+Open data
-Basic information
Entry | Database: PDB / ID: 6tbk | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a beta galactosidase with inhibitor | ||||||
Components | Beta-galactosidase, putative, bgl35A | ||||||
Keywords | HYDROLASE / beta galactosidase / inhibitor | ||||||
Function / homology | Function and homology information beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / vacuole / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Cellvibrio japonicus Ueda107 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Offen, W. / Davies, G. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Molecules / Year: 2020 Title: Mechanistic Insights into the Chaperoning of Human Lysosomal-Galactosidase Activity: Highly Functionalized Aminocyclopentanes and C -5a-Substituted Derivatives of 4- epi -Isofagomine. Authors: Weber, P. / Thonhofer, M. / Averill, S. / Davies, G.J. / Santana, A.G. / Muller, P. / Nasseri, S.A. / Offen, W.A. / Pabst, B.M. / Paschke, E. / Schalli, M. / Torvisco, A. / Tschernutter, M. ...Authors: Weber, P. / Thonhofer, M. / Averill, S. / Davies, G.J. / Santana, A.G. / Muller, P. / Nasseri, S.A. / Offen, W.A. / Pabst, B.M. / Paschke, E. / Schalli, M. / Torvisco, A. / Tschernutter, M. / Tysoe, C. / Windischhofer, W. / Withers, S.G. / Wolfsgruber, A. / Wrodnigg, T.M. / Stutz, A.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tbk.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tbk.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 6tbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tbk_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tbk_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6tbk_validation.xml.gz | 163.9 KB | Display | |
Data in CIF | 6tbk_validation.cif.gz | 240.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbk ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbk | HTTPS FTP |
-Related structure data
Related structure data | 6tbfC 6tbgC 6tbhC 6tbiC 6tbjC 4d1iS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 62127.023 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: Beta-galactosidase without predicted signal sequence and with N-terminal his tag Source: (gene. exp.) Cellvibrio japonicus Ueda107 (bacteria) Gene: bgl35A, CJA_2707 / Production host: Escherichia coli (E. coli) / References: UniProt: B3PBE0, beta-galactosidase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-N0Q / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016 |
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→63.2 Å / Num. obs: 650269 / % possible obs: 95.8 % / Redundancy: 2.1 % / CC1/2: 0.995 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 1.6→1.63 Å / Num. unique obs: 31475 / CC1/2: 0.678 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D1I Resolution: 1.6→63.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.835 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE (DIMETHYLAMINO)NAPHTHALENE GROUPS OF THE LIGAND HAVE NOT BEEN MODELLED AS THERE IS INSUFFICIENT DENSITY, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE (DIMETHYLAMINO)NAPHTHALENE GROUPS OF THE LIGAND HAVE NOT BEEN MODELLED AS THERE IS INSUFFICIENT DENSITY, AND THE SULFONYL GROUP IS ONLY MODELLED IN THE ACTIVE SITES OF MOLECULES A AND D. THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT SOME ATOMS. IN SOME OF THE MOLECULES THE LOOPS BETWEEN THR432 AND GLU449 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH CHAIN BREAKS WHERE RESIDUES COULD NOT BE PLACED.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.96 Å2 / Biso mean: 26.906 Å2 / Biso min: 13.96 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→63.2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|