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- PDB-7w93: Crystal structure of E.coli pseudouridine kinase PsuK complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w93 | ||||||
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Title | Crystal structure of E.coli pseudouridine kinase PsuK complexed with N1-methyl-pseudouridine | ||||||
![]() | PfkB domain protein | ||||||
![]() | SUGAR BINDING PROTEIN / Kinase / sugar / pseudouridine / m1-pseudouridine / mRNA vaccine | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, K.J. / Li, X.J. / Wu, B.X. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK. Authors: Li, X. / Li, K. / Guo, W. / Wen, Y. / Meng, C. / Wu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.6 KB | Display | ![]() |
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PDB format | ![]() | 111.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.8 KB | Display | ![]() |
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Full document | ![]() | 798.7 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vkpSC ![]() 7vskC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 33781.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-8IZ / |
#3: Chemical | ChemComp-K / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 22% w/v Poly(acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 41758 / % possible obs: 98.5 % / Redundancy: 28.2 % / Biso Wilson estimate: 32.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.026 / Rrim(I) all: 0.148 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.462 / Num. unique obs: 5922 / CC1/2: 0.651 / Rpim(I) all: 0.301 / Rrim(I) all: 1.498 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VKP Resolution: 1.9→29.19 Å / SU ML: 0.2182 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.169 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 74.5586871219 Å / Origin y: -19.8952284959 Å / Origin z: -3.95126651783 Å
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Refinement TLS group | Selection details: all |