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Yorodumi- PDB-5okb: High resolution structure of native Gan1D, a putative 6-phospho-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5okb | |||||||||
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Title | High resolution structure of native Gan1D, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus | |||||||||
Components | Putative 6-phospho-beta-galactobiosidase | |||||||||
Keywords | HYDROLASE / 6-beta-phospho-galactosidase / glycoside hydrolase / GH1 / Gan1D | |||||||||
Function / homology | Function and homology information 6-phospho-beta-galactosidase / 6-phospho-beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.331 Å | |||||||||
Authors | Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G. | |||||||||
Citation | Journal: FEBS J. / Year: 2017 Title: Structural basis for enzyme bifunctionality - the case of Gan1D from Geobacillus stearothermophilus. Authors: Lansky, S. / Zehavi, A. / Belrhali, H. / Shoham, Y. / Shoham, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5okb.cif.gz | 877.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5okb.ent.gz | 729.5 KB | Display | PDB format |
PDBx/mmJSON format | 5okb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5okb ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5okb | HTTPS FTP |
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-Related structure data
Related structure data | 5ok7C 5okaC 5okeC 5okgC 5okhC 5okjC 5okkC 5okqC 5okrC 5oksC 4zeh 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
#1: Protein | Mass: 56209.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: gan1D / Production host: Escherichia coli (E. coli) / References: UniProt: W8QF82, 6-phospho-beta-galactosidase #2: Chemical | ChemComp-IMD / #3: Chemical | #4: Chemical | ChemComp-PO4 / #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: 2.15 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-19% PEG 8K, 3% MPD, 0.1M imidazole buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→40 Å / Num. obs: 429175 / % possible obs: 95.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.4 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZEH 4zeh Resolution: 1.331→30.829 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.331→30.829 Å
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Refine LS restraints |
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LS refinement shell |
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