+Open data
-Basic information
Entry | Database: PDB / ID: 7owh | ||||||
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Title | Odinarchaeota Adenylate kinase (OdinAK) native structure | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / Asgard group | ||||||
Function / homology | AAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / Adenylate kinase Function and homology information | ||||||
Biological species | Candidatus Odinarchaeota archaeon LCB_4 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 7owh.cif.gz | 253.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7owh.ent.gz | 205.1 KB | Display | PDB format |
PDBx/mmJSON format | 7owh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owh ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owh | HTTPS FTP |
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-Related structure data
Related structure data | 7oweSC 7owjC 7owkC 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.) Candidatus Odinarchaeota archaeon LCB_4 (archaea) Gene: adkA_1, OdinLCB4_00710 / Variant: Odinarchaeaota / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9N9I8, adenylate kinase #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.4 Å3/Da / Density % sol: 48.67 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Bis-Tris Propane pH 7.0, 0.1 M, PEG 3350 12%, CuCl2 83 microM. Protein stored in 0.030 M MOPS, 0.05 M NaCl, pH 6.8 |
-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: 0.9762 Å |
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: 1.85→49.08 Å / Num. obs: 113276 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.85→1.88 Å / Rmerge(I) obs: 2.028 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11096 / CC1/2: 0.646 / Rpim(I) all: 0.813 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7owe Resolution: 1.85→49.08 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.41 / 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: 149.26 Å2 / Biso mean: 45.7032 Å2 / Biso min: 18.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→49.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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