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Yorodumi- PDB-4zep: Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zep | ||||||
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Title | Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose | ||||||
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 catabolic process / beta-glucosidase activity / cytosol Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Lansky, S. / Zehavi, A. / Dvir, H. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: To Be Published Title: Structure of Gan1D, a 6-phospho-beta-galactosidase from Geobacillus stearothermophilus, in complex with 6-phospho-glucose 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 | 4zep.cif.gz | 215.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zep.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zep_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4zep_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4zep_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 4zep_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/4zep ftp://data.pdbj.org/pub/pdb/validation_reports/ze/4zep | HTTPS FTP |
-Related structure data
Related structure data | 4ze4S 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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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: Sugar | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IMD / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-18% 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: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→50 Å / Num. obs: 55496 / % possible obs: 99.5 % / Redundancy: 3.9 % / Rsym value: 0.085 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.21→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.3 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZE4 Resolution: 2.21→28.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.029 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.187 / 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: 34.236 Å2
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Refinement step | Cycle: 1 / Resolution: 2.21→28.31 Å
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Refine LS restraints |
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