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- PDB-5hxz: Structure-function analysis of functionally diverse members of th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hxz | ||||||
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Title | Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes | ||||||
![]() | 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. / Balotra, S. / Wilding, M. / Newman, J. / 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 | ![]() | 279.8 KB | Display | ![]() |
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PDB format | ![]() | 224.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5hweC ![]() 5hxuSC ![]() 5hy0C ![]() 5hy1C ![]() 5hy2C ![]() 5hy4C 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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Unit cell |
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Components
#1: Protein | Mass: 41188.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein was at 15 mg/mL; reservoir was 2.5 M ammonium sulfate, 0.1 M bis-tris at pH 6.5; vapor diffusion sitting drops of 150 nL plus 150 nL; done at 20 C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 2.36→45.3 Å / Num. obs: 61689 / % possible obs: 99.9 % / Redundancy: 7.4 % / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.36→2.42 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.6 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5hxu Resolution: 2.36→45.3 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R: 0.469 / ESU R Free: 0.265 / 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: 31.438 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→45.3 Å
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Refine LS restraints |
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