+Open data
-Basic information
Entry | Database: PDB / ID: 5t3b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of BpGH50 | ||||||
Components | Glycoside Hydrolase | ||||||
Keywords | HYDROLASE / (alpha/alpha)6 barrel / glycoside hydrolase | ||||||
Function / homology | Glycoside hydrolase superfamily / Uncharacterized protein Function and homology information | ||||||
Biological species | Bacteroides plebeius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Giles, K. / Pluvinage, B. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Proteins / Year: 2017 Title: Structure of a glycoside hydrolase family 50 enzyme from a subfamily that is enriched in human gut microbiome bacteroidetes. Authors: Giles, K. / Pluvinage, B. / Boraston, A.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5t3b.cif.gz | 428.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5t3b.ent.gz | 350.5 KB | Display | PDB format |
PDBx/mmJSON format | 5t3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t3b_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5t3b_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 5t3b_validation.xml.gz | 43.9 KB | Display | |
Data in CIF | 5t3b_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/5t3b ftp://data.pdbj.org/pub/pdb/validation_reports/t3/5t3b | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54689.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides plebeius (bacteria) / Gene: BACPLE_01683 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5CY86 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 17-25% PEG 3350, 0.04-0.1M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92017 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92017 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→71.95 Å / Num. obs: 176279 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.9 / CC1/2: 0.844 / % possible all: 95.6 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→71.95 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.538 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.047 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.69 Å2 / Biso mean: 16.817 Å2 / Biso min: 5.66 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→71.95 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|