2
MethodPISA
3
C: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3268
Polymers34,8752
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-39 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.838, 69.474, 95.288
Angle α, β, γ (deg.)90.000, 116.888, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11F-395-

HOH

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Components

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 17437.734 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: sodC1, AAP89_24585, ABO94_13165, AF480_24525, AF488_17800, AF489_22535, AIC76_23135, AU613_25900, AXR84_22600, AXU58_25005, C2253_23510, CD48_19550, CE87_24875, CET98_19490, CQG18_24025, CVR97_ ...Gene: sodC1, AAP89_24585, ABO94_13165, AF480_24525, AF488_17800, AF489_22535, AIC76_23135, AU613_25900, AXR84_22600, AXU58_25005, C2253_23510, CD48_19550, CE87_24875, CET98_19490, CQG18_24025, CVR97_00185, D4369_24860, D4380_23405, D4401_24550, D4E62_23815, D6360_24640, D7F20_18080, D7H43_24310, DD95_21320, DJ388_22940, DKJ11_15870, DKU57_23325, DLM31_21285, DO698_19845, DOJ90_22365, DOQ88_23710, DQ848_24435, DRM14_23695, DSF69_10260, DSR36_22945, DUW48_23400, EBO41_23675, EBP31_23480, EGU67_12495, EHB24_23490, EHC98_23755, EIW53_22710, F0A00_10055, F0A01_03930, F0A02_16630, F0A03_14260, F0A04_11295, F0A05_20695, F0A06_10485, F0U66_16995, FKA80_23505, FKA81_22545, FKA82_23465, FKA83_23450, FKA84_23540, FKA85_22415, FKA86_23320, FKA87_22565, FKA88_23655, FKA89_19440, FKA90_23025, FKA91_22685, FKA92_23550, FKA93_23530, FKA94_23705, FKA95_23590, FKA96_23695, FKA97_23460, FKA98_23465, FKA99_23670, FKB00_23595, FKB01_23750, FKB02_23725, FKB03_23595, FKB12_23280, FKB15_23500, FKB18_22510, FKB19_23085, FYL57_20425, FYL66_21285, FYL68_13470, FYL69_02095, FYL71_08605, FYL73_12165, FYL74_21170, FYL75_22020, FYL77_03645, FYL81_07750, FYL84_20475, FYL90_20575, FYL92_04365, FYL93_18435, FYL94_21135, FYL96_21895, FYM06_15765, FYM08_18765, FYM09_02430, FYM54_04305, FZ992_22195, FZ993_21050, FZ994_04265, FZ995_00435, FZ996_12505, FZ997_14980, FZ998_14695, FZ999_05915, GW08_24555, JO10_24570, LZ63_20420, NCTC13348_01621, NG18_23390, NU83_09530, QA89_23615, QD15_24180, RJ78_24990, SAMEA4398682_02945, Y934_24990, YG50_23900, YI33_24375, YR17_24730, ZB89_24710, ZC54_24870
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS
References: UniProt: A0A0D6GQL3, UniProt: P0CW86*PLUS, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.16 Å3/Da / Density % sol: 42.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mg/ml SODC1 plus 1.2 mM trachaeal cytotoxin in 20 mM Tris pH 6.6 150 mM NaCl set up as hanging drop with mother liquor Bis-Tris 0.05M, Ammonium Sulfate 0.05M, 30% Pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.528→84.987 Å / Num. obs: 187907 / % possible obs: 79.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 14.4
Reflection shellResolution: 1.528→1.639 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5352 / CC1/2: 0.768 / Rpim(I) all: 0.297 / Rrim(I) all: 0.671 / % possible all: 21

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20190607)data processing
XDSVERSION Mar 15, 2019 BUILT=20190606data reduction
STARANISOVersion 2.2.19data scaling
PHENIX1.17phasing
PHENIX1.17refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D52

6d52


Resolution: 1.7→35.88 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.1984
RfactorNum. reflection% reflection
Rfree0.2189 3497 1.86 %
Rwork0.1785 --
obs0.1792 187907 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 32 849 7697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087031
X-RAY DIFFRACTIONf_angle_d1.03069539
X-RAY DIFFRACTIONf_chiral_restr0.05381041
X-RAY DIFFRACTIONf_plane_restr0.00691264
X-RAY DIFFRACTIONf_dihedral_angle_d5.7949971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.2611100.24745789X-RAY DIFFRACTION76.72
1.72-1.750.3091220.23126432X-RAY DIFFRACTION85
1.75-1.770.27711380.22367259X-RAY DIFFRACTION95.82
1.77-1.80.28251430.21327446X-RAY DIFFRACTION99.7
1.8-1.830.25011440.20737585X-RAY DIFFRACTION99.72
1.83-1.860.22681430.18977482X-RAY DIFFRACTION99.82
1.86-1.90.26861430.18497568X-RAY DIFFRACTION99.82
1.9-1.930.24251480.18217571X-RAY DIFFRACTION99.9
1.93-1.970.2461400.17067464X-RAY DIFFRACTION99.78
1.97-2.020.16821430.17127552X-RAY DIFFRACTION99.79
2.02-2.060.21181430.16797561X-RAY DIFFRACTION99.82
2.06-2.110.17961430.16657508X-RAY DIFFRACTION99.57
2.11-2.170.231420.17167541X-RAY DIFFRACTION99.62
2.17-2.230.22571420.17487479X-RAY DIFFRACTION99.43
2.24-2.310.26111400.16647513X-RAY DIFFRACTION99.36
2.31-2.390.23471440.16287473X-RAY DIFFRACTION97.74
2.39-2.490.2321360.16147202X-RAY DIFFRACTION96.55
2.49-2.60.19421440.16567529X-RAY DIFFRACTION99.88
2.6-2.740.22961460.16297574X-RAY DIFFRACTION99.86
2.74-2.910.24181430.16677524X-RAY DIFFRACTION99.83
2.91-3.130.17321360.16437520X-RAY DIFFRACTION99.71
3.13-3.450.17261410.16677517X-RAY DIFFRACTION99.39
3.45-3.940.21171430.16787465X-RAY DIFFRACTION98.93
3.94-4.970.15491410.16257366X-RAY DIFFRACTION97.2
4.97-35.880.31281390.24957490X-RAY DIFFRACTION99.3

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