+Open data
-Basic information
Entry | Database: PDB / ID: 6tbi | ||||||
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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 / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Cellvibrio japonicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Offen, W. / Davies, G. | ||||||
Funding support | United Kingdom, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tbi.cif.gz | 1.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6tbi.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6tbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tbi ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tbi | HTTPS FTP |
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-Related structure data
Related structure data | 6tbfC 6tbgC 6tbhC 6tbjC 6tbkC 4d1iS S: Starting model for refinement C: citing same article (ref.) |
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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 (bacteria) / Gene: bgl35A, CJA_2707 / Production host: Escherichia coli (E. coli) / References: UniProt: B3PBE0, beta-galactosidase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-N8V / ( #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→116.1 Å / Num. obs: 865389 / % possible obs: 96.4 % / Redundancy: 3.4 % / CC1/2: 0.996 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.46→1.48 Å / Num. unique obs: 41941 / CC1/2: 0.662 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D1I Resolution: 1.46→116.1 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.651 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY THE HYDROCARBON TAILS OF THE LIGAND MOLECULES ARE EITHER MODELLED WITH LOWERED OCCUPANCY ATOMS OR WITHOUT SOME ATOMS. THE LOOPS 433-447 HAVE BEEN MODELLED AT REDUCED OCCUPANCY OR WITH GAPS IN SOME OF THE MOLECULES.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 119.37 Å2 / Biso mean: 22.723 Å2 / Biso min: 12.09 Å2
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Refinement step | Cycle: final / Resolution: 1.46→116.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.498 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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