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- PDB-5oc2: Crystal structure of Asp295Cys/Lys303Cys Amadoriase I mutant from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oc2 | ||||||
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Title | Crystal structure of Asp295Cys/Lys303Cys Amadoriase I mutant from Aspergillus Fumigatus | ||||||
![]() | Fructosyl amine:oxygen oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / thermoresistance / flavin dependant enzyme / glycated aminoacid | ||||||
Function / homology | ![]() fructosyl-amino acid oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rigoldi, F. / Donini, S. / Gautieri, A. / Parisini, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Thermal stabilization of the deglycating enzyme Amadoriase I by rational design. Authors: Rigoldi, F. / Donini, S. / Giacomina, F. / Sorana, F. / Redaelli, A. / Bandiera, T. / Parisini, E. / Gautieri, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193 KB | Display | ![]() |
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PDB format | ![]() | 150.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 922.6 KB | Display | ![]() |
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Full document | ![]() | 938.3 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 51.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oc3C ![]() 4wctS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51298.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: O42629, UniProt: Q4WIF5*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium citrate pH 5.6 14% Peg4K 5 % dimethyl sulfoxide |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.82 Å / Num. obs: 22860 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.165 / Net I/av σ(I): 10.6 / Net I/σ(I): 10.59 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3316 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4wct Resolution: 2.85→46.371 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.17 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→46.371 Å
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Refine LS restraints |
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LS refinement shell |
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