+Open data
-Basic information
Entry | Database: PDB / ID: 5nbo | ||||||
---|---|---|---|---|---|---|---|
Title | Bacteroides ovatus mixed linkage glucan PUL (MLGUL) GH16 | ||||||
Components | Glycosyl hydrolase family 16 | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH16 | ||||||
Function / homology | Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Glycosyl hydrolase family 16 Function and homology information | ||||||
Biological species | Bacteroides ovatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hemsworth, G.R. / Tamura, K. / Dejean, G. / Rogers, T.E. / Pudlo, N.A. / Urs, K. / Jain, N. / Martens, E.C. / Brumer, H. / Davies, G.J. | ||||||
Citation | Journal: Cell Rep / Year: 2017 Title: Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides. Authors: Tamura, K. / Hemsworth, G.R. / Dejean, G. / Rogers, T.E. / Pudlo, N.A. / Urs, K. / Jain, N. / Davies, G.J. / Martens, E.C. / Brumer, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5nbo.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5nbo.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nbo_validation.pdf.gz | 436.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5nbo_full_validation.pdf.gz | 436.1 KB | Display | |
Data in XML | 5nbo_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5nbo_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nbo ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nbo | HTTPS FTP |
-Related structure data
Related structure data | 5nbpC 4crqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30651.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02741 / Production host: Escherichia coli (E. coli) / References: UniProt: A7LY25 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.83 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM MES pH 6 200 mM LiCl2 15-25% Peg-6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.23 Å / Num. obs: 45483 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.053 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2 / Num. unique obs: 2726 / CC1/2: 0.669 / Rpim(I) all: 0.365 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4crq Resolution: 1.8→49.23 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.699 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / 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: 18.72 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→49.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|