+Open data
-Basic information
Entry | Database: PDB / ID: 6hri | ||||||
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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 | 6hri.cif.gz | 62.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hri.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 6hri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hri_validation.pdf.gz | 466 KB | Display | wwPDB validaton report |
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Full document | 6hri_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 6hri_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 6hri_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hri ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hri | HTTPS FTP |
-Related 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: 23535.217 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: 1.93 Å3/Da / Density % sol: 36.14 % |
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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: 0.97622 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.03→34.2 Å / Num. obs: 76651 / % possible obs: 85 % / Redundancy: 1.9 % / Net I/σ(I): 18.67 |
Reflection shell | Resolution: 1.03→1.07 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→36.07 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.492 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.033 / 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: 13.079 Å2
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Refinement step | Cycle: 1 / Resolution: 1.03→36.07 Å
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Refine LS restraints |
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