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- PDB-3t6x: Crystal Structure of Steccherinum ochraceum Laccase obtained by m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t6x | |||||||||
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Title | Crystal Structure of Steccherinum ochraceum Laccase obtained by multi-crystals composite data collection technique (20% dose) | |||||||||
![]() | Laccase![]() | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ferraroni, M. / Briganti, F. / Matera, I. / Kolomytseva, M. / Golovleva, L. / Scozzafava, A. / Chernykh, A.M. | |||||||||
![]() | ![]() Title: Reaction intermediates and redox state changes in a blue laccase from Steccherinum ochraceum observed by crystallographic high/low X-ray dose experiments. Authors: Ferraroni, M. / Matera, I. / Chernykh, A. / Kolomytseva, M. / Golovleva, L.A. / Scozzafava, A. / Briganti, F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.8 KB | Display | ![]() |
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PDB format | ![]() | 261.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3t6vSC ![]() 3t6wC ![]() 3t6zC ![]() 3t71C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | ![]() Mass: 52829.312 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / | ![]() |
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-Non-polymers , 5 types, 1504 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / ![]() #4: Chemical | ChemComp-SO4 / ![]() #5: Chemical | ChemComp-GOL / ![]() #6: Chemical | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.21 % |
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Crystal grow![]() | Temperature: 296 K / pH: 9 Details: 1.9 M ammonium sulphate, 0.01 M zinc chloride, pH 9.0, vapor diffusion, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC, 225 MM / Detector: CCD / Date: Dec 2, 2007 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111), HORIZONTALLY FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→19.87 Å / Num. obs: 92472 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.08 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6.74 |
Reflection shell | Resolution: 2.15→2.28 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.97 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3T6V Resolution: 2.15→19.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.818 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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