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- PDB-5in2: Crystal structure of extra cellular Cu/Zn Superoxide Dismutase fr... -

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Basic information

Entry
Database: PDB / ID: 5in2
TitleCrystal structure of extra cellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors
ComponentsExtracellular superoxide dismutase [Cu-Zn]
KeywordsOXIDOREDUCTASE / Ec Ov-SOD / Onchcerca Volvulus / prodrug
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding / extracellular region
Similarity search - Function
Copper/Zinc superoxide dismutase signature 1. / 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
Similarity search - Domain/homology
AZIDE ION / COPPER (II) ION / TRIETHYLENE GLYCOL / Extracellular superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesOnchocerca volvulus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMoustafa, A. / Betzel, C. / Perbandt, M.
Funding support Egypt, Germany, 2items
OrganizationGrant numberCountry
Minstry of Higher Education Egypt
DAAD Germany
CitationJournal: To Be Published
Title: Crystal structure of extracellular Cu/Zn Superoxide Dismutase from Onchocerca volvulus at 1.5 Angstrom; Insight into novel binding site and new inhibitors
Authors: Moustafa, A. / Betzel, C. / Perbandt, M.
History
DepositionMar 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6438
Polymers16,0981
Non-polymers5457
Water1,65792
1
A: Extracellular superoxide dismutase [Cu-Zn]
hetero molecules

A: Extracellular superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,28516
Polymers32,1962
Non-polymers1,09014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Unit cell
Length a, b, c (Å)58.410, 58.410, 77.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Extracellular superoxide dismutase [Cu-Zn] / EC-SOD


Mass: 16097.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Onchocerca volvulus (invertebrata) / Gene: sod-4, sod2 / Plasmid: pASKIBA16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07449, superoxide dismutase

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Non-polymers , 8 types, 99 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 % w/v PEG 20 000, 20 % v/v PEG MME 550, 0.03 M of each ethylene glycol and 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.55→25.292 Å / Num. obs: 22806 / % possible obs: 100 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.1
Reflection shellHighest resolution: 1.55 Å / Rmerge(I) obs: 0.42

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KBE

3kbe


Resolution: 1.55→25.292 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 17.31
RfactorNum. reflection% reflection
Rfree0.181 1185 5.2 %
Rwork0.1596 --
obs0.1607 22776 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→25.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 27 92 1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091171
X-RAY DIFFRACTIONf_angle_d1.241580
X-RAY DIFFRACTIONf_dihedral_angle_d13.279411
X-RAY DIFFRACTIONf_chiral_restr0.053173
X-RAY DIFFRACTIONf_plane_restr0.006211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.62050.2441570.20072658X-RAY DIFFRACTION100
1.6205-1.7060.22811350.18352652X-RAY DIFFRACTION100
1.706-1.81280.1891510.16162650X-RAY DIFFRACTION100
1.8128-1.95270.16661270.14482721X-RAY DIFFRACTION100
1.9527-2.14920.18481240.13662682X-RAY DIFFRACTION100
2.1492-2.45990.16461570.14142684X-RAY DIFFRACTION100
2.4599-3.09840.17581720.15892708X-RAY DIFFRACTION100
3.0984-25.29560.18091620.16852836X-RAY DIFFRACTION100

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