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Open data
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Basic information
Entry | Database: PDB / ID: 6zs1 | ||||||
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Title | Chaetomium thermophilum CuZn-superoxide dismutase | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | METAL BINDING PROTEIN / thermophilic fungus / superoxide / antioxidant / thermostability / metalloenzyme / metal-binding protein | ||||||
Function / homology | ![]() intracellular zinc ion homeostasis / superoxide dismutase / superoxide dismutase activity / cell redox homeostasis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Papageorgiou, A.C. / Mohsin, I. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 369.4 KB | Display | ![]() |
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PDB format | ![]() | 239.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 73.5 KB | Display | |
Data in CIF | ![]() | 112.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f1gS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | 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.) ![]() Gene: CTHT_0013440 / Production host: ![]() |
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-Non-polymers , 6 types, 2493 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CU / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.9 % / Description: Bipyramids |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: NaK phosphate 1.2-1.4 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Apr 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8047 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→38.59 Å
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Refine LS restraints |
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LS refinement shell |
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