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Open data
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Basic information
Entry | Database: PDB / ID: 5x98 | ||||||
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Title | Y162F mutant of thermus thermophilus HB8 thymidylate kinase | ||||||
![]() | Thymidylate kinase | ||||||
![]() | TRANSFERASE / Nucleotide monophosphate kinase | ||||||
Function / homology | ![]() dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K. | ||||||
![]() | ![]() Title: Structural and functional roles of dynamically correlated residues in thymidylate kinase. Authors: Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.3 KB | Display | ![]() |
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PDB format | ![]() | 126.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.6 KB | Display | ![]() |
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Full document | ![]() | 451.4 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5x86C ![]() 5x8aC ![]() 5x8bC ![]() 5x8cC ![]() 5x8dC ![]() 5x8jC ![]() 5x8kC ![]() 5x8vC ![]() 5x99C ![]() 5xakC ![]() 5xalC ![]() 5xt8C ![]() 5x7jS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 21993.543 Da / Num. of mol.: 2 / Mutation: Y162F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: tmk, TTHA1607 / Production host: ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.11 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 0.1M Magnesium formate dehydrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→37.81 Å / Num. obs: 33617 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.35 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.76→1.79 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X7J Resolution: 1.76→37.81 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.058 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 23.742 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→37.81 Å
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Refine LS restraints |
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