+Open data
-Basic information
Entry | Database: PDB / ID: 5onk | ||||||
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Title | Native YndL | ||||||
Components | YndL | ||||||
Keywords | HYDROLASE / PGA hydrolases | ||||||
Function / homology | Poly-gamma-glutamate hydrolase / Poly-gamma-glutamate hydrolase, zinc-binding motif superfamily / Poly-gamma-glutamate hydrolase / hydrolase activity / plasma membrane / CITRATE ANION / IMIDAZOLE / Gamma-polyglutamate hydrolase PghL / UPF0714 protein YndL Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 Å | ||||||
Authors | Ramaswamy, S. / Rasheed, M. / Morelli, C. / Calvio, C. / Sutton, B. / Pastore, A. | ||||||
Citation | Journal: FEBS J. / Year: 2018 Title: The structure of PghL hydrolase bound to its substrate poly-gamma-glutamate. Authors: Ramaswamy, S. / Rasheed, M. / Morelli, C.F. / Calvio, C. / Sutton, B.J. / Pastore, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5onk.cif.gz | 63.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5onk.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 5onk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5onk_validation.pdf.gz | 474.5 KB | Display | wwPDB validaton report |
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Full document | 5onk_full_validation.pdf.gz | 478.9 KB | Display | |
Data in XML | 5onk_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 5onk_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5onk ftp://data.pdbj.org/pub/pdb/validation_reports/on/5onk | HTTPS FTP |
-Related structure data
Related structure data | 5onjC 5onlC 6hriC 6hrjC 3a9lS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23985.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_0239 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164XNU3, UniProt: O31815*PLUS |
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-Non-polymers , 5 types, 243 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-FLC / | #5: Chemical | ChemComp-IMD / | #6: 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: 1.89 Å3/Da / Density % sol: 34.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1 Ammonium sulphate, 0.15 Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.6 - 2.3 | |||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2017 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.03→34.2 Å / Num. obs: 76651 / % possible obs: 85 % / Redundancy: 1.9 % / Biso Wilson estimate: 11.75 Å2 / Net I/av σ(I): 2.2 / Net I/σ(I): 18.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A9L Resolution: 1.03→34.2 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.482 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.419 Å2
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Refinement step | Cycle: 1 / Resolution: 1.03→34.2 Å
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Refine LS restraints |
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