+Open data
-Basic information
Entry | Database: PDB / ID: 3q5z | ||||||
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Title | Crystal structure of virulent allele ROP5B pseudokinase domain | ||||||
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 / SIRAS / Resolution: 1.9 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 | 3q5z.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q5z.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 3q5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/3q5z ftp://data.pdbj.org/pub/pdb/validation_reports/q5/3q5z | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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-EDO / #3: 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: 2.16 Å3/Da / Density % sol: 43.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG-3350, 0.3M Sodium malonate, 0.01M MgCl2, pH 5.0, 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: Aug 6, 2009 / Details: Rh coated flat mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 28779 / % possible obs: 98.7 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.054 / Χ2: 1.012 / Net I/σ(I): 15.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SIRAS |
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-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.9→36.727 Å / Occupancy max: 1 / Occupancy min: 0.45 / SU ML: 0.25 / 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: 61.489 Å2 / ksol: 0.435 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.09 Å2 / Biso mean: 42.2784 Å2 / Biso min: 20.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→36.727 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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