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- PDB-6vbt: The P212121 Crystal structure of SodCI Superoxide Dismutase with ... -

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Basic information

Entry
Database: PDB / ID: 6vbt
TitleThe P212121 Crystal structure of SodCI Superoxide Dismutase with 2 molecules in the asymmetric unit at 1.7 A resolution
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsOXYGEN BINDING / Superoxide Dismutase / enzyme / 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
Similarity search - Function
Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
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 / SAD / 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 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1336
Polymers34,8752
Non-polymers2584
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Light Scattering SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-14 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.052, 57.428, 120.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Superoxide dismutase [Cu-Zn]


Mass: 17437.734 Da / Num. of mol.: 2
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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
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 0.1M KCN, 30% polyethylene glycol monomethyl ether 2000 (unbuffered)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
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: 1.487→60.274 Å / Num. obs: 36880 / % possible obs: 72.1 % / Redundancy: 12.4 % / Biso Wilson estimate: 15.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Net I/σ(I): 13.7
Reflection shellResolution: 1.487→1.631 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1844 / CC1/2: 0.866 / Rpim(I) all: 0.218 / Rrim(I) all: 0.651 / % possible all: 15.1
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
autoPROCv1.0.5data processing
XDSVERSION Mar 15, 2019 BUILT=20190606data reduction
STARANISOVersion 2.2.19 (11-May-2019data scaling
AutoSol1.17.1phasing
PHENIX1.17.1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→33.57 Å / SU ML: 0.1767 / Cross valid method: FREE R-VALUE / Phase error: 20.0265
RfactorNum. reflection% reflection
Rfree0.2123 3392 5.41 %
Rwork0.1748 --
obs0.1768 62649 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 4 414 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00472343
X-RAY DIFFRACTIONf_angle_d0.75193185
X-RAY DIFFRACTIONf_chiral_restr0.0456347
X-RAY DIFFRACTIONf_plane_restr0.0075424
X-RAY DIFFRACTIONf_dihedral_angle_d3.10411913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.28911030.28331754X-RAY DIFFRACTION68.37
1.72-1.750.28481080.24851897X-RAY DIFFRACTION74.87
1.75-1.780.23771290.22942269X-RAY DIFFRACTION87.45
1.78-1.810.26921320.20622339X-RAY DIFFRACTION91.28
1.81-1.840.25391400.20272419X-RAY DIFFRACTION95.02
1.84-1.870.23011440.19832509X-RAY DIFFRACTION99.62
1.87-1.910.24581450.19772632X-RAY DIFFRACTION99.96
1.91-1.950.22841470.19282518X-RAY DIFFRACTION99.89
1.95-1.990.26811450.20012574X-RAY DIFFRACTION100
1.99-2.030.24551420.1922546X-RAY DIFFRACTION100
2.03-2.090.22751500.2022577X-RAY DIFFRACTION100
2.09-2.140.19991490.18352534X-RAY DIFFRACTION99.89
2.14-2.20.24551470.18392589X-RAY DIFFRACTION100
2.2-2.280.20071430.17192543X-RAY DIFFRACTION100
2.28-2.360.21171460.1652551X-RAY DIFFRACTION100
2.36-2.450.23581520.1682557X-RAY DIFFRACTION98.29
2.45-2.560.22631480.16692552X-RAY DIFFRACTION100
2.56-2.70.20881430.17092541X-RAY DIFFRACTION100
2.7-2.870.21981470.16572564X-RAY DIFFRACTION100
2.87-3.090.18521480.16222549X-RAY DIFFRACTION100
3.09-3.40.20921490.16642574X-RAY DIFFRACTION99.71
3.4-3.890.19831430.162560X-RAY DIFFRACTION100
3.89-4.90.14351460.13782551X-RAY DIFFRACTION99.59
4.9-33.570.21551460.182558X-RAY DIFFRACTION99.82

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