[English] 日本語
Yorodumi- PDB-3ueq: Crystal structure of amylosucrase from Neisseria polysaccharea in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ueq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of amylosucrase from Neisseria polysaccharea in complex with turanose | |||||||||
Components | Amylosucrase | |||||||||
Keywords | TRANSFERASE / beta/alpha-barrel / glycoside hydrolase / amylose synthesis / sucrose isomerization / glucosyltransferase / carbohydrate | |||||||||
Function / homology | Function and homology information amylosucrase / amylosucrase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Neisseria polysaccharea (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Guerin, F. / Pizzut-Serin, S. / Potocki-Veronese, G. / Guillet, V. / Mourey, L. / Remaud-Simeon, M. / Andre, I. / Tranier, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Investigation of the Thermostability and Product Specificity of Amylosucrase from the Bacterium Deinococcus geothermalis. Authors: Guerin, F. / Barbe, S. / Pizzut-Serin, S. / Potocki-Veronese, G. / Guieysse, D. / Guillet, V. / Monsan, P. / Mourey, L. / Remaud-Simeon, M. / Andre, I. / Tranier, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ueq.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ueq.ent.gz | 120.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ueq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ueq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ueq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ueq_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 3ueq_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/3ueq ftp://data.pdbj.org/pub/pdb/validation_reports/ue/3ueq | HTTPS FTP |
-Related structure data
Related structure data | 3ucqC 3uerC 1g5aS 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
#1: Protein | Mass: 71888.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria polysaccharea (bacteria) / Strain: ATCC 43768 / Gene: ams / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZEU2, amylosucrase |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-3)-beta-D-fructofuranose / beta-turanose |
#3: Sugar | ChemComp-OTU / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
Sequence details | G537D MUTATION IS A PCR ARTIFACT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30% PEG 6000, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→29.27 Å / Num. all: 58575 / Num. obs: 55312 / % possible obs: 99.47 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.85→1.95 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G5A Resolution: 1.85→29.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.438 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.555 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→29.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
|