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- PDB-6d52: Superoxide dismutase SodCI of Salmonella enterica serovar Typhimu... -

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Basic information

Entry
Database: PDB / ID: 6d52
TitleSuperoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6 Angstrom resolution
ComponentsSuperoxide dismutase [Cu-Zn] 1
KeywordsOXIDOREDUCTASE / Superoxide dismutase / SOD / Cu-Zn superoxide dismutase
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / periplasmic space / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn] 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNewhouse IX, P.W. / Forest, K.T. / Satyshur, K.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)IOS 1353674 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007215 United States
CitationJournal: to be published
Title: Superoxide dismutase SodCI of Salmonella enterica serovar Typhimurium at 1.6 Angstrom resolution
Authors: Newhouse IX, P.W. / Satyshur, K.A. / Forest, K.T. / Slauch, J.M.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
Item: _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
B: Superoxide dismutase [Cu-Zn] 1
D: Superoxide dismutase [Cu-Zn] 1
C: Superoxide dismutase [Cu-Zn] 1
A: Superoxide dismutase [Cu-Zn] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,26712
Polymers69,7514
Non-polymers5168
Water11,872659
1
B: Superoxide dismutase [Cu-Zn] 1
A: Superoxide dismutase [Cu-Zn] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1336
Polymers34,8752
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-13 kcal/mol
Surface area13550 Å2
MethodPISA
2
D: Superoxide dismutase [Cu-Zn] 1
C: Superoxide dismutase [Cu-Zn] 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1336
Polymers34,8752
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-14 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.530, 68.571, 122.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Superoxide dismutase [Cu-Zn] 1 / sodCI


Mass: 17437.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 4/74) (bacteria)
Strain: 4/74 / Gene: sodC1, sodC, STM474_1035 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: E8XDJ8, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 8000, sodium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9839 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9839 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 73177 / % possible obs: 96.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 16.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Net I/σ(I): 17.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5783 / CC1/2: 0.894 / Rpim(I) all: 0.209 / Rrim(I) all: 0.517 / % possible all: 77.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2992)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EQW

1eqw


Resolution: 1.6→28 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 19.07
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1773 2.4 %random
Rwork0.1597 ---
obs0.1603 73159 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4575 0 8 659 5242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074783
X-RAY DIFFRACTIONf_angle_d0.8756501
X-RAY DIFFRACTIONf_dihedral_angle_d12.8812877
X-RAY DIFFRACTIONf_chiral_restr0.052708
X-RAY DIFFRACTIONf_plane_restr0.006861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62290.32681100.31484285X-RAY DIFFRACTION73
1.6229-1.64710.2721150.26754676X-RAY DIFFRACTION79
1.6471-1.67290.26791260.24164997X-RAY DIFFRACTION85
1.6729-1.70030.23651410.22315313X-RAY DIFFRACTION91
1.7003-1.72960.2321320.20865615X-RAY DIFFRACTION95
1.7296-1.7610.22661430.19675762X-RAY DIFFRACTION98
1.761-1.79490.23241390.18245835X-RAY DIFFRACTION99
1.7949-1.83150.21211560.16785855X-RAY DIFFRACTION100
1.8315-1.87140.17391380.16945912X-RAY DIFFRACTION100
1.8714-1.91490.16491470.1475858X-RAY DIFFRACTION100
1.9149-1.96280.19261410.14975914X-RAY DIFFRACTION100
1.9628-2.01580.15931490.15365869X-RAY DIFFRACTION100
2.0158-2.07510.19251440.15195861X-RAY DIFFRACTION100
2.0751-2.14210.16781470.14565892X-RAY DIFFRACTION100
2.1421-2.21860.17911420.14985885X-RAY DIFFRACTION100
2.2186-2.30740.17121460.15085842X-RAY DIFFRACTION100
2.3074-2.41230.18611440.15095908X-RAY DIFFRACTION100
2.4123-2.53940.21031440.15935898X-RAY DIFFRACTION100
2.5394-2.69840.19131370.15595861X-RAY DIFFRACTION100
2.6984-2.90660.17721450.15625866X-RAY DIFFRACTION100
2.9066-3.19870.19151400.15635911X-RAY DIFFRACTION100
3.1987-3.66070.16461380.1535861X-RAY DIFFRACTION100
3.6607-4.60870.15391480.13195883X-RAY DIFFRACTION100
4.6087-27.90460.18581440.17335868X-RAY DIFFRACTION100

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