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Yorodumi- PDB-4jcm: Crystal structure of Gamma-CGTASE from Alkalophilic bacillus clar... -
+Open data
-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 | ||||||
Components | Cyclodextrin glucanotransferase | ||||||
Keywords | TRANSFERASE / IBETA/ALPHA J8 BARREL / ALPHA-AMYLASE FAMILY / CYCLIZATION / BINDING GLUCOSE / BINDING CATION CALCIUM | ||||||
Function / homology | Function and homology information starch binding / transferase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus clarkii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Wu, L. / Yang, D. / Zhou, J. / Wu, J. / Chen, J. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jcm.cif.gz | 318.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jcm.ent.gz | 255.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcm ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcm | HTTPS FTP |
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-Related structure data
Related structure data | 1cdgS 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
-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.) Bacillus clarkii (bacteria) / Gene: cgt / Plasmid: PET20B(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B9A1J6, cyclomaltodextrin glucanotransferase |
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-Non-polymers , 7 types, 536 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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