+Open data
-Basic information
Entry | Database: PDB / ID: 6gya | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Amylase in complex with branched ligand | |||||||||
Components | A-amylase | |||||||||
Keywords | HYDROLASE / Amylase Glycoside Hydrolase | |||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding Similarity search - Function | |||||||||
Biological species | Alicyclobacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Agirre, J. / Moroz, O. / Meier, S. / Brask, J. / Munch, A. / Hoff, T. / Andersen, C. / Wilson, K.S. / Davies, G.J. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: The structure of the AliC GH13 alpha-amylase from Alicyclobacillus sp. reveals the accommodation of starch branching points in the alpha-amylase family. Authors: Agirre, J. / Moroz, O. / Meier, S. / Brask, J. / Munch, A. / Hoff, T. / Andersen, C. / Wilson, K.S. / Davies, G.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6gya.cif.gz | 393.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6gya.ent.gz | 322.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/6gya ftp://data.pdbj.org/pub/pdb/validation_reports/gy/6gya | HTTPS FTP |
---|
-Related structure data
Related structure data | 6gxvSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 4 - 484 / Label seq-ID: 4 - 484
NCS ensembles :
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53984.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: in complex with branched ligand / Source: (gene. exp.) Alicyclobacillus sp. (bacteria) / Variant: 18711 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A3P8MUS3 |
---|
-Sugars , 4 types, 15 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #6: Sugar | ChemComp-GLC / #7: Sugar | |
---|
-Non-polymers , 3 types, 239 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.21 Å3/Da / Density % sol: 76.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG3350, 0.1M BTP pH 8.5, 0.2% Na2SO4 / PH range: 8.0-8.5 / Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→66.9 Å / Num. obs: 92496 / % possible obs: 100 % / Redundancy: 10 % / Biso Wilson estimate: 50.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.14 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.96→3.03 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.74 / Num. unique obs: 6812 / Rrim(I) all: 0.83 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GXV Resolution: 2.95→66.86 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.089 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.37 / ESU R Free: 0.232 / 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: 56.439 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.95→66.86 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|