+
Open data
-
Basic information
Entry | Database: PDB / ID: 4ao5 | ||||||
---|---|---|---|---|---|---|---|
Title | B. subtilis prophage dUTPase YosS in complex with dUMP | ||||||
![]() | SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEO TIDOHYDROLASE YOSS | ||||||
![]() | HYDROLASE / HOMOTRIMERIC DUTPASES / PHE-LID | ||||||
Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Nafria, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S. | ||||||
![]() | ![]() Title: Tying Down the Arm in Bacillus Dutpase: Structure and Mechanism Authors: Garcia-Nafria, J. / Timm, J. / Harrison, C. / Turkenburg, J.P. / Wilson, K.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 387.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 316.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 47.3 KB | Display | |
Data in CIF | ![]() | 67.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aooC ![]() 4aozC ![]() 4apzC ![]() 4b0hC ![]() 2xcdS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16397.756 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UMP / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.17 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 14% PEG 3350, 0.1 M SODIUM MALONATE, 0.1 M, BIS-TRIS PROPANE PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 28, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.8 Å / Num. obs: 131522 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2XCD Resolution: 1.6→70.65 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.92 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 21.005 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→70.65 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|