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- PDB-5cu9: CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), APO -

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Basic information

Entry
Database: PDB / ID: 5cu9
TitleCANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), APO
ComponentsCell surface Cu-only superoxide dismutase 5
KeywordsOXIDOREDUCTASE / ANTIOXIDANT / OXIDATIVE BURST / ZINC LOOP / DISULFIDE BOND / EXTRACELLULAR
Function / homology
Function and homology information


symbiont defense to host-produced reactive oxygen species / cellular response to superoxide / hyphal cell wall / fungal-type cell wall / evasion of host immune response / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / side of membrane ...symbiont defense to host-produced reactive oxygen species / cellular response to superoxide / hyphal cell wall / fungal-type cell wall / evasion of host immune response / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / side of membrane / cellular response to oxidative stress / copper ion binding / cell surface / extracellular region
Similarity search - Function
Filamin/ABP280 repeat-like / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell surface Cu-only superoxide dismutase 5
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWaninger-Saroni, J.J. / Taylor, A.B. / Hart, P.J. / Galaleldeen, A.
CitationJournal: To Be Published
Title: CANDIDA ALBICANS SUPEROXIDE DISMUTASE 5 (SOD5), APO
Authors: Waninger-Saroni, J.J. / Taylor, A.B. / Hart, P.J. / Galaleldeen, A.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell surface Cu-only superoxide dismutase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0893
Polymers16,8971
Non-polymers1922
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.531, 37.699, 102.875
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 Cell surface Cu-only superoxide dismutase 5 / Predicted GPI-anchored protein 3


Mass: 16896.715 Da / Num. of mol.: 1 / Fragment: UNP residues 27-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: SOD5, PGA3, SOD31, CaO19.2060, CaO19.9607 / Plasmid: pAG8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q5AD07, superoxide dismutase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.48→102.87 Å / Num. obs: 22964 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.042 / Net I/σ(I): 16.6
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N3T

4n3t


Resolution: 1.48→51.438 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1994 8.71 %Random selection
Rwork0.2023 ---
obs0.2071 22891 98.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.7 Å2
Refinement stepCycle: LAST / Resolution: 1.48→51.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1147 0 10 59 1216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051189
X-RAY DIFFRACTIONf_angle_d0.9381618
X-RAY DIFFRACTIONf_dihedral_angle_d10.606430
X-RAY DIFFRACTIONf_chiral_restr0.068180
X-RAY DIFFRACTIONf_plane_restr0.004213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.5170.42251410.35291482X-RAY DIFFRACTION100
1.517-1.5580.38391410.32071481X-RAY DIFFRACTION100
1.558-1.60390.36151400.30411467X-RAY DIFFRACTION100
1.6039-1.65570.35291430.28721495X-RAY DIFFRACTION100
1.6557-1.71480.38771430.27021494X-RAY DIFFRACTION100
1.7148-1.78350.28621360.25031454X-RAY DIFFRACTION99
1.7835-1.86470.28051440.21761499X-RAY DIFFRACTION100
1.8647-1.9630.28211420.20581499X-RAY DIFFRACTION99
1.963-2.0860.26941420.20291479X-RAY DIFFRACTION99
2.086-2.2470.2861440.20241501X-RAY DIFFRACTION99
2.247-2.47320.24631440.20491507X-RAY DIFFRACTION99
2.4732-2.8310.26971440.20551502X-RAY DIFFRACTION98
2.831-3.56660.2541420.18891491X-RAY DIFFRACTION96
3.5666-51.46860.19691480.1691546X-RAY DIFFRACTION94

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