+Open data
-Basic information
Entry | Database: PDB / ID: 1pez | |||||||||
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Title | Bacillus circulans strain 251 mutant A230V | |||||||||
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: 2.32 Å | |||||||||
Authors | Rozeboom, H.J. / Dijkstra, B.W. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Conversion of Cyclodextrin Glycosyltransferase into a Starch Hydrolase by Directed Evolution: The Role of Alanine 230 in Acceptor Subsite +1 Authors: Leemhuis, H. / Rozeboom, H.J. / Wilbrink, M. / Euverink, G.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 | 1pez.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pez.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 1pez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pez_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1pez_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1pez_validation.xml.gz | 34.1 KB | Display | |
Data in CIF | 1pez_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/1pez ftp://data.pdbj.org/pub/pdb/validation_reports/pe/1pez | HTTPS FTP |
-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: 74533.344 Da / Num. of mol.: 1 / Mutation: A230V 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, 4 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
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#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
#4: Polysaccharide |
-Non-polymers , 5 types, 773 molecules
#5: Chemical | #6: Chemical | ChemComp-MPD / ( | #7: Chemical | ChemComp-ACY / #8: Chemical | ChemComp-EPE / | #9: 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: 2.84 Å3/Da / Density % sol: 56.65 % | ||||||||||||||||||||
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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: Oct 20, 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: 2.32→25 Å / Num. all: 36647 / Num. obs: 36647 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.32→2.41 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3433 / % possible all: 95.2 |
Reflection | *PLUS Num. measured all: 356544 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 95.2 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1D3C Resolution: 2.32→23 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1846278.44 / Data cutoff high rms absF: 1846278.44 / 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: 54.9705 Å2 / ksol: 0.340232 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.32→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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