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Open data
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Basic information
Entry | Database: PDB / ID: 8glr | ||||||
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Title | FrlB - Deglycase for 6-phosphofructose lysine | ||||||
![]() | SIS domain-containing protein | ||||||
![]() | SUGAR BINDING PROTEIN / deglycase / fructose-lysine metabolism / Amadori compound / sugar isomerase domain | ||||||
Function / homology | Fructosamine deglycase FrlB / Fructosamine deglycase FrlB, SIS domain 1 / carbohydrate derivative metabolic process / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / carbohydrate derivative binding / SIS domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bell, C.E. / Gopalan, V. / Kovvali, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the catalytic mechanism of a bacterial deglycase essential for utilization of fructose-lysine. Authors: Kovvali, S. / Gao, Y. / Cool, A. / Lindert, S. / Wysocki, V.H. / Bell, C.E. / Gopalan, 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 | ![]() | 84.4 KB | Display | ![]() |
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PDB format | ![]() | 60.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.6 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a3nS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38440.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: AIT36_19960, BG493_20030, G0K88_001622, G0K89_001219, G0K90_002095, G0K94_001269, G0K95_001240, G0L00_000266, G0L02_001295, G0L86_001412, G0M06_001202, G0M13_000979, G0M18_002254, G0M22_001196, ...Gene: AIT36_19960, BG493_20030, G0K88_001622, G0K89_001219, G0K90_002095, G0K94_001269, G0K95_001240, G0L00_000266, G0L02_001295, G0L86_001412, G0M06_001202, G0M13_000979, G0M18_002254, G0M22_001196, G0M25_001016, G0M29_001211, G0M46_001199, G0M48_001460, G4F88_04075, G4F89_20295, G4F91_19950, G4F92_04075, GXC51_00580, GXC56_00580, GXG40_00580, GYJ28_003810 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES (pH 7.5) and 1.0 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å |
Detector | Type: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Dec 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→45.1 Å / Num. obs: 28584 / % possible obs: 94.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.091 / Χ2: 1.279 / Net I/av σ(I): 20.7 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.83→1.88 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 28564 / Rpim(I) all: 0.214 / Rrim(I) all: 0.511 / Χ2: 1.295 / % possible all: 84.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2a3n Resolution: 1.83→45.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.349 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.357 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→45.09 Å
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Refine LS restraints |
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