[English] 日本語
![](img/lk-miru.gif)
- PDB-8i5s: Crystal structure of TxGH116 D593N acid/base mutant from Thermoan... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8i5s | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of TxGH116 D593N acid/base mutant from Thermoanaerobacterium xylanolyticum with 2-deoxy-2-fluoroglucoside | ||||||||||||
![]() | beta-glucosidase![]() | ||||||||||||
![]() | ![]() | ||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pengthaisong, S. / Ketudat Cairns, J.R. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation. Authors: Pengthaisong, S. / Piniello, B. / Davies, G.J. / Rovira, C. / Ketudat Cairns, J.R. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 188.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8i5oC ![]() 8i5pC ![]() 8i5qC ![]() 8i5rC ![]() 8i5tC ![]() 8i5uC ![]() 5bvuS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 91793.195 Da / Num. of mol.: 1 / Mutation: D593A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LX-11 / Gene: Thexy_2211 / Plasmid: PET30A / Production host: ![]() ![]() ![]() ![]() |
---|
-Sugars , 2 types, 3 molecules ![](data/chem/img/G2F.gif)
![](data/chem/img/NFG.gif)
![](data/chem/img/NFG.gif)
#2: Sugar | ChemComp-G2F / |
---|---|
#6: Sugar |
-Non-polymers , 4 types, 622 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-EDO / | ![]() #7: Water | ChemComp-HOH / | ![]() |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % |
---|---|
Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.18 M AMMONIUM SULFATE, 22% PEG 3000, 0.1 M MES, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→35 Å / Num. obs: 141041 / % possible obs: 98.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.45→1.5 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 12918 / CC1/2: 0.787 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5BVU Resolution: 1.45→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.112 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 57.62 Å2 / Biso mean: 18.256 Å2 / Biso min: 8.76 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|