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- PDB-5zbk: Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zbk | ||||||
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Title | Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 in complex with AMP | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.6 KB | Display | ![]() |
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PDB format | ![]() | 33.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.5 KB | Display | ![]() |
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Full document | ![]() | 802.7 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zbjC ![]() 5zblC ![]() 5itsS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 21758.934 Da / Num. of mol.: 1 / Mutation: E115A 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 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-AMP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: ammonium phosphate dibasic, citrate pH 5.5, sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 23, 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: 2.3→54 Å / Num. obs: 10160 / % possible obs: 97.3 % / Redundancy: 4.3 % / CC1/2: 0.912 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.063 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.349 / Num. unique obs: 493 / CC1/2: 0.713 / Rpim(I) all: 0.162 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ITS Resolution: 2.3→54 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.463 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.214 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.94 Å2 / Biso mean: 16.208 Å2 / Biso min: 3.01 Å2
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Refinement step | Cycle: final / Resolution: 2.3→54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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