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- PDB-5zb0: 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: 5zb0 | ||||||
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Title | Crystal structure of thymidylate kinase in complex with ADP and TDP 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 | ![]() | 180.4 KB | Display | ![]() |
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PDB format | ![]() | 141.4 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 ![]() 5zb4C 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, 375 molecules ![](data/chem/img/TYD.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.84 % |
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Crystal grow | Temperature: 295 K / Method: microbatch Details: 0.2M MgCl2.6H2O, 0.1M Tris hydrochloride, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→50.01 Å / Num. obs: 107494 / % possible obs: 98.4 % / Redundancy: 4 % / CC1/2: 0.9818 / Rpim(I) all: 0.026 / Net I/σ(I): 37.12 |
Reflection shell | Resolution: 1.19→1.21 Å / CC1/2: 0.855 / Rpim(I) all: 0.203 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5X7J Resolution: 1.19→50.01 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.849 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.357 Å2
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Refinement step | Cycle: 1 / Resolution: 1.19→50.01 Å
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Refine LS restraints |
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