+Open data
-Basic information
Entry | Database: PDB / ID: 1pj9 | |||||||||
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Title | Bacillus circulans strain 251 loop mutant 183-195 | |||||||||
Components | Cyclomaltodextrin glucanotransferase | |||||||||
Keywords | TRANSFERASE / glycosyltransferase / cyclodextrin | |||||||||
Function / homology | Function and homology information cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus circulans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | |||||||||
Authors | Rozeboom, H.J. / Dijkstra, B.W. | |||||||||
Citation | Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / Year: 2004 Title: Improved thermostability of bacillus circulans cyclodextrin glycosyltransferase by the introduction of a salt bridge Authors: Leemhuis, H. / Rozeboom, H.J. / Dijkstra, B.W. / Dijkhuizen, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pj9.cif.gz | 168.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pj9.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/1pj9 ftp://data.pdbj.org/pub/pdb/validation_reports/pj/1pj9 | HTTPS FTP |
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-Related structure data
Related structure data | 1d3cS 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: 74649.461 Da / Num. of mol.: 1 / Mutation: T185S, T186Y, N188D, K192R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251 / Plasmid: pDP66k- / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 References: UniProt: P43379, cyclomaltodextrin glucanotransferase |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | #3: Polysaccharide | #4: Sugar | ChemComp-GLC / | |
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-Non-polymers , 4 types, 805 molecules
#5: Chemical | ChemComp-MPD / ( | ||||
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#6: Chemical | #7: Chemical | #8: 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: 2.81 Å3/Da / Density % sol: 56.27 % | ||||||||||||||||||||||||
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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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 23, 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→50 Å / Num. all: 57530 / Num. obs: 57530 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 7.8 / Num. unique all: 5528 / % possible all: 96.3 |
Reflection | *PLUS Lowest resolution: 32 Å / Num. obs: 57077 / % possible obs: 98.8 % / Num. measured all: 363420 |
Reflection shell | *PLUS % possible obs: 96.3 % / Mean I/σ(I) obs: 8.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1D3C Resolution: 2→31.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2283082.17 / Data cutoff high rms absF: 2283082.17 / 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: 76.6193 Å2 / ksol: 0.428511 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→31.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 32 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 |