+Open data
-Basic information
Entry | Database: PDB / ID: 5hy1 | ||||||
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Title | high resolution structure of barbiturase | ||||||
Components | Barbiturase | ||||||
Keywords | HYDROLASE / Toblerone fold / pyrimidine catabolism | ||||||
Function / homology | Function and homology information barbiturase / barbiturase activity / uracil catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Peat, T.S. / Scott, C. / Balotra, S. / Wilding, M. / Newman, J. | ||||||
Citation | Journal: Appl. Environ. Microbiol. / Year: 2017 Title: High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes. Authors: Peat, T.S. / Balotra, S. / Wilding, M. / Hartley, C.J. / Newman, J. / Scott, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hy1.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hy1.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hy1_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 5hy1_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 5hy1_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 5hy1_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/5hy1 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/5hy1 | HTTPS FTP |
-Related structure data
Related structure data | 5hweSC 5hxuC 5hxzC 5hy0C 5hy2C 5hy4C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41188.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: bar / Plasmid: pET14b variant / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8RSQ2, barbiturase | ||
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#2: Chemical | ChemComp-WDL / | ||
#3: Chemical | ChemComp-NA / | ||
#4: Chemical | #5: 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: 1.99 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein at 16 mg/,mL in 50 mM ADA pH 6.5, 50 mM NaCl mixed with 2.45 M ammonium sulfate, 10% glycerol; 150 nL plus 150 nL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→41.2 Å / Num. obs: 22146 / % possible obs: 99.6 % / Redundancy: 14.4 % / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.01→2.06 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HWE Resolution: 2.01→41.2 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.557 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.172 / 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: 28.651 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→41.2 Å
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Refine LS restraints |
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