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Yorodumi- PDB-4ike: Crystal Structure of a partly open ATP-lid of liganded Adenylate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ike | ||||||
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Title | Crystal Structure of a partly open ATP-lid of liganded Adenylate kinase | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / tansferase (phosphotransferase) / phosphoryl transfer / nucleotide binding / phosphoryl transfer of nucleotides | ||||||
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: 1.48 Å | ||||||
Authors | Cho, Y.-J. / Kern, D. | ||||||
Citation | Journal: To be Published Title: The ATP-Lid Opened Adenylate Kinase with Fully Occupied Substrates Authors: Cho, Y.-J. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ike.cif.gz | 196.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ike.ent.gz | 157.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ike.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/4ike ftp://data.pdbj.org/pub/pdb/validation_reports/ik/4ike | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23269.057 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: adk, Aquifex, aq_078 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66490, adenylate kinase #2: Chemical | #3: Chemical | #4: 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: 2.19 Å3/Da / Density % sol: 43.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9998 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2009 |
Radiation | Monochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→34.82 Å / Num. all: 66860 / Num. obs: 66831 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→33.04 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 20.58 / 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: 1.48→33.04 Å
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Refine LS restraints |
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LS refinement shell |
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