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Yorodumi- PDB-3q60: Crystal structure of virulent allele ROP5B pseudokinase domain bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q60 | ||||||
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Title | Crystal structure of virulent allele ROP5B pseudokinase domain bound to ATP | ||||||
Components | ROP5B | ||||||
Keywords | TRANSFERASE / pseudokinase / toxoplasma / 551.m00238 / ROP5 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å | ||||||
Authors | Reese, M.L. / Boothroyd, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: A conserved non-canonical motif in the pseudoactive site of the ROP5 pseudokinase domain mediates its effect on Toxoplasma virulence. Authors: Reese, M.L. / Boothroyd, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q60.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q60.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q60_validation.pdf.gz | 790.9 KB | Display | wwPDB validaton report |
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Full document | 3q60_full_validation.pdf.gz | 792.5 KB | Display | |
Data in XML | 3q60_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 3q60_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q60 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q60 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41218.145 Da / Num. of mol.: 1 / Fragment: Pseudokinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ROP5B;TGGT1_042710 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: F2YGR7*PLUS, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-ATP / | ||||
#3: Chemical | ChemComp-MLI / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | GENOMIC SEQUENCE ENCODING THE PROTEIN HAS BEEN DEPOSITED IN GENBANK ACCESSION HQ916448. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG-3350, 0.3M Sodium malonate, 0.02M MgCl2, 0.01M ATP, pH 5.5, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2010 / Details: Rh coated flat mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→50 Å / Num. obs: 40071 / % possible obs: 98.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.072 / Χ2: 0.986 / Net I/σ(I): 11.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 / Resolution: 1.72→30.219 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.464 Å2 / ksol: 0.42 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.31 Å2 / Biso mean: 30.6359 Å2 / Biso min: 12.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→30.219 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: 10
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