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- PDB-5mhv: The study of the X-ray induced enzymatic reduction of molecular o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mhv | |||||||||
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Title | The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from Steccherinum murashkinskyi.The fourth structure of the series with total exposition time 93 min. | |||||||||
![]() | 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: Structural study of the X-ray-induced enzymatic reduction of molecular oxygen to water by Steccherinum murashkinskyi laccase: insights into the reaction mechanism. Authors: Polyakov, K.M. / Gavryushov, S. / Ivanova, S. / Fedorova, T.V. / Glazunova, O.A. / Popov, A.N. / Koroleva, O.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mejC ![]() 5mewC ![]() 5mhuC ![]() 5mhwC ![]() 5mhxC ![]() 5mhyC ![]() 5mhzC ![]() 5mi1C ![]() 5mi2C ![]() 5miaC ![]() 5mibC ![]() 5micC ![]() 5midC ![]() 5mieC ![]() 5migC 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: 53411.746 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 , 5 types, 690 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | #5: Chemical | ChemComp-CIT / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.92 % Description: The crystal is a tetragonal prism with Dimension 0.3 x 0.2 x 0.15 mm. |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Protein solution (12mg/ml, 002M K-phosphate buffer, pH 6.5). Reservoir solution (0.1M citrate-phosphate buffer pH4.0, 0.2M ammonium acetat, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 27, 2009 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→67.52 Å / Num. obs: 116915 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 20 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 10.79 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→67.52 Å
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Refine LS restraints |
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