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Open data
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Basic information
Entry | Database: PDB / ID: 7c27 | ||||||
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Title | Glycosidase F290Y at pH4.5 | ||||||
![]() | Isomaltose glucohydrolase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() isomaltose glucohydrolase / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tagami, T. / Kikuchi, A. / Okuyama, M. / Kimura, A. | ||||||
![]() | ![]() Title: Structural insights reveal the second base catalyst of isomaltose glucohydrolase. Authors: Tagami, T. / Chen, M. / Furunaga, Y. / Kikuchi, A. / Sadahiro, J. / Lang, W. / Okuyama, M. / Tanaka, Y. / Iwasaki, T. / Yao, M. / Kimura, 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 | ![]() | 99.5 KB | Display | ![]() |
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PDB format | ![]() | 70.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5z3aC ![]() 5z3bC ![]() 5z3cC ![]() 5z3dSC ![]() 5z3eC ![]() 5z3fC ![]() 7c24C ![]() 7c25C ![]() 7c26C 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 on special symmetry positions |
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Components
#1: Protein | Mass: 44060.059 Da / Num. of mol.: 1 / Mutation: F290Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Plasmid: pET28a / Production host: ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-GOL / ![]() #3: Chemical | ChemComp-CIT / | ![]() #4: Chemical | ChemComp-NH4 / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.91→46.92 Å / Num. obs: 39724 / % possible obs: 99.9 % / Redundancy: 26.4 % / CC1/2: 0.998 / Rrim(I) all: 0.242 / Rsym value: 0.238 / Net I/σ(I): 0.107 |
Reflection shell | Resolution: 1.91→2.02 Å / Redundancy: 26.7 % / Mean I/σ(I) obs: 0.01 / Num. unique obs: 6298 / CC1/2: 0.429 / Rrim(I) all: 3.722 / Rsym value: 3.651 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5Z3D Resolution: 1.91→46.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.339 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.12 Details: Hydrogens have been added in their riding positions
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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: 36.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→46.92 Å
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Refine LS restraints |
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LS refinement shell |
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