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- PDB-5k7a: Crystal structure of laccase fron Thermus thermophilus HB27 (sodi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k7a | ||||||
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Title | Crystal structure of laccase fron Thermus thermophilus HB27 (sodium nitrate 1.5 min) | ||||||
![]() | Laccase![]() | ||||||
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Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Rudino-Pinera, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Preserving metalic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase Authors: Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Stojanoff, V. / Rudino-Pinera, 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 | ![]() | 132.1 KB | Display | ![]() |
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PDB format | ![]() | 101.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xu9S 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 on special symmetry positions |
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Components
#1: Protein | ![]() Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: UNP residues 24-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-MPD / ( ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES, pH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.5→19.719 Å / Num. obs: 79274 / % possible obs: 97.3 % / Observed criterion σ(I): 3.65 / Redundancy: 4.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 4.39 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.49 / % possible all: 86.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 2XU9 Resolution: 1.5→19.719 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.16 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.49 Å2 / Biso mean: 14.8381 Å2 / Biso min: 0 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.719 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28
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