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Yorodumi- PDB-4gi6: Crystal structure of the MUTB F164L mutant in complex with glucose -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gi6 | ||||||
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Title | Crystal structure of the MUTB F164L mutant in complex with glucose | ||||||
Components | Sucrose isomerase | ||||||
Keywords | ISOMERASE / Enzyme complex / Tim-barrel(beta/alpha)8 / Sucrose isomerase / Glycoside hydrolase / Trehalulose synthase / GH13 family(cazy database) / Calcium binding | ||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / sucrose alpha-glucosidase activity / sucrose catabolic process / maltose catabolic process / maltose alpha-glucosidase activity / amino acid transport / alpha-amylase activity / isomerase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Rhizobium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Lipski, A. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gi6.cif.gz | 252.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gi6.ent.gz | 200.7 KB | Display | PDB format |
PDBx/mmJSON format | 4gi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/4gi6 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/4gi6 | HTTPS FTP |
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-Related structure data
Related structure data | 4gi8C 4gi9C 4giaC 4ginC 4h2cC 1zjbS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 63904.832 Da / Num. of mol.: 2 / Fragment: MUTB fragment, UNP residues 28-584 / Mutation: F164L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG660.12 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q2PS28, UniProt: M1E1F3*PLUS, EC: 5.4.11.99 #3: Sugar | ChemComp-GLC / | |
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-Non-polymers , 4 types, 903 molecules
#2: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-TRS / | #6: 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: 2.53 Å3/Da / Density % sol: 51.35 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97559 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2008 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97559 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→15 Å / Num. all: 69351 / Num. obs: 68858 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.117 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.15→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12519 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1ZJB Resolution: 2.15→14.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.89 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.232 / ESU R Free: 0.188 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→14.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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