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- PDB-5zb4: Crystal structure of thymidylate kinase in complex with ADP and T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5zb4 | ||||||
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Title | Crystal structure of thymidylate kinase in complex with ADP and TMP from thermus thermophilus HB8 | ||||||
![]() | Thymidylate kinase | ||||||
![]() | TRANSFERASE / NMP kinase | ||||||
Function / homology | ![]() dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / dTTP biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K. | ||||||
![]() | ![]() Title: Insights into product release dynamics through structural analyses of thymidylate kinase. Authors: Chaudhary, S.K. / Iyyappan, Y. / Elayappan, M. / 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 | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 70.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5x7jSC ![]() 5zaxC ![]() 5zb0C S: Starting model for refinement C: citing same article ( |
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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: 22009.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / Gene: tmk, TTHA1607 Production host: ![]() ![]() References: UniProt: Q5SHX3, dTMP kinase |
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-Non-polymers , 5 types, 184 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TMP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.44 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / Details: 0.2M CaCl2.2H2O, 20% w/v 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: Jul 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→19.74 Å / Num. obs: 26814 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.75 |
Reflection shell | Resolution: 1.92→1.95 Å / Rmerge(I) obs: 0.168 / CC1/2: 0.983 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X7J Resolution: 1.92→19.74 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.704 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.16 / 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: 15.586 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→19.74 Å
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Refine LS restraints |
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