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Yorodumi- PDB-5eje: Crystal structure of E. coli Adenylate kinase G56C/T163C double m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eje | |||||||||
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Title | Crystal structure of E. coli Adenylate kinase G56C/T163C double mutant in complex with Ap5a | |||||||||
Components | Adenylate kinase | |||||||||
Keywords | TRANSFERASE / Adenylate kinase / G56C and T163C variant / disulfide bond / Ap5A ligand | |||||||||
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 / phosphorylation ...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 / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Sauer, U.H. / Kovermann, M. / Grundstrom, C. / Wolf-Watz, M. / Sauer-Eriksson, A.E. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural basis for ligand binding to an enzyme by a conformational selection pathway. Authors: Kovermann, M. / Grundstrom, C. / Sauer-Eriksson, A.E. / Sauer, U.H. / 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 | 5eje.cif.gz | 186.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eje.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 5eje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5eje ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5eje | HTTPS FTP |
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-Related structure data
Related structure data | 4akeS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23668.160 Da / Num. of mol.: 2 / Mutation: G56C and T163C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: E24377A / ETEC / Gene: adk, EcE24377A_0513 / Production host: Escherichia coli (E. coli) References: UniProt: A7ZIN4, UniProt: P69441*PLUS, adenylate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.69 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Purified AdK in 50 mM NaCl and 30 mM MES buffer, pH 6.0 was concentrated to 13 mg/ml and co-crystallized with a 5 molar excess of Ap5a. A typical drop contained 1 microL of protein mixed ...Details: Purified AdK in 50 mM NaCl and 30 mM MES buffer, pH 6.0 was concentrated to 13 mg/ml and co-crystallized with a 5 molar excess of Ap5a. A typical drop contained 1 microL of protein mixed with 1 microL of precipitant and equilibrated against 1 mL reservoir solution containing 26-28% PEG 8K, 10 mM CoCl2 and 0.1 M NaOAc, pH 5.8). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.038 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.8 Å / Num. obs: 37833 / % possible obs: 99.6 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.99 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AKE Resolution: 1.9→26.8 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 25.76 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→26.8 Å
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Refine LS restraints |
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LS refinement shell |
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