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Open data
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Basic information
Entry | Database: PDB / ID: 1ki9 | ||||||
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Title | Adenylate kinase from Methanococcus thermolithotrophicus | ||||||
![]() | adenylate kinase | ||||||
![]() | SIGNALING PROTEIN / TRANSFERASE / kinase / phosphotransferase | ||||||
Function / homology | ![]() adenylate kinase / adenylate kinase activity / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Criswell, A.R. / Konisky, J. / Phillips Jr., G.N. | ||||||
![]() | ![]() Title: Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus Authors: Criswell, A.R. / Bae, E. / Stec, B. / Konisky, J. / Phillips Jr., G.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.9 KB | Display | ![]() |
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PDB format | ![]() | 97.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 460.6 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1khtC ![]() 1nksS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21486.764 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: adk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 1999 / Details: confocal |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 27043 / Num. obs: 25623 / % possible obs: 94.7 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.068 |
Reflection | *PLUS Highest resolution: 2.76 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 2.76 Å / Lowest resolution: 2.95 Å / % possible obs: 94.4 % / Rmerge(I) obs: 0.175 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1NKS Resolution: 2.76→30.78 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 157151.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.3445 Å2 / ksol: 0.33371 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.76→30.78 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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