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- PDB-2yaq: X-ray induced reduction of laccase from Thermus thermophilus HB27... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2yaq | ||||||
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Title | X-ray induced reduction of laccase from Thermus thermophilus HB27 (75. 0-87.5 percent dose) | ||||||
![]() | LACCASE![]() | ||||||
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Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Serrano-Posada, H. / Rudino-Pinera, E. | ||||||
![]() | ![]() Title: X-Ray-Induced Catalytic Active-Site Reduction of a Multicopper Oxidase: Structural Insights Into the Proton-Relay Mechanism and O2-Reduction States. Authors: Serrano-Posada, H. / Centeno-Leija, S. / Rojas-Trejo, S.P. / Rodriguez-Almazan, C. / 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 | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xu9SC ![]() 2xuwC ![]() 2xvbC ![]() 2yaeC ![]() 2yafC ![]() 2yahC ![]() 2yamC ![]() 2yaoC ![]() 2yapC ![]() 2yarC ![]() 4ai7C 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 / Fragment: MATURE FORM, RESIDUES 24-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 528 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/OH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-MPD / ( ![]() #4: Chemical | ChemComp-MRD / ( ![]() #5: Chemical | ChemComp-OH / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON ...THE SEQUENCE AT THE UNIPROT DEPOSIT Q72HW2 POSITION 53 IS OCCUPIED BY A LEUCINE BUT THE ELECTRON DENSITY CLEARLY SUPPORTS THE PRESENCE OF AN ISOLEUCINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % / Description: NONE |
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Crystal grow![]() | pH: 7.5 / Details: 0.1M HEPES PH 7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2010 Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING. |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→29 Å / Num. obs: 44918 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.1 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2XU9 Resolution: 1.8→28.704 Å / SU ML: 0.17 / σ(F): 0.41 / Phase error: 14.66 / 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 / Bsol: 57.126 Å2 / ksol: 0.373 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→28.704 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.9997 Å / Origin y: -19.8766 Å / Origin z: 3.807 Å
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Refinement TLS group | Selection details: RESID 95 AND CHAIN A |