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- PDB-4jcm: Crystal structure of Gamma-CGTASE from Alkalophilic bacillus clar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jcm | ||||||
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Title | Crystal structure of Gamma-CGTASE from Alkalophilic bacillus clarkii at 1.65 Angstrom resolution | ||||||
![]() | Cyclodextrin glucanotransferase | ||||||
![]() | TRANSFERASE / IBETA/ALPHA J8 BARREL / ALPHA-AMYLASE FAMILY / CYCLIZATION / BINDING GLUCOSE / BINDING CATION CALCIUM | ||||||
Function / homology | ![]() starch binding / transferase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, L. / Yang, D. / Zhou, J. / Wu, J. / Chen, J. | ||||||
![]() | ![]() Title: The Crystal Structure of Gamma-Cgtase from Alkalophilic Bacillus Clarkii at 1.65 Angstrom Resolution. Authors: Wu, L. / Yang, D. / Li, J. / Zhou, J. / Wu, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.1 KB | Display | ![]() |
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PDB format | ![]() | 255.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.5 KB | Display | ![]() |
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Full document | ![]() | 484.4 KB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cdgS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 78429.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B9A1J6, cyclomaltodextrin glucanotransferase |
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-Non-polymers , 7 types, 536 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1M BICINE PH9.0, 2.0M (NH4)2SO4, 0.05M NACL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 22, 2010 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 82111 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 8.8 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 1.65→1.71 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CDG Resolution: 1.65→32.65 Å / SU ML: 0.17 / σ(F): 0.09 / Phase error: 18.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.25 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→32.65 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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