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- PDB-6rhi: Single crystal serial study of the X-ray induced enzymatic reduct... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rhi | |||||||||
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Title | Single crystal serial study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi at sub-atomic resolution. Ninth structure of the series with 1215 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 | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 248.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6rghC ![]() 6rgpC ![]() 6rhhC ![]() 6rhoC ![]() 6rhpC ![]() 6rhrC ![]() 6rhuC ![]() 6rhxC ![]() 6ri0C ![]() 6ri2C ![]() 6ri4C ![]() 6ri6C ![]() 6ri8C ![]() 6riiC ![]() 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
#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 #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-OXY / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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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). |
-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: 1.01→70 Å / Num. obs: 277996 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / CC1/2: 0.997 / Rrim(I) all: 0.076 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.01→1.04 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 20426 / CC1/2: 0.723 / Rrim(I) all: 0.699 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5E9N Resolution: 1.01→67.4 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.76 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.018 / ESU R Free: 0.019 / 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: 11.818 Å2
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Refinement step | Cycle: 1 / Resolution: 1.01→67.4 Å
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Refine LS restraints |
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