+
Open data
-
Basic information
Entry | Database: PDB / ID: 5olq | ||||||
---|---|---|---|---|---|---|---|
Title | Rhamnogalacturonan lyase | ||||||
![]() | Rhamnogalacturonan lyase | ||||||
![]() | LYASE / Pectin / PL9 / polysaccharide lyase family 9 / Rhamnogalacturonan lyase / endo-acting enzyme | ||||||
Function / homology | ![]() carbon-oxygen lyase activity, acting on polysaccharides / alpha-galactosidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Basle, A. / Luis, A.S. / Gilbert, H.J. | ||||||
![]() | ![]() Title: Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides. Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / ...Authors: Luis, A.S. / Briggs, J. / Zhang, X. / Farnell, B. / Ndeh, D. / Labourel, A. / Basle, A. / Cartmell, A. / Terrapon, N. / Stott, K. / Lowe, E.C. / McLean, R. / Shearer, K. / Schuckel, J. / Venditto, I. / Ralet, M.C. / Henrissat, B. / Martens, E.C. / Mosimann, S.C. / Abbott, D.W. / Gilbert, H.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 558.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 454.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 457.8 KB | Display | |
Data in XML | ![]() | 57.9 KB | Display | |
Data in CIF | ![]() | 91 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5olpC ![]() 5olrC ![]() 5olsC ![]() 5opjC ![]() 1ru4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 56980.395 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HMPREF2534_01516 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.72 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 mM sodium/potassium phosphate 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→39.65 Å / Num. obs: 221195 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.48→1.51 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 10868 / CC1/2: 0.736 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1RU4 Resolution: 1.48→39.65 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.218 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.158 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.48→39.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|