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- PDB-4re3: Different transition state conformations for the hydrolysis of be... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4re3 | ||||||
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Title | Different transition state conformations for the hydrolysis of beta-mannosides and beta-glucosides in the rice Os7BGlu26 family GH1 beta-mannosidase/beta-glucosidase | ||||||
![]() | Beta-mannosidase/beta-glucosidase | ||||||
![]() | HYDROLASE / GH1 | ||||||
Function / homology | ![]() beta-mannosidase / beta-D-fucosidase activity / beta-mannosidase activity / beta-galactosidase activity / beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R. | ||||||
![]() | ![]() Title: A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides Authors: Tankrathok, A. / Iglesias-Fernandez, J. / Williams, R.J. / Pengthaisong, S. / Baiya, S. / Hakki, Z. / Robinson, R.C. / Hrmova, M. / Rovira, C. / Williams, S.J. / Ketudat Cairns, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.6 KB | Display | ![]() |
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PDB format | ![]() | 87.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481 KB | Display | ![]() |
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Full document | ![]() | 484.2 KB | Display | |
Data in XML | ![]() | 20.1 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4re2C ![]() 4re4C ![]() 4jhoS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 57703.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET32A / Production host: ![]() ![]() References: UniProt: B5ABY0, UniProt: A2YPH1*PLUS, beta-mannosidase |
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-Non-polymers , 5 types, 126 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GIM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/GIM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-TRS / | #4: Chemical | ChemComp-EPE / | #5: Chemical | ChemComp-GIM / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: 0.8M K/Na tartrate, 0.1 M HEPES, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 22658 / Num. obs: 22658 / % possible obs: 99.9 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.55→2.64 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JHO Resolution: 2.55→24.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.318 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.424 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.804 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→24.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.545→2.611 Å / Total num. of bins used: 20
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