+
Open data
-
Basic information
Entry | Database: PDB / ID: 5zbj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 | ||||||
![]() | Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / AMP nucleosidase / AMP nucleosidase activity / cytokinin biosynthetic process / hydrolase activity, hydrolyzing N-glycosyl compounds / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seo, H. / Kim, K.-J. | ||||||
![]() | ![]() Title: Structural insight into molecular mechanism of cytokinin activating protein from Pseudomonas aeruginosa PAO1. Authors: Seo, H. / Kim, K.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 53.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 468.8 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zbkC ![]() 5zblC ![]() 5itsS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21816.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4923 / Plasmid: pET30a / Production host: ![]() ![]() References: UniProt: P48636, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
---|
-Non-polymers , 5 types, 106 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-IMD / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: ammonium phosphate dibasic, imidazole pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2017 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→54.11 Å / Num. obs: 18128 / % possible obs: 98.1 % / Redundancy: 5 % / CC1/2: 0.804 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.036 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.89→1.93 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 845 / CC1/2: 0.944 / Rpim(I) all: 0.158 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5ITS Resolution: 1.89→54.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.718 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.118 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.68 Å2 / Biso mean: 22.512 Å2 / Biso min: 10.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→54.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.894→1.943 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|