+
Open data
-
Basic information
Entry | Database: PDB / ID: 5oyc | ||||||
---|---|---|---|---|---|---|---|
Title | GH5 endo-xyloglucanase from Cellvibrio japonicus | ||||||
![]() | Cellulase, putative, cel5D | ||||||
![]() | HYDROLASE / endo-xyloglucanase | ||||||
Function / homology | ![]() glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Attia, M. / Nelson, C.E. / Offen, W.A. / Jain, N. / Gardner, J.G. / Davies, G.J. / Brumer, H. | ||||||
![]() | ![]() Title: In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions. Authors: Attia, M.A. / Nelson, C.E. / Offen, W.A. / Jain, N. / Davies, G.J. / Gardner, J.G. / Brumer, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 346 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 280.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 819.8 KB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 52.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oydC ![]() 5oyeC ![]() 3zmrS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44396.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminally his-tagged catalytic domain of putative cellulase Cel5D Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B3PD52, xyloglucan-specific endo-beta-1,4-glucanase |
---|
-Non-polymers , 6 types, 616 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/2PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-2PE / | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 5.5 / Details: ammonium sulfate, MES buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→82.45 Å / Num. obs: 112339 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5530 / CC1/2: 0.699 / Rpim(I) all: 0.695 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ZMR.PDB Resolution: 1.6→82.45 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.13 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.083 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS UNMODELLED DENSITY BETWEEN SOME SIDE CHAINS AS FOLLOWS:ASN132 ARG334 AND TRP143 IN BOTH MOL, GLN172 AND TYR173 IN BOTH MOL, AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THERE IS UNMODELLED DENSITY BETWEEN SOME SIDE CHAINS AS FOLLOWS:ASN132 ARG334 AND TRP143 IN BOTH MOL, GLN172 AND TYR173 IN BOTH MOL, AND BETWEEN TYR328 OF BOTH MOL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.972 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→82.45 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|