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Yorodumi- PDB-4h8v: Crystal structure of the trehalulose synthase MUTB in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h8v | ||||||
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Title | Crystal structure of the trehalulose synthase MUTB in complex with trehalulose | ||||||
Components | Sucrose isomerase | ||||||
Keywords | ISOMERASE / NATIVE ENZYME / 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: 1.95 Å | ||||||
Authors | Lipski, A. / Ravaud, S. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: To be Published Title: Insights into product binding in sucrose isomerases from crystal structures of MutB from Rhizobium sp. Authors: Lipski, A. / Watzlawick, H. / Ravaud, S. / Robert, X. / 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 | 4h8v.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h8v.ent.gz | 206.5 KB | Display | PDB format |
PDBx/mmJSON format | 4h8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/4h8v ftp://data.pdbj.org/pub/pdb/validation_reports/h8/4h8v | HTTPS FTP |
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-Related structure data
Related structure data | 4h7vC 4h8hC 4h8uC 4ha1C 1zjaS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 63938.848 Da / Num. of mol.: 2 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: PHWG315 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q2PS28, UniProt: M1E1F6*PLUS, EC: 5.4.11.99 #2: Chemical | #3: Sugar | #4: 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: 2.65 Å3/Da / Density % sol: 53.59 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 12% PEG20000, 0.1M Na cacodylate, 0.01M L-cysteine, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 2005 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→35.5 Å / Num. all: 95875 / Num. obs: 90958 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 25.8 Å2 / Rsym value: 0.09 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.95→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.16 / Num. unique all: 26719 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1ZJA Resolution: 1.95→35.5 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 28.52 / 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: 1.95→35.5 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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