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Open data
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Basic information
Entry | Database: PDB / ID: 5hwe | ||||||
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Title | high resolution structure of barbiturase | ||||||
![]() | Barbiturase | ||||||
![]() | HYDROLASE / Toblerone fold / pyrimidine catabolism | ||||||
Function / homology | ![]() barbiturase / barbiturase activity / uracil catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peat, T.S. / Scott, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 458.9 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hxuC ![]() 5hxzC ![]() 5hy0C ![]() 5hy1C ![]() 5hy2C ![]() 5hy4C ![]() 4bvqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MHA / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.15 % |
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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; reservoir of 2.45 M ammonium sulfate, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 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: 1.707→41.5 Å / Num. obs: 36498 / % possible obs: 99.7 % / Redundancy: 7.2 % / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.707→1.74 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4BVQ Resolution: 1.71→41.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.17 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.101 / 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: 19.557 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→41.5 Å
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Refine LS restraints |
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