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Yorodumi- PDB-4hph: The crystal structure of isomaltulose synthase mutant E295Q from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hph | |||||||||
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Title | The crystal structure of isomaltulose synthase mutant E295Q from Erwinia rhapontici NX5 in complex with its natural substrate sucrose | |||||||||
Components | Sucrose isomerase | |||||||||
Keywords | ISOMERASE / Tim barrel / hydrolase / calcium binding | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / : / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / amino acid transport / isomerase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Erwinia rhapontici (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Xu, Z. / Li, S. / Xu, H. / Zhou, J. | |||||||||
Citation | Journal: Plos One / Year: 2013 Title: The Structural Basis of Erwinia rhapontici Isomaltulose Synthase Authors: Xu, Z. / Li, S. / Li, J. / Li, Y. / Feng, X. / Wang, R. / Xu, H. / Zhou, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hph.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hph.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/4hph ftp://data.pdbj.org/pub/pdb/validation_reports/hp/4hph | HTTPS FTP |
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-Related structure data
Related structure data | 4howSC 4hozC 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
#1: Protein | Mass: 65830.195 Da / Num. of mol.: 1 / Fragment: UNP residues 42-600 / Mutation: E295Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erwinia rhapontici (bacteria) / Strain: NX5 / Gene: PalI / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D9MPF2, isomaltulose synthase |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 30% PEG 6000, 0.1M Bicine, 10% Glycerol, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0442 Å |
Detector | Detector: CCD / Date: May 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0442 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 434369 / Num. obs: 434369 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.021 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.663 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HOW Resolution: 1.7→34.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.965 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 23.315 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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