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- PDB-1to4: Structure of the cytosolic Cu,Zn SOD from S. mansoni -

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Basic information

Entry
Database: PDB / ID: 1to4
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 / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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. / da Silva, C.T.H.P. / de Araujo, A.P.U. / Tanaka, T. / Tanaka, M. / Garratt, R.C.
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: Advisory / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,41412
Polymers63,8994
Non-polymers5168
Water13,962775
1
A: Superoxide dismutase
B: 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 area1250 Å2
ΔGint-11 kcal/mol
Surface area13870 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 area1240 Å2
ΔGint-11 kcal/mol
Surface area13790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.27, 95.08, 78.41
Angle α, β, γ (deg.)90.00, 103.55, 90.00
Int Tables number4
Space group name H-MP1211
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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / 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, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.55→18 Å / Num. obs: 80845 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rsym value: 0.051 / Net I/σ(I): 24.8
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 9.2 / Rsym value: 0.126 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.09refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→18 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.915 / SU ML: 0.035 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4056 5 %RANDOM
Rwork0.157 ---
obs0.158 80801 99.7 %-
all-80801 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.071 Å0.076 Å
Refinement stepCycle: LAST / Resolution: 1.55→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 8 775 5259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.926129
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8545617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43124.898196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.98415701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8061516
X-RAY DIFFRACTIONr_chiral_restr0.1120.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023496
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.225
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.53013
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71324757
X-RAY DIFFRACTIONr_scbond_it2.56531532
X-RAY DIFFRACTIONr_scangle_it4.0674.51366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.213 301
Rwork0.185 5622
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11130.029-0.10560.4269-0.15160.270.00990.0085-0.0068-0.00070.00030.0107-0.01520.0001-0.01010.0104-0.00070.00020.01790.00250.013720.440210.5720.0276
20.10240.0302-0.10680.25460.10530.2491-0.021-0.0083-0.0072-0.00690.0025-0.00150.0105-0.00670.01850.0002-0.00080.0020.02650.00050.020113.7928-10.600216.7471
30.0899-0.089-0.04780.52330.02240.29810.00210.01140.00080.0098-0.0126-0.0392-0.0213-0.01480.01050.02930.0055-0.00210.00740.0030.00679.792860.045337.7102
40.10680.1284-0.03290.3982-0.1290.13110.0088-0.0001-0.00080.0358-0.00480.0033-0.01090.0044-0.0040.03730.00270.00230.00920.00140.0037.799881.244255.6636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1534 - 156
2X-RAY DIFFRACTION2BB1 - 1534 - 156
3X-RAY DIFFRACTION3CC1 - 1534 - 156
4X-RAY DIFFRACTION4DD1 - 1534 - 156

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