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Yorodumi- PDB-3uq6: Adenosine kinase from Schistosoma mansoni in complex with adenosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uq6 | ||||||
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Title | Adenosine kinase from Schistosoma mansoni in complex with adenosine and AMP | ||||||
Components | Adenosine kinase, putative | ||||||
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: 2.3 Å | ||||||
Authors | Romanello, L. / Cassago, A. / Bachega, F.R. / Garatt, R.C. / DeMarco, R. / 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 | 3uq6.cif.gz | 278.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uq6.ent.gz | 224 KB | Display | PDB format |
PDBx/mmJSON format | 3uq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/3uq6 ftp://data.pdbj.org/pub/pdb/validation_reports/uq/3uq6 | HTTPS FTP |
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-Related structure data
Related structure data | 3uq9C 3vaqC 3vasC 4dc3C 1bx4S 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
#1: Protein | Mass: 41609.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 37oC / Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: AK2, Smp_008360 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: C4PZB4, UniProt: G4V7G8*PLUS, adenosine kinase #2: Chemical | #3: Chemical | #4: Chemical | #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: 51.73 % |
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Crystal grow | Temperature: 293 K Details: 100mM Bis-tris, 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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 26, 2008 |
Radiation | Monochromator: DCM SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→180.53 Å / Num. obs: 35871 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.552 / % possible all: 88.6 |
-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 1BX4 Resolution: 2.3→49.958 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 25.57 / 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: 43.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→49.958 Å
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Refine LS restraints |
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LS refinement shell |
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