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- PDB-6rii: Single crystal serial study of the inhibition of laccases from St... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rii | |||||||||
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Title | Single crystal serial study of the inhibition of laccases from Steccherinum murashkinskyi by fluoride anions at sub-atomic resolution. Fourth structure of the series with 1200 KGy dose. | |||||||||
![]() | Laccase 2 | |||||||||
![]() | OXIDOREDUCTASE / MULTI COPPER OXIDASE / LACCASE / COMPLEX WITH MOLECULAR OXYGEN | |||||||||
Function / homology | ![]() hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Polyakov, K.M. / Gavryushov, S. / Fedorova, T.V. / Glazunova, O.A. / Popov, A.N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The subatomic resolution study of laccase inhibition by chloride and fluoride anions using single-crystal serial crystallography: insights into the enzymatic reaction mechanism. Authors: Polyakov, K.M. / Gavryushov, S. / Fedorova, T.V. / Glazunova, O.A. / Popov, A.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 312.5 KB | Display | ![]() |
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PDB format | ![]() | 252 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 49.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rghC ![]() 6rgpC ![]() 6rhhC ![]() 6rhiC ![]() 6rhoC ![]() 6rhpC ![]() 6rhrC ![]() 6rhuC ![]() 6rhxC ![]() 6ri0C ![]() 6ri2C ![]() 6ri4C ![]() 6ri6C ![]() 6ri8C ![]() 6rikC ![]() 6rilC ![]() 5e9nS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 53310.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 943 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/F.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/F.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-F / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 4 Details: CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 20 MM K-PHOSPHATE BUFFER, PH 6.5) RESERVOIR SOLUTION (0.1 M CITRATE-PHOSPHATE BUFFER PH 4.0, 0.2 M AMMONIUM ACETATE, 25% PEG 4000). ...Details: CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 20 MM K-PHOSPHATE BUFFER, PH 6.5) RESERVOIR SOLUTION (0.1 M CITRATE-PHOSPHATE BUFFER PH 4.0, 0.2 M AMMONIUM ACETATE, 25% PEG 4000). Before collecting the diffraction data, the crystal was soaked in reservoir solution containing 0.1 M NaF. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→70 Å / Num. obs: 307638 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / CC1/2: 0.996 / Rrim(I) all: 0.074 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 0.97→1 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 21761 / CC1/2: 0.717 / Rrim(I) all: 0.74 / % possible all: 94.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E9N Resolution: 0.97→67.36 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.55 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.114 Å2
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Refinement step | Cycle: 1 / Resolution: 0.97→67.36 Å
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Refine LS restraints |
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