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Yorodumi- PDB-5okh: Conservatively refined structure of Gan1D-WT, a putative 6-phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5okh | ||||||
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Title | Conservatively refined structure of Gan1D-WT, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in the C2 spacegroup | ||||||
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 catabolic process / beta-glucosidase activity / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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 | 5okh.cif.gz | 215.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5okh.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 5okh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5okh_validation.pdf.gz | 469.8 KB | Display | wwPDB validaton report |
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Full document | 5okh_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 5okh_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 5okh_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/5okh ftp://data.pdbj.org/pub/pdb/validation_reports/ok/5okh | HTTPS FTP |
-Related structure data
Related structure data | 5ok7C 5okaC 5okbSC 5okeC 5okgC 5okjC 5okkC 5okqC 5okrC 5oksC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 56209.715 Da / Num. of mol.: 2 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-GOL / | #3: Chemical | #4: Chemical | ChemComp-TRS / | #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: 2.48 Å3/Da / Density % sol: 50.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16-19% PEG8K, 3% MPD, 0.1M imidazole buffer pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→25.6 Å / Num. obs: 76802 / % possible obs: 99.9 % / Redundancy: 3.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.98→2.02 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4553 / CC1/2: 0.929 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OKB Resolution: 1.98→25.593 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.37 / 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: 1.98→25.593 Å
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Refine LS restraints |
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LS refinement shell |
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