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Yorodumi- PDB-4dc3: Adenosine kinase from Schistosoma mansoni in complex with 2-fluor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dc3 | ||||||
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Title | Adenosine kinase from Schistosoma mansoni in complex with 2-fluoroadenosine | ||||||
Components | Adenosine kinase | ||||||
Keywords | TRANSFERASE / ribokinase | ||||||
Function / homology | Function and homology information adenosine kinase / adenosine kinase activity / purine ribonucleoside salvage / nucleotide binding Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Romanello, L. / Bachega, F.R. / Garatt, R.C. / DeMarco, R. / Brandao-neto, J. / Pereira, H.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues. Authors: Romanello, L. / Bachega, J.F. / Cassago, A. / Brandao-Neto, J. / Demarco, R. / Garratt, R.C. / Pereira, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dc3.cif.gz | 283.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dc3.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 4dc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/4dc3 ftp://data.pdbj.org/pub/pdb/validation_reports/dc/4dc3 | HTTPS FTP |
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-Related structure data
Related structure data | 3uq6C 3uq9C 3vaqSC 3vasC C: citing same article (ref.) 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: 41572.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 37oC / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: adenosine kinase, Smp_008360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4V7G8, adenosine kinase #2: Chemical | ChemComp-ADN / | #3: Chemical | #4: Chemical | ChemComp-2FA / | #5: 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: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM Bis-tris pH 6.1-6.7, 200mM LiSO4, 16-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.1-6.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9611 Å | ||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2011 / Details: Compound Refractive Lenses | ||||||||||||||||||
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.9611 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.4→47.61 Å / Num. all: 32370 / Num. obs: 30864 / % possible obs: 90.34 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.5 Å2 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3VAQ Resolution: 2.4→47.61 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.29 / σ(F): 1.33 / Phase error: 22.8 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6884 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.61 Å
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Refine LS restraints |
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LS refinement shell |
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