[English] 日本語
Yorodumi- PDB-7owe: Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a -
+Open data
-Basic information
Entry | Database: PDB / ID: 7owe | ||||||
---|---|---|---|---|---|---|---|
Title | Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Phosphotransferase / Odinarchaeota Adenylate kinase / AP5A | ||||||
Function / homology | AAA domain / adenylate kinase / adenylate kinase activity / phosphorylation / P-loop containing nucleoside triphosphate hydrolase / BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase Function and homology information | ||||||
Biological species | Candidatus Odinarchaeota archaeon LCB_4 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Grundstrom, C. / Aberg-Zingmark, E. / Verma, A. / Wolf-Watz, M. / Sauer, U.H. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7owe.cif.gz | 244.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7owe.ent.gz | 200.5 KB | Display | PDB format |
PDBx/mmJSON format | 7owe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7owe ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7owe | HTTPS FTP |
---|
-Related structure data
Related structure data | 7owhC 7owjC 7owkC 7owlC 1ki9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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-AP5 / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.4 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Drop E7 PACT Screen: 0.2 M NaAc, 20% PEG 3550. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→71.6 Å / Num. obs: 42150 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.056 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.98 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4139 / CC1/2: 0.626 / Rpim(I) all: 0.846 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ki9 Resolution: 2.75→71.582 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.2 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.31 Å2 / Biso mean: 93.4972 Å2 / Biso min: 44.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→71.582 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|