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Yorodumi- PDB-3bmw: Cyclodextrin glycosyl transferase from Thermoanerobacterium therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bmw | ||||||||||||
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Title | Cyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P complexed with a maltoheptaose inhibitor | ||||||||||||
Components | Cyclomaltodextrin glucanotransferase | ||||||||||||
Keywords | TRANSFERASE / glycosidase / thermostable / family 13 glycosyl hydrolas / ligand / substrate / acarbose / Glycosyltransferase / Metal-binding / Secreted | ||||||||||||
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 | Thermoanaerobacterium thermosulfurigenes (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||||||||
Authors | Rozeboom, H.J. / van Oosterwijk, N. / Dijkstra, B.W. | ||||||||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution. Authors: Kelly, R.M. / Leemhuis, H. / Rozeboom, H.J. / van Oosterwijk, N. / Dijkstra, B.W. / Dijkhuizen, L. #1: Journal: J.Biol.Chem. / Year: 1998 Title: Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1 Authors: Wind, R.D. / Uitdehaag, J.C.M. / Buitelaar, R.M. / Dijkstra, B.W. / Dijkhuizen, L. #2: Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1 Authors: Knegtel, R.M.A. / Wind, R.D. / Rozeboom, H.J. / Kalk, K.H. / Buitelaar, R.M. / Dijkhuizen, L. / Dijkstra, B.W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bmw.cif.gz | 180.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bmw.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bmw_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3bmw_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3bmw_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 3bmw_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/3bmw ftp://data.pdbj.org/pub/pdb/validation_reports/bm/3bmw | HTTPS FTP |
-Related structure data
Related structure data | 3bmvC 1a47S S: Starting model for refinement C: citing same article (ref.) |
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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: 75508.109 Da / Num. of mol.: 1 / Mutation: S77P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium thermosulfurigenes (bacteria) Strain: EM1 / Gene: amyA / Plasmid: PCSCGT-TT / Production host: Bacillus subtilis (bacteria) / Strain (production host): DB104A References: UniProt: P26827, cyclomaltodextrin glucanotransferase |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
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#3: Polysaccharide | alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose |
-Non-polymers , 6 types, 1168 molecules
#5: Chemical | ChemComp-ACI / | ||||||||
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#6: Chemical | #7: Chemical | ChemComp-CL / | #8: Chemical | #9: Chemical | ChemComp-GOL / #10: 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: 2.72 Å3/Da / Density % sol: 54.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20% Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2007 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.5 Å / Num. all: 102676 / Num. obs: 102676 / % possible obs: 94.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.115 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / Num. unique all: 11370 / Rsym value: 0.223 / % possible all: 72.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1A47 Resolution: 1.6→49.48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.142 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.246 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→49.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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