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Open data
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Basic information
Entry | Database: PDB / ID: 7owj | ||||||
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Title | Odinarchaeota Adenylate kinase (OdinAK) in complex with GTP | ||||||
![]() | Adenylate kinase | ||||||
![]() | TRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group / GTP | ||||||
Function / homology | AAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / GUANOSINE-5'-TRIPHOSPHATE / Adenylate kinase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aberg-Zingmark, E. / Grundstrom, C. / Verma, A. / Wolf-Watz, M. / Sauer, U.H. / Sauer-Eriksson, A.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. Authors: Verma, A. / Aberg-Zingmark, E. / Sparrman, T. / Mushtaq, A.U. / Rogne, P. / Grundstrom, C. / Berntsson, R. / Sauer, U.H. / Backman, L. / Nam, K. / Sauer-Eriksson, E. / 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 | ![]() | 247.3 KB | Display | ![]() |
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PDB format | ![]() | 201.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 45.1 KB | Display | |
Data in CIF | ![]() | 60.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oweSC ![]() 7owhC ![]() 7owkC ![]() 7owlC S: Starting model for refinement 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22883.516 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: adkA_1, OdinLCB4_00710 / Variant: Odinarchaeaota / Production host: ![]() ![]() #2: Chemical | ChemComp-GTP / #3: 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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein in: 0.030 M MOPS, 0.050M NaCl, pH 6.8. Drop: 1:1 of Bis-Tris Propane pH 6.5 - 0.1 M, PEG 3350 12% Odin 0.853 mM, GTP 8.53 mM |
-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: Mar 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.27 Å / Num. obs: 46830 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.088 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / Num. unique obs: 4562 / CC1/2: 0.708 / Rpim(I) all: 0.548 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7owe Resolution: 2.5→49.27 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.74 / Stereochemistry target values: ML
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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 max: 323.44 Å2 / Biso mean: 51.5686 Å2 / Biso min: 13.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→49.27 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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