[English] 日本語
Yorodumi- PDB-7ehh: Crystal structure of alpha-glucosidase from Weissella cibaria BKK... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ehh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of alpha-glucosidase from Weissella cibaria BKK1 in complex with maltose | ||||||
Components | alpha-glucosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase / maltooligosaccharides / carbohydrate metabolism / CARBOHYDRATE | ||||||
Biological species | Weissella cibaria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Krusong, K. / Wangpaiboon, K. / Kim, S. / Mori, T. / Hakoshima, T. | ||||||
Funding support | Thailand, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: A GH13 alpha-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. Authors: Wangpaiboon, K. / Laohawuttichai, P. / Kim, S.Y. / Mori, T. / Nakapong, S. / Pichyangkura, R. / Pongsawasdi, P. / Hakoshima, T. / Krusong, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ehh.cif.gz | 285.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ehh.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ehh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ehh_validation.pdf.gz | 869.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ehh_full_validation.pdf.gz | 874.2 KB | Display | |
Data in XML | 7ehh_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 7ehh_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/7ehh ftp://data.pdbj.org/pub/pdb/validation_reports/eh/7ehh | HTTPS FTP |
-Related structure data
Related structure data | 7d9bSC 7d9cC 7dcgC 7dchC 7ehiC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 68398.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Weissella cibaria (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: alpha-glucosidase |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 441 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|---|
Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.45 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: Ammonium sulfate, dioxane, MES |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 67707 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.72 Å2 / Rpim(I) all: 0.089 / Rrim(I) all: 0.229 / Net I/σ(I): 19.51 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique obs: 6686 / CC1/2: 0.249 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D9B Resolution: 2→32.18 Å / SU ML: 0.1737 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.175 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→32.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|