[English] 日本語
Yorodumi- PDB-1v3m: Crystal structure of F283Y mutant cyclodextrin glycosyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v3m | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of F283Y mutant cyclodextrin glycosyltransferase complexed with a pseudo-tetraose derived from acarbose | |||||||||
Components | Cyclomaltodextrin glucanotransferase | |||||||||
Keywords | TRANSFERASE / CGTase / Cyclodextrin / Acarbose | |||||||||
Function / homology | Function and homology information cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. | |||||||||
Citation | Journal: PROTEIN SCI. / Year: 2004 Title: Role of Phe283 in enzymatic reaction of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp.1011: Substrate binding and arrangement of the catalytic site Authors: Kanai, R. / Haga, K. / Akiba, T. / Yamane, K. / Harata, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: X-ray Structure of Cyclodextrin Glucano-transferase from Alkalophilic Bacillus Sp. 1011. Comparison of Two Independent Molecules at 1.8 Angstrom Resolution Authors: Harata, K. / Haga, K. / Nakamura, A. / Aoyagi, M. / Yamane, K. #2: Journal: J.Biochem.(Tokyo) / Year: 2003 Title: Effects of essential carbohydrate/aromatic stacking interaction with Tyr100 and Phe259 on substrate binding of cyclodextrin glycosyltransferase from alkalophilic Bacillus sp. 1011 Authors: Haga, K. / Kanai, R. / Sakamoto, O. / Aoyagi, M. / Harata, K. / Yamane, K. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v3m.cif.gz | 293.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v3m.ent.gz | 233.6 KB | Display | PDB format |
PDBx/mmJSON format | 1v3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v3m_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1v3m_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1v3m_validation.xml.gz | 57.5 KB | Display | |
Data in CIF | 1v3m_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/1v3m ftp://data.pdbj.org/pub/pdb/validation_reports/v3/1v3m | HTTPS FTP |
-Related structure data
Related structure data | 1v3jC 1v3kC 1v3lC 1pamS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 75246.086 Da / Num. of mol.: 2 / Mutation: F283Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: 1011 / Plasmid: pTUE254 / Production host: Escherichia coli (E. coli) / Strain (production host): ME8417 References: UniProt: P05618, cyclomaltodextrin glucanotransferase |
---|
-Sugars , 4 types, 10 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | #4: Sugar | ChemComp-GLC / #6: Sugar | |
---|
-Non-polymers , 3 types, 691 molecules
#5: Chemical | #7: Chemical | ChemComp-CA / #8: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | The depositors believe that Pro452 and Gly454 are correct and that swissprot is incorrect at these positions. |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG3000, SODIUM CITRATE, 2-PROPANOL, CALCIUM CHLORIDE, ACARBOSE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Jun 18, 2001 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→18.9 Å / Num. obs: 103110 / Observed criterion σ(F): 5.58 / Redundancy: 2.58 % / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 1.82→1.88 Å / Num. unique all: 498 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PAM Resolution: 2→10 Å / Isotropic thermal model: ISOTROPIC / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
|