+Open data
-Basic information
Entry | Database: PDB / ID: 7owk | ||||||
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Title | Odinarchaeota Adenylate kinase (OdinAK) in complex with dTTP | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group / dTTP | ||||||
Function / homology | AAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / THYMIDINE-5'-TRIPHOSPHATE / Adenylate kinase Function and homology information | ||||||
Biological species | Odinarchaeota archaeon | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Aberg-Zingmark, E. / Grundstrom, C. / Verma, A. / Wolf-Watz, M. / Sauer, U.H. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Sci Adv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7owk.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7owk.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 7owk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owk ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owk | HTTPS FTP |
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-Related structure data
Related structure data | 7oweSC 7owhC 7owjC 7owlC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Odinarchaeota archaeon (strain LCB_4) (archaea) Strain: LCB_4 / Gene: adkA_1, OdinLCB4_00710 / Variant: Odinarchaeaota / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9I8, adenylate kinase #2: Chemical | ChemComp-TTP / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein: 0.030 M MOPS, 0.050 M NaCl pH 7.0. Precipitant: Bis-Tris Propane pH 7.0, 0.1 M, PEG 3350 15-18% Odin 0.732 milliM, dTTP 5.8 milliM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→48.57 Å / Num. obs: 23925 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.356 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 3.017 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2363 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OWE Resolution: 3.1→48.567 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.07 / 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: 244.78 Å2 / Biso mean: 70.3 Å2 / Biso min: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→48.567 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
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