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Yorodumi- PDB-3wms: The crystal structure of Y195I mutant alpha-cyclodextrin glycosyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wms | ||||||
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Title | The crystal structure of Y195I mutant alpha-cyclodextrin glycosyltransferase from Paenibacillus macerans | ||||||
Components | Alpha-cyclodextrin glucanotransferase | ||||||
Keywords | TRANSFERASE / Tim barrel / IgG-like beta-barrel / Cyclodextrin glycosyltransferase | ||||||
Function / homology | Function and homology information cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / transferase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Paenibacillus macerans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xie, T. / Hou, Y.J. / Li, D.F. / Yue, Y. / Qian, S.J. / Chao, Y.P. | ||||||
Citation | Journal: J.Biotechnol. / Year: 2014 Title: Structural basis of a mutant Y195I alpha-cyclodextrin glycosyltransferase with switched product specificity from alpha-cyclodextrin to beta-/ gamma-cyclodextrin Authors: Xie, T. / Hou, Y.J. / Li, D.F. / Yue, Y. / Qian, S.J. / Chao, Y.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wms.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wms.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wms_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 3wms_full_validation.pdf.gz | 434.4 KB | Display | |
Data in XML | 3wms_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3wms_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/3wms ftp://data.pdbj.org/pub/pdb/validation_reports/wm/3wms | HTTPS FTP |
-Related structure data
Related structure data | 3bmwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 78302.352 Da / Num. of mol.: 1 / Mutation: Y195I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus macerans (bacteria) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: S5ZJ19, UniProt: P04830*PLUS, cyclomaltodextrin glucanotransferase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 30% PEG 4000, 0.2M Sodium acetate trihydrate, 0.1M Tris hydrochloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.09 Å / Num. all: 30397 / Num. obs: 30397 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 31.38 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.502 / Net I/σ(I): 4.2 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 10 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.502 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BMW Resolution: 2.3→24.641 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 1.33 / Phase error: 24.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8924 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→24.641 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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