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- PDB-5h56: ADP and dTDP bound Crystal structure of thymidylate kinase (aq_96... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5h56 | ||||||
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Title | ADP and dTDP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5 | ||||||
![]() | Thymidylate kinase | ||||||
![]() | TRANSFERASE / Kinase / Rossmann Fold / Product-bound | ||||||
Function / homology | ![]() dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Biswas, A. / Jeyakanthan, J. / Sekar, K. / Kuramitsu, S. / Yokoyama, S. | ||||||
![]() | ![]() Title: Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate Authors: Biswas, A. / Shukla, A. / Chaudhary, S.K. / Santhosh, R. / 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 | ![]() | 106.4 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4s2eC ![]() 4s35C ![]() 5h5bC ![]() 5h5kC ![]() 5xaiC ![]() 5xb2C ![]() 5xb3C ![]() 5xb5C ![]() 5xbhC ![]() 2pbrS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22402.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: VF5 / Gene: tmk, aq_969 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 330 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/TYD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TYD.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5, 45% MPD, 0.2M CaCl2, 10mM Mg, 10mM dTDP, 10mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 42940 / % possible obs: 97.8 % / Redundancy: 7 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 7.51 / Num. unique all: 3578 / % possible all: 82.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PBR Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.657 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.096 / 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: 14.244 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50 Å
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Refine LS restraints |
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