[English] 日本語
![](img/lk-miru.gif)
- PDB-4yhe: NATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYS... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yhe | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | NATIVE BACTEROIDETES-AFFILIATED GH5 CELLULASE LINKED WITH A POLYSACCHARIDE UTILIZATION LOCUS | |||||||||||||||||||||
![]() | GH5 | |||||||||||||||||||||
![]() | HYDROLASE / beta alpha barrel / glycoside hydrolase / metagenomics | |||||||||||||||||||||
Function / homology | ![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Naas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G.H. / Pope, P.B. | |||||||||||||||||||||
Funding support | ![]() ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Structural Features of a Bacteroidetes-Affiliated Cellulase Linked with a Polysaccharide Utilization Locus. Authors: Naas, A.E. / MacKenzie, A.K. / Dalhus, B. / Eijsink, V.G. / Pope, P.B. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 183 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 427.1 KB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 59.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 9 - 397 / Label seq-ID: 1 - 389
NCS oper:
|
-
Components
#1: Protein | Mass: 43681.637 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Synthetic DNA Source: (gene. exp.) ![]() Plasmid: pNIC-CH / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.02 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Sodium Cacodylate,40% v/v 2-Methyl-2,4-pentanediol, 5% w/v PEG8000 Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.85→65.51 Å / Num. obs: 74499 / % possible obs: 98.6 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.047 / Net I/σ(I): 8.9 / Num. measured all: 273972 / Scaling rejects: 51 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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: 65.81 Å2 / Biso mean: 25.762 Å2 / Biso min: 11.48 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→65.51 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
|