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- PDB-4gin: Crystal structure of the MUTB R284C mutant from crystals soaked w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gin | ||||||
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Title | Crystal structure of the MUTB R284C mutant from crystals soaked with the inhibitor deoxynojirimycin | ||||||
![]() | Sucrose isomerase | ||||||
![]() | ISOMERASE / MUTANT ENZYME / TIM-BARREL(BETA/ALPHA)8 / SUCROSE ISOMERASE / GLYCOSIDE HYDROLASE / TREHALULOSE SYNTHASE / GH13 FAMILY(CAZY DATABASE) / CALCIUM BINDING | ||||||
Function / homology | ![]() glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / maltose alpha-glucosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport / isomerase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lipski, A. / Ravaud, S. / Robert, X. / Haser, R. / Aghajari, N. | ||||||
![]() | ![]() Title: Mutations inducing an active-site aperture in Rhizobium sp. sucrose isomerase confer hydrolytic activity Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / Rhimi, M. / Haser, R. / Mattes, R. / Aghajari, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 267.1 KB | Display | ![]() |
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PDB format | ![]() | 211.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.7 KB | Display | ![]() |
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Full document | ![]() | 432.3 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 43.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gi6C ![]() 4gi8C ![]() 4gi9C ![]() 4giaC ![]() 4h2cC ![]() 1zjaS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 66815.344 Da / Num. of mol.: 1 / Mutation: R284C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99 | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.26 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, 12%(w/v) PEG20000, 0.01M L-Cysteine, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 3, 2004 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9699 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.85 Å / Num. all: 55036 / Num. obs: 55036 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.113 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.9→2.02 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZJA Resolution: 1.9→44.85 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 15.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→44.85 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 11.4763 Å / Origin y: 12.5386 Å / Origin z: 14.8503 Å
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Refinement TLS group | Selection details: all |