[English] 日本語
Yorodumi- PDB-4go9: CRYSTAL STRUCTURE of the TREHALULOSE SYNTHASE MUTANT, MUTB D415N,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4go9 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE of the TREHALULOSE SYNTHASE MUTANT, MUTB D415N, in COMPLEX with TRIS | ||||||
Components | Sucrose isomerase | ||||||
Keywords | ISOMERASE / MUTANT ENZYME / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / maltose catabolic process / maltose alpha-glucosidase activity / amino acid transport / alpha-amylase activity / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas mesoacidophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Lipski, A. / Ravaud, S. / Robert, X. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: To be Published / Year: 2013 Title: CRYSTAL STRUCTURE of the TREHALULOSE SYNTHASE MUTB, MUTANT D415N, in COMPLEX with TRIS Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Haser, R. / Mattes, R. / Aghajari, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4go9.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4go9.ent.gz | 207 KB | Display | PDB format |
PDBx/mmJSON format | 4go9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/4go9 ftp://data.pdbj.org/pub/pdb/validation_reports/go/4go9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pwgS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 63937.863 Da / Num. of mol.: 2 / Fragment: MUTB fragment, UNP residues 28-584 / Mutation: D415N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas mesoacidophila (bacteria) / Gene: mutB / Plasmid: PHWG660.2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2PS28, EC: 5.4.11.99 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.07 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 12% (w/v) PEG20000, 0.01M L-Cysteine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9699 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2004 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40.83 Å / Num. all: 67242 / Num. obs: 67185 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 21.99 Å2 / Rsym value: 0.112 / Net I/σ(I): 9.36 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.16 / Num. unique all: 8384 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2PWG Resolution: 2.2→40.8 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.71 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|