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- PDB-4nzy: Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nzy | ||||||
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Title | Crystal structure (type-2) of dTMP kinase (st1543) from Sulfolobus Tokodaii Strain7 | ||||||
![]() | Probable thymidylate kinase | ||||||
![]() | TRANSFERASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Biswas, A. / Jeyakanthan, J. / Sekar, K. / Kuramitsu, S. / Yokoyama, S. | ||||||
![]() | ![]() Title: Insight into Substrate Binding Mechanism in Thymidylate Kinase based on Intrinsic Dynamics of the Active Site Authors: Biswas, A. / 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 | ![]() | 100.4 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 506.3 KB | Display | ![]() |
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Full document | ![]() | 510.2 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 24631.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 8 types, 195 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EPE / | ||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PG4 / | #7: Chemical | ChemComp-PGE / | #8: Chemical | ChemComp-1PE / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50% PEG 200, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K , temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Details: RH Coated Bent-Cyrindrical MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 25941 / Num. obs: 25941 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.53 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 6.42 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 24.541 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→26.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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