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Yorodumi- PDB-4jl5: A high resolution structure of Aquifex Adenylate kinase with 2 ADP's -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jl5 | ||||||
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Title | A high resolution structure of Aquifex Adenylate kinase with 2 ADP's | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / phosphoryl transfer | ||||||
Function / homology | Function and homology information nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Cho, Y.-J. / Kern, D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: The energy landscape of adenylate kinase during catalysis. Authors: Kerns, S.J. / Agafonov, R.V. / Cho, Y.J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Alber, T. / Hagan, M.F. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jl5.cif.gz | 285.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jl5.ent.gz | 236.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jl5 ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jl5 | HTTPS FTP |
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-Related structure data
Related structure data | 3sr0C 4cf7C 4jkyC 4jl6C 4jl8C 4jlaC 4jlbC 4jldC 4jloC 4jlpC C: citing same article (ref.) |
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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
#1: Protein | Mass: 22982.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: adk, aq_078 / Production host: Escherichia coli (E. coli) / References: UniProt: O66490, adenylate kinase #2: Chemical | ChemComp-ADP / #3: Water | ChemComp-HOH / | |
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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: 2.14 Å3/Da / Density % sol: 42.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.1M Sodium Acetate trihydrate, 0.2M Ammonium Acetate, 30% w/v Polyethylene Glycol 4000, 20mM MgCl2, 20mM ADP , pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99186 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99186 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→28.96 Å / Num. all: 1560689 / Num. obs: 111370 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.24→1.31 Å / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.7 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→28.96 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 13.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.743 Å2 / ksol: 0.441 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.24→28.96 Å
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Refine LS restraints |
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LS refinement shell |
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