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Yorodumi- PDB-5y9b: Crystal structure of Bacillus licheniformis Gamma glutamyl transp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y9b | ||||||
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Title | Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with DON | ||||||
Components | (Gamma glutamyl ...) x 2 | ||||||
Keywords | TRANSFERASE / Gamma glutamyl transpeptidase / Bacillus licheniformis / DON | ||||||
Function / homology | Function and homology information gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process Similarity search - Function | ||||||
Biological species | Bacillus licheniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Goel, M. / Kumari, S. / Pal, R. / Gupta, R. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine Authors: Goel, M. / Kumari, S. / Pal, R. / Gupta, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y9b.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y9b.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 5y9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/5y9b ftp://data.pdbj.org/pub/pdb/validation_reports/y9/5y9b | HTTPS FTP |
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-Related structure data
Related structure data | 5y8xC 5xluS 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
-Gamma glutamyl ... , 2 types, 2 molecules AB
#1: Protein | Mass: 43538.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q65KZ6*PLUS, gamma-glutamyltransferase |
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#2: Protein | Mass: 20534.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q65KZ6*PLUS, gamma-glutamyltransferase |
-Non-polymers , 4 types, 149 molecules
#3: Chemical | #4: Chemical | ChemComp-DON / | #5: Chemical | ChemComp-EDO / | #6: 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: 2.19 Å3/Da / Density % sol: 43.88 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, 100 mM NaCl, 200 mM MgCl2, MPD, 100 mM Tris-Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35 Å / Num. obs: 29483 / % possible obs: 97.1 % / Redundancy: 10 % / Rpim(I) all: 0.024 / Χ2: 1.18 / Net I/σ(I): 29.39 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 9 % / Mean I/σ(I) obs: 2.73 / Num. unique obs: 1288 / Χ2: 0.91 / % possible all: 86.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XLU Resolution: 2.15→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.009 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.204 / 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: 40.59 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→35 Å
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