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Yorodumi- PDB-8rj4: E. coli adenylate kinase in complex with two ADP molecules and Mg... -
+Open data
-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 | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / ATP:AMP PHOSPHOTRANSFERASE / ENERGY METABOLISM / AP4A HYDROLYSIS / POTENTIAL MOONLIGHTING PROTEIN | ||||||
Function / homology | Function and homology information purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Tischlik, S. / Ronge, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Sci Adv / Year: 2024 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: Journal: Biochemistry / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rj4.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rj4.ent.gz | 151.7 KB | Display | PDB format |
PDBx/mmJSON format | 8rj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rj4_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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Full document | 8rj4_full_validation.pdf.gz | 4.4 MB | Display | |
Data in XML | 8rj4_validation.xml.gz | 37.5 KB | Display | |
Data in CIF | 8rj4_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rj/8rj4 ftp://data.pdbj.org/pub/pdb/validation_reports/rj/8rj4 | HTTPS FTP |
-Related structure data
Related structure data | 8rj6C 8rj9C 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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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.) Escherichia coli (E. coli) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→44.71 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.06 / 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 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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