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Open data
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Basic information
Entry | Database: PDB / ID: 4mkh | ||||||
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Title | Crystal structure of a stable adenylate kinase variant AKv18 | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / Adenylate kinase / Zinc Finger / transferase activity / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation | ||||||
Function / homology | ![]() nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity ...nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moon, S. / Bae, E. | ||||||
![]() | ![]() Title: An integrated approach for thermal stabilization of a mesophilic adenylate kinase. Authors: Moon, S. / Jung, D.K. / 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 | ![]() | 106.2 KB | Display | ![]() |
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PDB format | ![]() | 79.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 970.1 KB | Display | ![]() |
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Full document | ![]() | 975.8 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mkfC ![]() 4mkgSC 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: 24967.594 Da / Num. of mol.: 1 Mutation: L3I,Q16L,G17A,R19K,D23K,K69R,G73S,D75S,Y103M,K105R,E114Q,D116R,D118E,V119E,S169T,T179M,Q180A,D184A,S187D,E188S,G190E,Y191V,A193V,Q198E,Q199R,Q202E,F205Y,K209D,D210V,L211I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | ChemComp-AP5 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 310.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.6M ammonium citrate pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 310.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2012 |
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: 1.5→50 Å / Num. all: 33561 / Num. obs: 33460 / % possible obs: 99.7 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3318 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MKG Resolution: 1.5→27.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.826 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.353 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.6 Å
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Refine LS restraints |
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