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- PDB-4ike: Crystal Structure of a partly open ATP-lid of liganded Adenylate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ike | ||||||
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Title | Crystal Structure of a partly open ATP-lid of liganded Adenylate kinase | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / tansferase (phosphotransferase) / phosphoryl transfer / nucleotide binding / phosphoryl transfer of nucleotides | ||||||
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 / intracellular membrane-bounded organelle / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cho, Y.-J. / Kern, D. | ||||||
![]() | ![]() Title: The ATP-Lid Opened Adenylate Kinase with Fully Occupied Substrates Authors: Cho, Y.-J. / Kern, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 196.7 KB | Display | ![]() |
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PDB format | ![]() | 157.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 23269.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2009 |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→34.82 Å / Num. all: 66860 / Num. obs: 66831 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→33.04 Å
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Refine LS restraints |
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LS refinement shell |
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