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Yorodumi- PDB-4jl8: A various kinds of ADP conformations in the Adenylate kinase acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jl8 | ||||||
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Title | A various kinds of ADP conformations in the Adenylate kinase active site | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / phosphoryl transfer reaction | ||||||
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: 1.79 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 | 4jl8.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jl8.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 4jl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/4jl8 ftp://data.pdbj.org/pub/pdb/validation_reports/jl/4jl8 | HTTPS FTP |
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-Related structure data
Related structure data | 3sr0C 4cf7C 4jkyC 4jl5C 4jl6C 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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1 |
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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 / Fragment: transferase 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: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 291 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, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.79→37.96 Å / Num. all: 511723 / Num. obs: 42592 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.56 Å2 / Net I/σ(I): 14.5 | |||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→37.96 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8416 / SU ML: 0.49 / σ(F): 1.33 / Phase error: 22.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.648 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.64 Å2 / Biso mean: 23.0515 Å2 / Biso min: 6.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→37.96 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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