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- PDB-1ot1: Bacillus circulans strain 251 Cyclodextrin glycosyl transferase m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ot1 | |||||||||
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Title | Bacillus circulans strain 251 Cyclodextrin glycosyl transferase mutant D135A | |||||||||
![]() | Cyclomaltodextrin glucanotransferase | |||||||||
![]() | TRANSFERASE / glycosyl transferase / cyclodextrin | |||||||||
Function / homology | ![]() cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Rozeboom, H.J. / Dijkstra, B.W. | |||||||||
![]() | ![]() Title: The fully conserved Asp residue in Conserved sequence region I of the alpha-amylase Family is crucial for the Catalytic Site Architecture and Activity Authors: Leemhuis, H. / Rozeboom, H.J. / Dijkstra, B.W. / Dijkhuizen, L. | |||||||||
History |
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Remark 999 | Authors informed that after reinterpretation of sequence data, residue 400 is Ser and not Cys. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.1 KB | Display | ![]() |
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PDB format | ![]() | 132.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ot2C ![]() 1d3cS C: citing same article ( 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: 74515.414 Da / Num. of mol.: 1 / Mutation: D135A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 3 types, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | |
-Non-polymers , 5 types, 835 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ACY / #8: Chemical | ChemComp-EPE / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.29 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: MPD, Ca, HEPES, maltose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Lawson, C.L., (1994) J. Mol. Biol., 236, 590. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 22, 2002 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 59675 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 50.9 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 15.5 / Num. unique all: 5751 / % possible all: 97.4 |
Reflection | *PLUS Num. obs: 59255 / Num. measured all: 437820 |
Reflection shell | *PLUS % possible obs: 97.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1D3C Resolution: 2→24.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2247700.93 / Data cutoff high rms absF: 2247700.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.6349 Å2 / ksol: 0.352309 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→24.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.181 / Rfactor Rwork: 0.16 |