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Open data
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Basic information
Entry | Database: PDB / ID: 4qbi | ||||||
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Title | Crystal structure of a stable adenylate kinase variant AKlse6 | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / Adenylate kinase / Zinc finger / transferase activity / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation | ||||||
Function / homology | ![]() CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / zinc ion binding ...CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moon, S. / Bae, E. | ||||||
![]() | ![]() Title: Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases. Authors: Moon, S. / Bannen, R.M. / Rutkoski, T.J. / Phillips Jr., G.N. / Bae, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.5 KB | Display | ![]() |
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PDB format | ![]() | 155.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 977.3 KB | Display | ![]() |
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Full document | ![]() | 983.6 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dl0C ![]() 4qbfC ![]() 4qbgC ![]() 4qbhC ![]() 1zinS 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
#1: Protein | Mass: 24414.111 Da / Num. of mol.: 2 / Mutation: 40 mutations Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: adk / Production host: ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 26.5% (w/v) polyethylene glycol 4000, 150mM magnesium acetate, 100mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 21, 2013 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 54822 / Num. obs: 54822 / % possible obs: 100 % |
Reflection shell | Resolution: 1.67→1.73 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZIN Resolution: 1.67→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.856 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.099 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.438 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→50 Å
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Refine LS restraints |
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