+Open data
-Basic information
Entry | Database: PDB / ID: 8pej | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CjGH35 with a Galactosidase Activity-Based Probe | |||||||||
Components | Beta-galactosidase, putative, bgl35A | |||||||||
Keywords | HYDROLASE / Beta-galactosidase / Complex / Activity-based Probe | |||||||||
Function / homology | Function and homology information beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Cellvibrio japonicus Ueda107 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Offen, W.A. / Davies, G.J. | |||||||||
Funding support | United Kingdom, European Union, 2items
| |||||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2023 Title: The development of a broad-spectrum retaining beta-exo-galactosidase activity-based probe. Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / ...Authors: Kuo, C.L. / Su, Q. / van den Nieuwendijk, A.M.C.H. / Beenakker, T.J.M. / Offen, W.A. / Willems, L.I. / Boot, R.G. / Sarris, A.J. / Marques, A.R.A. / Codee, J.D.C. / van der Marel, G.A. / Florea, B.I. / Davies, G.J. / Overkleeft, H.S. / Aerts, J.M.F.G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pej.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pej.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 8pej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/8pej ftp://data.pdbj.org/pub/pdb/validation_reports/pe/8pej | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 62127.023 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: beta-galactosidase without signal peptide and with N-terminal hexahistidine 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-YGX / ( #4: Chemical | ChemComp-ACT / #5: 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: 2.71 Å3/Da / Density % sol: 54.57 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→99.32 Å / Num. obs: 802827 / % possible obs: 96.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.061 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.0467 / Mean I/σ(I) obs: 2 / Num. unique obs: 37248 / CC1/2: 0.719 / Rpim(I) all: 0.0467 / Rrim(I) all: 0.66 / % possible all: 90 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→82.544 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.198 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.063 Details: Hydrogens have been added in their riding positions There was incomplete electron density for loop 434 - 445, which has been modelled at partial occupancy or left partially unmodelled for each chain.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.647 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→82.544 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|