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- PDB-8rj4: E. coli adenylate kinase in complex with two ADP molecules and Mg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rj4 | ||||||
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Title | E. coli adenylate kinase in complex with two ADP molecules and Mg2+ as a result of enzymatic AP4A hydrolysis | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / ATP:AMP PHOSPHOTRANSFERASE / ENERGY METABOLISM / AP4A HYDROLYSIS / POTENTIAL MOONLIGHTING PROTEIN | ||||||
Function / homology | ![]() purine ribonucleotide interconversion / ADP biosynthetic process / 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 ...purine ribonucleotide interconversion / ADP biosynthetic process / 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 / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tischlik, S. / Ronge, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase. Authors: Abdul Raafik, A.T. / Tischlik, S. / Nagy, T.M. / Phoeurk, C. / Schierholtz, L. / Aden, J. / Rogne, P. / Drescher, M. / Nam, K. / Sauer-Eriksson, A.E. / Wolf-Watz, M. #1: ![]() Title: Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by Authors: Tischlik, S. / Oelker, M. / Rogne, P. / Sauer-Eriksson, A.E. / Drescher, M. / Wolf-Watz, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.2 KB | Display | ![]() |
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PDB format | ![]() | 151.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 37.5 KB | Display | |
Data in CIF | ![]() | 53.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rj6C ![]() 8rj9C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 23620.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ADP / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: 24 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→44.71 Å / Num. obs: 55145 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 36.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.083 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.11→2.19 Å / Rmerge(I) obs: 1.452 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5433 / CC1/2: 0.668 / Rpim(I) all: 0.903 |
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.36 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→44.71 Å
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LS refinement shell |
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