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Open data
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Basic information
Entry | Database: PDB / ID: 7vkp | ||||||
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Title | Crystal structure of E.coli pseudouridine kinase PsuK | ||||||
![]() | PfkB domain protein | ||||||
![]() | RNA BINDING PROTEIN / pseudouridine / kinase / yeiC | ||||||
Function / homology | pfkB family of carbohydrate kinases signature 1. / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / kinase activity / PfkB domain protein![]() | ||||||
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 | ![]() | 154.9 KB | Display | ![]() |
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PDB format | ![]() | 102 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.8 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vskC ![]() 7w93C ![]() 7c1yS 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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Unit cell |
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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.) ![]() ![]() Strain: B / BL21-DE3 / Gene: ECBD_1492 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting 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 PILATUS 6M / Detector: PIXEL / Date: Sep 21, 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: 2.3→30 Å / Num. obs: 24045 / % possible obs: 99.9 % / Redundancy: 21 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.029 / Rrim(I) all: 0.151 / Net I/σ(I): 22.25 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2362 / CC1/2: 0.294 / CC star: 0.674 / Rpim(I) all: 0.169 / Rrim(I) all: 0.549 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C1Y Resolution: 2.3→29.18 Å / SU ML: 0.2796 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 23.7643 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: 42.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.18 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: 74.4502827355 Å / Origin y: -20.2127539345 Å / Origin z: -3.90177952866 Å
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Refinement TLS group | Selection details: all |