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- PDB-3mnd: Crystallographic analysis of the cystosolic cu/zn Superoxide dism... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mnd | ||||||
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Title | Crystallographic analysis of the cystosolic cu/zn Superoxide dismutase from taenia solium | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
![]() | OXIDOREDUCTASE / CU/ZN-SUPEROXIDE DISMUTASE / METAL-MEDIATED SELF-ASSEMBLY | ||||||
Function / homology | ![]() superoxide dismutase / superoxide dismutase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hernandez-Santoyo, A. / Rodriguez-Romero, A. | ||||||
![]() | ![]() Title: Crystal structure of Cu / Zn superoxide dismutase from Taenia solium reveals metal-mediated self-assembly Authors: Hernandez-Santoyo, A. / Landa, A. / Gonzalez-Mondragon, E. / Pedraza-Escalona, M. / Parra-Unda, R. / Rodriguez-Romero, A. #1: Journal: Int.J.Parasitol. / Year: 2002 Title: Cloning, production and characterisation of a recombinant Cu/Zn superoxide dismutase from Taenia solium. Authors: Castellanos-Gonzalez, A. / Jimenez, L. / Landa, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.6 KB | Display | ![]() |
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PDB format | ![]() | 51.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1to4S 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
#1: Protein | Mass: 15613.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 42.24 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 20% w/v polyethylene glycol monomethyl ether 2,000, in hexahydrate 0.1 M Tris buffer pH 8.5 and 0.01 M Nickel (II) chloridE., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 14, 2005 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.64 Å / Num. obs: 13829 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.94 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7 |
Reflection shell | Highest resolution: 2.2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TO4 Resolution: 2.2→39.64 Å / SU ML: 0.28 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.96 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.64 Å
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Refine LS restraints |
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LS refinement shell |
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