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- PDB-5g3f: Preserving Metallic Sites Affected by Radiation Damage the CuT2 C... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5g3f | ||||||
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Title | Preserving Metallic Sites Affected by Radiation Damage the CuT2 CAse in Thermus Thermophilus Multicopper Oxidase | ||||||
![]() | THERMUS THERMOPHILUS MULTICOPPER OXIDASE | ||||||
![]() | OXIDOREDUCTASE / MULTICOPPER OXIDASA / RADIATION DAMAGE / METALLIC SITES / MACROMOLECULAR CRYSTALLOGRAPHY / RADICAL SCAVENGERS | ||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / ferroxidase activity / outer membrane-bounded periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Rudino, E. | ||||||
![]() | ![]() Title: Preserving Metallic Sites Affected by Radiation Damage the Cut2 Case in Thermus Thermophilus Multicopper Oxidase Authors: Ruiz-Arellano, R. / Diaz, A. / Rosas, E. / Stojanoff, V. / Rudino, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
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PDB format | ![]() | 93.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 458.4 KB | Display | ![]() |
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Full document | ![]() | 462.7 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g3bC ![]() 5g3cC ![]() 5g3dC ![]() 5g3eC ![]() 5g3gC ![]() 5g3hC ![]() 2yaeS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48791.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 379 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-MRD / ( #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→19.72 Å / Num. obs: 292656 / % possible obs: 98.4 % / Observed criterion σ(I): 19.25 / Redundancy: 6.3 % / Biso Wilson estimate: 12.87 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.79→1.86 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.04 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YAE Resolution: 1.82→19.707 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 16.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→19.707 Å
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Refine LS restraints |
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LS refinement shell |
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