+Open data
-Basic information
Entry | Database: PDB / ID: 4jky | ||||||
---|---|---|---|---|---|---|---|
Title | Cobalt between two ADP's in the active site of adenylate kinase | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / phosphoryl transfer reaction / Cobalt binding | ||||||
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: 2.373 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4jky.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4jky.ent.gz | 76.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/4jky ftp://data.pdbj.org/pub/pdb/validation_reports/jk/4jky | HTTPS FTP |
---|
-Related structure data
Related structure data | 3sr0C 4cf7C 4jl5C 4jl6C 4jl8C 4jlaC 4jlbC 4jldC 4jloC 4jlpC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.95 % |
---|---|
Crystal grow | Temperature: 298 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, ADP(17.3mM) and CoCl2(41.2mM), pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.6086 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.6086 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→56.28 Å / Num. all: 33838 / Num. obs: 18108 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.23 Å2 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2.37→2.5 Å / Rmerge(I) obs: 0.198 / % possible all: 97.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.373→53.463 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.7834 / SU ML: 0.78 / σ(F): 1.34 / Phase error: 28.17 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.056 Å2 / ksol: 0.296 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.33 Å2 / Biso mean: 41.5628 Å2 / Biso min: 15.17 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.373→53.463 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
|