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- PDB-1to5: Structure of the cytosolic Cu,Zn SOD from S. mansoni -

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Basic information

Entry
Database: PDB / ID: 1to5
TitleStructure of the cytosolic Cu,Zn SOD from S. mansoni
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / beta-barrel
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / 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
ACETATE ION / COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCardoso, R.M.F. / Silva, C.H.T.P. / Ulian de Araujo, A.P. / Tanaka, T. / Tanaka, M. / Garratt, R.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni.
Authors: Cardoso, R.M. / Silva, C.H. / Ulian de Araujo, A.P. / Tanaka, T. / Tanaka, M. / Garratt, R.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Expression and preliminary X-ray diffraction studies of cytosolic Cu,Zn superoxide dismutase from Schistosoma mansoni
Authors: Cardoso, R.M.F. / Silva, C.H.T.P. / Araujo, A.P.U. / Tanaka, T. / Tanaka, M. / Garratt, R.C.G.
History
DepositionJun 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)64,47413
Polymers63,8994
Non-polymers5759
Water10,971609
1
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2667
Polymers31,9492
Non-polymers3175
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-11 kcal/mol
Surface area14000 Å2
MethodPISA
2
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2076
Polymers31,9492
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-10 kcal/mol
Surface area13840 Å2
MethodPISA
3
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules

C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,47413
Polymers63,8994
Non-polymers5759
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area4480 Å2
ΔGint-27 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.64, 78.24, 95.18
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains two Cu,Zn SOD biological dimers

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Components

#1: Protein
Superoxide dismutase /


Mass: 15974.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SOD / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q01137, 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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.22 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 30% PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5408 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 19, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5408 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. all: 29152 / Num. obs: 25229 / % possible obs: 86.5 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rsym value: 0.08 / Net I/σ(I): 17.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 2088 / Rsym value: 0.172 / % possible all: 72.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1289 -random
Rwork0.176 ---
all-25185 --
obs-25185 86.8 %-
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--0.75 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→58.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 12 609 5099
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_mcangle_it1.9
X-RAY DIFFRACTIONc_mcbond_it1.24
X-RAY DIFFRACTIONc_scangle_it2.61
X-RAY DIFFRACTIONc_scbond_it1.91
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.293 195 -
Rwork0.194 --
obs-3687 77.8 %

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