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- PDB-6zs1: Chaetomium thermophilum CuZn-superoxide dismutase -

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Basic information

Entry
Database: PDB / ID: 6zs1
TitleChaetomium thermophilum CuZn-superoxide dismutase
ComponentsSuperoxide dismutase [Cu-Zn]
KeywordsMETAL BINDING PROTEIN / thermophilic fungus / superoxide / antioxidant / thermostability / metalloenzyme / metal-binding protein
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / copper ion binding
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
COPPER (II) ION / PHOSPHATE ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsPapageorgiou, A.C. / Mohsin, I.
Citation
Journal: Protein Pept.Lett. / Year: 2021
Title: Crystal Structure of a Cu,Zn Superoxide Dismutase From the Thermophilic Fungus Chaetomium thermophilum.
Authors: Mohsin, I. / Zhang, L.Q. / Li, D.C. / Papageorgiou, A.C.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2010
Title: Expression, purification and crystallization of Chaetomium thermophilum Cu,Zn superoxide dismutase.
Authors: Wakadkar, S. / Zhang, L.-Q. / Li, D.-C. / Haikarainen, T. / Dhavala, P. / Papageorgiou, A.C.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: citation / database_2 / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Cu-Zn]
B: Superoxide dismutase [Cu-Zn]
C: Superoxide dismutase [Cu-Zn]
D: Superoxide dismutase [Cu-Zn]
E: Superoxide dismutase [Cu-Zn]
F: Superoxide dismutase [Cu-Zn]
G: Superoxide dismutase [Cu-Zn]
H: Superoxide dismutase [Cu-Zn]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,10846
Polymers130,9528
Non-polymers2,15538
Water44,2272455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-295 kcal/mol
Surface area49490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.110, 89.110, 310.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Superoxide dismutase [Cu-Zn]


Mass: 16369.033 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: There is clear density for Ile at residue 48 (coordinate file numbering) despite the original sequence contains a Thr at the same position YVE sequence at the N-terminal belongs to the ...Details: There is clear density for Ile at residue 48 (coordinate file numbering) despite the original sequence contains a Thr at the same position YVE sequence at the N-terminal belongs to the expression vector secretion signal
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0013440 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: G0S1F8, superoxide dismutase

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Non-polymers , 6 types, 2493 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.76 Å3/Da / Density % sol: 55.9 % / Description: Bipyramids
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: NaK phosphate 1.2-1.4 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8047 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8047 Å / Relative weight: 1
ReflectionResolution: 1.56→38.59 Å / Num. obs: 194568 / % possible obs: 98 % / Redundancy: 5 % / Biso Wilson estimate: 19.25 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.008 / Net I/σ(I): 15
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 29651 / CC1/2: 0.416 / Rrim(I) all: 0.146 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f1g

1f1g


Resolution: 1.56→38.59 Å / SU ML: 0.2459 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0058
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2044 9737 5.01 %
Rwork0.1727 184679 -
obs0.1743 194416 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.81 Å2
Refinement stepCycle: LAST / Resolution: 1.56→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9012 0 86 2455 11553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00899358
X-RAY DIFFRACTIONf_angle_d1.046812746
X-RAY DIFFRACTIONf_chiral_restr0.06331447
X-RAY DIFFRACTIONf_plane_restr0.00691716
X-RAY DIFFRACTIONf_dihedral_angle_d14.25193380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.610.42248960.390617244X-RAY DIFFRACTION91.32
1.61-1.680.36739420.342717680X-RAY DIFFRACTION94
1.68-1.750.30329590.271318131X-RAY DIFFRACTION96.28
1.75-1.840.2689870.23818550X-RAY DIFFRACTION98.5
1.84-1.960.24099910.191318807X-RAY DIFFRACTION99.97
1.96-2.110.20679930.163318867X-RAY DIFFRACTION100
2.11-2.320.20279900.165918829X-RAY DIFFRACTION99.98
2.32-2.660.19919920.160618856X-RAY DIFFRACTION99.98
2.66-3.350.18149950.150518876X-RAY DIFFRACTION99.99
3.35-38.590.15479920.133618839X-RAY DIFFRACTION99.45

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