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Yorodumi- PDB-4ze4: Structure of Gan1D, a putative 6-phospho-beta-galactosidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ze4 | ||||||
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Title | Structure of Gan1D, a putative 6-phospho-beta-galactosidase from Geobacillus stearothermophilus | ||||||
Components | Putative 6-phospho-beta-galactobiosidase | ||||||
Keywords | HYDROLASE / TIM-barrel / dimer / glycoside hydrolase / 6-phospho-beta-galactosidase | ||||||
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 / Resolution: 1.92 Å | ||||||
Authors | Lansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To Be Published Title: To be published Authors: Lansky, S. / Zehavi, A. / Dvir, 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 | 4ze4.cif.gz | 210.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ze4.ent.gz | 173.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ze4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4ze4 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4ze4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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 | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 17% PEG 8K, 3% MPD, 0.1 M 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: 1.92→40 Å / Num. obs: 86922 / % possible obs: 99.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.92→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 1.92→31.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.433 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 33.825 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→31.9 Å
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Refine LS restraints |
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