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Yorodumi- PDB-4ott: Crystal structure of the gamma-glutamyltranspeptidase from Bacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ott | ||||||
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Title | Crystal structure of the gamma-glutamyltranspeptidase from Bacillus licheniformis. | ||||||
Components |
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Keywords | HYDROLASE / Ntn hydrolase | ||||||
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: 2.98 Å | ||||||
Authors | Merlino, A. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2014 Title: Low resolution X-ray structure of gamma-glutamyltranspeptidase from Bacillus licheniformis: Opened active site cleft and a cluster of acid residues potentially involved in the recognition of a metal ion. Authors: Lin, L.L. / Chen, Y.Y. / Chi, M.C. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ott.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ott.ent.gz | 89.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ott.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/4ott ftp://data.pdbj.org/pub/pdb/validation_reports/ot/4ott | HTTPS FTP |
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-Related structure data
Related structure data | 4otuC 3a75S 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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Unit cell |
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-Components
#1: Protein | Mass: 43578.473 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) / References: UniProt: A9YTT0, gamma-glutamyltransferase | ||
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#2: Protein | Mass: 20533.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus licheniformis (bacteria) / Strain: DSM 13 / ATCC 14580 / Gene: ggt, BL03798, BLi01364 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65KZ6, gamma-glutamyltransferase | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: Protein concentration 20 mg/ml, 20% PEG3350, 0.2 M MgCl2, 0.2 M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 29, 2013 / Details: mirror | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.95→50 Å / Num. all: 11668 / Num. obs: 11668 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB code 3A75 Resolution: 2.98→26.25 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.831 / SU B: 17.415 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.101 / 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: 38.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.98→26.25 Å
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Refine LS restraints |
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