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Open data
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Basic information
Entry | Database: PDB / ID: 4typ | ||||||
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Title | Crystal structure of an adenylate kinase mutant--AKm1 | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / adenylate kinase / ATP binding | ||||||
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: Crystal structures of thermally stable adenylate kinase mutants designed by local structural entropy optimization and structure-guided mutagenesis Authors: Moon, S. / 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 | ![]() | 330.2 KB | Display | ![]() |
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PDB format | ![]() | 271.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4tyqC ![]() 4mkgS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 24456.176 Da / Num. of mol.: 4 Mutation: L3I, G17A, R19K, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, Y109H, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180K, D184A, S187D, E188S, G190E, Y191V, A193R, ...Mutation: L3I, G17A, R19K, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, Y109H, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180K, D184A, S187D, E188S, G190E, Y191V, A193R, Q198E, I201M, Q202E, D203K, Y205F, A206K, V208L, K209R, D210E, G213Q, K216A, K217R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-AP5 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 18% (w/v) polyethylene glycol 3350, 100mM lithium sulfate, 100mM Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Monochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 20201 / Num. obs: 18989 / % possible obs: 94 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1 |
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Processing
Software | Name: REFMAC / Version: 5.8.0049 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 4MKG Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.808 / SU B: 77.842 / SU ML: 0.641 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / 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: 42.461 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→50 Å
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Refine LS restraints |
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