[English] 日本語
![](img/lk-miru.gif)
- PDB-7op6: Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-conf... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7op6 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Bacteroides thetaiotaomicron mannosidase GH2 with beta-manno-configured cyclophellitol aziridine | ||||||||||||
![]() | Beta-mannosidase | ||||||||||||
![]() | HYDROLASE / mannosidase / cyclophellitol aziridine | ||||||||||||
Function / homology | ![]() beta-mannosidase / beta-mannosidase activity / glycoprotein catabolic process / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | McGregor, N.G.S. / Beenakker, T.J.M. / Kuo, C. / Wong, C. / Offen, W.A. / Armstrong, Z. / Codee, J.D.C. / Aerts, J.M.F.G. / Florea, B.I. / Overkleeft, H.S. / Davies, G.J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 379.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 298.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 66.7 KB | Display | |
Data in CIF | ![]() | 99.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7odjC ![]() 7omiC ![]() 7omsC ![]() 7op7C ![]() 2je8S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 98291.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: beta-mannosidase without signal peptide sequence and with C-terminal hexa-his tag Source: (gene. exp.) ![]() Gene: BT_0458 / Production host: ![]() ![]() |
---|
-Non-polymers , 8 types, 962 molecules ![](data/chem/img/BR.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JIW.gif)
![](data/chem/img/JIT.gif)
![](data/chem/img/VKH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/JIW.gif)
![](data/chem/img/JIT.gif)
![](data/chem/img/VKH.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Chemical | ChemComp-JIW / | #7: Chemical | ChemComp-JIT / | #8: Chemical | ChemComp-VKH / ( | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 3350, sodium bromide, MES buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→92.19 Å / Num. obs: 119933 / % possible obs: 98.6 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rpim(I) all: 0.049 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4 % / Num. unique obs: 5880 / CC1/2: 0.535 / Rpim(I) all: 0.522 / % possible all: 97.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2JE8 Resolution: 2.05→92.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.387 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.176 / 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: 91.93 Å2 / Biso mean: 33.93 Å2 / Biso min: 12.33 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→92.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|