[English] 日本語
![](img/lk-miru.gif)
- PDB-5hxu: Structure-function analysis of functionally diverse members of th... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5hxu | ||||||
---|---|---|---|---|---|---|---|
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 167.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 129 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 483.2 KB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 51.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hweC ![]() 5hxzC ![]() 5hy0C ![]() 5hy1C ![]() 5hy2C ![]() 5hy4C ![]() 4bvqS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 367 / Label seq-ID: 23 - 387
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41188.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 626 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MHA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MHA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 ...Details: Protein at 15 mg/mL; reservoir was 2.5 M ammonium sulfate with 10% (v/v) MMT buffer at pH 9; sitting drop setup with 150 nL plus 150 nL drops; crystals cryo-protected with AP/E core 150 basestock (Mobile 1, Australia). |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28221 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→45.7 Å / Num. obs: 67015 / % possible obs: 98.1 % / Redundancy: 26.6 % / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.83→1.87 Å / Redundancy: 20.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 81 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4bvq Resolution: 1.83→41.5 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.89 / SU B: 3.122 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.162 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.83→41.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|