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Yorodumi- PDB-3czk: Crystal Structure Analysis of Sucrose hydrolase(SUH) E322Q-sucros... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3czk | |||||||||
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Title | Crystal Structure Analysis of Sucrose hydrolase(SUH) E322Q-sucrose complex | |||||||||
Components | Sucrose hydrolase | |||||||||
Keywords | HYDROLASE / (alpha/beta)8-barrel | |||||||||
Function / homology | Function and homology information amylosucrase activity / carbohydrate metabolic process / hydrolase activity Similarity search - Function | |||||||||
Biological species | Xanthomonas axonopodis pv. glycines (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Kim, M.I. / Rhee, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structures and mutagenesis of sucrose hydrolase from Xanthomonas axonopodis pv. glycines: insight into the exclusively hydrolytic amylosucrase fold. Authors: Kim, M.I. / Kim, H.S. / Jung, J. / Rhee, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3czk.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3czk.ent.gz | 106.2 KB | Display | PDB format |
PDBx/mmJSON format | 3czk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3czk_validation.pdf.gz | 808.5 KB | Display | wwPDB validaton report |
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Full document | 3czk_full_validation.pdf.gz | 823.8 KB | Display | |
Data in XML | 3czk_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 3czk_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/3czk ftp://data.pdbj.org/pub/pdb/validation_reports/cz/3czk | HTTPS FTP |
-Related structure data
Related structure data | 3czeSC 3czgC 3czlC 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: 70420.070 Da / Num. of mol.: 1 / Mutation: E322Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. glycines (bacteria) Strain: 8ra / Gene: supH / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q6UVM5, sucrose alpha-glucosidase |
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#2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
#3: 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: 2.26 Å3/Da / Density % sol: 45.55 % / Mosaicity: 0.728 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M HEPES, 0.2M calcium acetate, 16% PEG 3000, 5mM DTT, 0.1M cesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2399 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 33073 / % possible obs: 99.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.074 / Χ2: 1.011 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CZE Resolution: 2.2→50 Å
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Solvent computation | Bsol: 49.808 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.08 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Xplor file |
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