+Open data
-Basic information
Entry | Database: PDB / ID: 4h7v | ||||||
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Title | MUTB inactive double mutant D200A-D415N in complex with GLUCOSE | ||||||
Components | Sucrose isomerase | ||||||
Keywords | ISOMERASE / ISOMALTULOSE SYNTHASE LIKE / TIM-BARREL / (BETA/ALPHA)8 / SUCROSE ISOMERASE / TREHALULOSE SYNTHASE / GH13 FAMILY (CAZY DATABASE) / CALCIUM BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizobium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lipski, A. / 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 | 4h7v.cif.gz | 258.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h7v.ent.gz | 202.3 KB | Display | PDB format |
PDBx/mmJSON format | 4h7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/4h7v ftp://data.pdbj.org/pub/pdb/validation_reports/h7/4h7v | HTTPS FTP |
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-Related structure data
Related structure data | 4h8hC 4h8uC 4h8vC 4ha1C 1zjbS 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: 63893.855 Da / Num. of mol.: 2 / Fragment: TREHALULOSE SYNTHASE MUTB, UNP residues 28-584 / Mutation: D415N, D200A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizobium (bacteria) / Strain: MX-45 / Gene: mutB / Plasmid: pHWG800.2 / 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: Chemical | ChemComp-GOL / | #5: 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: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG10000, 0.1M TRIS-HCL, pH 8.5, 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: 0.98081 Å |
Detector | Type: PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98081 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.2 Å / Num. all: 113616 / Num. obs: 105583 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 22.97 Å2 / Rsym value: 0.103 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.8→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.4 / Num. unique all: 28403 / % possible all: 92.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZJB Resolution: 1.8→42.2 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.12 / 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: 1.8→42.2 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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