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Open data
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Basic information
Entry | Database: PDB / ID: 5wq3 | ||||||
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Title | Crystal structure of type-II LOG from Corynebacterium glutamicum | ||||||
![]() | Cytokinin riboside 5'-monophosphate phosphoribohydrolase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() cytokinin riboside 5'-monophosphate phosphoribohydrolase activity / : / cytokinin biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seo, H. / Kim, K.-J. | ||||||
![]() | ![]() Title: Structural basis for a novel type of cytokinin-activating protein 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 | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | 111.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 503.2 KB | Display | ![]() |
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Full document | ![]() | 512.7 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wekS S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 29798.986 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A1B4WK77, UniProt: Q8NRE2*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds |
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-Non-polymers , 7 types, 257 molecules ![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-1PE / | ||||||
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#3: Chemical | ChemComp-GOL / | ||||||
#4: Chemical | ChemComp-PO4 / | ||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: PEG 3350, Lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 22, 2014 |
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: 1.95→50 Å / Num. obs: 47969 / % possible obs: 95.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.46 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WEK Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.368 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.03 Å2 / Biso mean: 32.901 Å2 / Biso min: 12.28 Å2
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Refinement step | Cycle: final / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.951→2.002 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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