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Yorodumi- PDB-1cwy: CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cwy | ||||||
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Title | CRYSTAL STRUCTURE OF AMYLOMALTASE FROM THERMUS AQUATICUS, A GLYCOSYLTRANSFERASE CATALYSING THE PRODUCTION OF LARGE CYCLIC GLUCANS | ||||||
Components | AMYLOMALTASE | ||||||
Keywords | TRANSFERASE / (BETA / ALPHA)8 BARREL | ||||||
Function / homology | Function and homology information 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / : / carbohydrate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å | ||||||
Authors | Przylas, I. / Tomoo, K. / Terada, Y. / Takaha, T. / Fuji, K. / Saenger, W. / Straeter, N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of amylomaltase from thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. Authors: Przylas, I. / Tomoo, K. / Terada, Y. / Takaha, T. / Fujii, K. / Saenger, W. / Strater, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cwy.cif.gz | 128.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cwy.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cwy_validation.pdf.gz | 362.4 KB | Display | wwPDB validaton report |
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Full document | 1cwy_full_validation.pdf.gz | 365.7 KB | Display | |
Data in XML | 1cwy_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 1cwy_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/1cwy ftp://data.pdbj.org/pub/pdb/validation_reports/cw/1cwy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 57293.039 Da / Num. of mol.: 1 / Fragment: MALQ Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) Plasmid: STARTING PLASMID PGEX-NDE, FINAL PLASMID WITH CLONED GENE PFQG8 Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: O87172, 4-alpha-glucanotransferase |
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#2: 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: 3.21 Å3/Da / Density % sol: 65.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, ETHYLENE GLYCOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.981 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 56277 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 7.4 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.8 / Rsym value: 33.7 / % possible all: 93.1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 40 Å / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Num. measured all: 347606 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 93.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→500 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: CNS_TOPPAR/PROTEIN_REP.PARAM CNS_ TOPPAR/WATER_REP.PARAM
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 78.04 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 500 Å / % reflection Rfree: 5.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.329 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.303 |