[English] 日本語
Yorodumi- PDB-5m0x: Structure of apo structure of GH36 alpha-galactosidase from Therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m0x | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of apo structure of GH36 alpha-galactosidase from Thermotoga maritima | ||||||
Components | Alpha-galactosidase | ||||||
Keywords | HYDROLASE / Alpha-galactosidase / glycoside hydrolase | ||||||
Function / homology | Function and homology information alpha-galactosidase / alpha-galactosidase activity / glycoside catabolic process / carbohydrate binding / carbohydrate metabolic process / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pengelly, R. / Gloster, T. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016 Title: Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars. Authors: Adamson, C. / Pengelly, R.J. / Shamsi Kazem Abadi, S. / Chakladar, S. / Draper, J. / Britton, R. / Gloster, T.M. / Bennet, A.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5m0x.cif.gz | 134 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5m0x.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 5m0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m0x_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5m0x_full_validation.pdf.gz | 442.3 KB | Display | |
Data in XML | 5m0x_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5m0x_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m0x ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m0x | HTTPS FTP |
-Related structure data
Related structure data | 5m12C 5m16C 5m1iC 1zy9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66198.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Differences at the N-terminus arise from the vector used for expression (primarily a His tag). Differences at the C-terminus arise from the lack of electron density meaning this part could not be modelled. Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: galA / Production host: Escherichia coli (E. coli) References: UniProt: O33835, UniProt: G4FEF4*PLUS, alpha-galactosidase | ||
---|---|---|---|
#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium sulfate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32.09 Å / Num. obs: 59066 / % possible obs: 99 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.6 / % possible all: 99.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZY9 Resolution: 1.8→32.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.278 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / 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: 29.643 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→32.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|