+Open data
-Basic information
Entry | Database: PDB / ID: 5zbj | ||||||
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Title | Crystal structure of type-I LOG from Pseudomonas aeruginosa PAO1 | ||||||
Components | Putative cytokinin riboside 5'-monophosphate phosphoribohydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Seo, H. / Kim, K.-J. | ||||||
Citation | Journal: Environ. Microbiol. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zbj.cif.gz | 53.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zbj.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/5zbj ftp://data.pdbj.org/pub/pdb/validation_reports/zb/5zbj | HTTPS FTP |
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-Related structure data
Related structure data | 5zbkC 5zblC 5itsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4923 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P48636, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 5 types, 106 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-IMD / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.88 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 76.68 Å2 / Biso mean: 22.512 Å2 / Biso min: 10.87 Å2
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Refinement step | Cycle: final / Resolution: 1.89→54.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.894→1.943 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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