+Open data
-Basic information
Entry | Database: PDB / ID: 4lv5 | ||||||
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Title | Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI | ||||||
Components |
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Keywords | Transferase/Hydrolase / immune related GTPase / guanine dissociation inhibitor / parasite effector / Transferase-Hydrolase complex | ||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to bacterium / defense response / cytokine-mediated signaling pathway / GDP binding ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / response to bacterium / defense response / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / protein kinase activity / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Toxoplasma gondii (eukaryote) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Reese, M.L. / Boothroyd, J.C. | ||||||
Citation | Journal: To be Published Title: Murine IRGa6 bound to Toxoplasma ROP5B, a pseudokinase GDI Authors: Reese, M.L. / Shah, N. / 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 | 4lv5.cif.gz | 182.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lv5.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lv5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4lv5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4lv5_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 4lv5_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/4lv5 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/4lv5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | biological unit is the same as asym. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 41218.145 Da / Num. of mol.: 1 / Fragment: UNP residues 175-541 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ROP5, ROP5B / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2YGR7 |
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#2: Protein | Mass: 48484.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Iigp1, Irga6 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9QZ85, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
-Non-polymers , 5 types, 492 molecules
#3: Chemical | ChemComp-ADP / | ||||
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#4: Chemical | ChemComp-BME / | ||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GDP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 0.1M Ammonium Citrate, pH 7.0, 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: 0.97945 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→39.33 Å / Num. obs: 92554 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.613 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.018 / Diffraction-ID: 1
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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: 3Q60 and then 1TPZ:A using phaser Resolution: 1.7→39.328 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.21 / σ(F): 1.97 / Phase error: 27.83 / 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 max: 85.77 Å2 / Biso mean: 38.0282 Å2 / Biso min: 17.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.328 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: 30
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