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- PDB-3tjy: Structure of the Pto-binding domain of HopPmaL generated by limit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tjy | ||||||
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Title | Structure of the Pto-binding domain of HopPmaL generated by limited chymotrypsin digestion | ||||||
![]() | Effector protein hopAB3 | ||||||
![]() | SIGNALING PROTEIN / type III effector / HopPmaL / Pseudomonas syringae / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helical bundle / Pto | ||||||
Function / homology | ![]() symbiont-mediated perturbation of host defense-related programmed cell death / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Singer, A.U. / Stein, A. / Xu, X. / Cui, H. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structural analysis of HopPmaL reveals the presence of a second adaptor domain common to the HopAB family of Pseudomonas syringae type III effectors. Authors: Singer, A.U. / Wu, B. / Yee, A. / Houliston, S. / Xu, X. / Cui, H. / Skarina, T. / Garcia, M. / Semesi, A. / Arrowsmith, C.H. / Savchenko, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 36.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2lf3C ![]() 2lf6C ![]() 3sviC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10655.572 Da / Num. of mol.: 1 / Fragment: HopPmaL / Mutation: none Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ES4326 / Gene: hopAB3, hopPmaL / Plasmid: p15TvLic / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | PROTEIN WAS CLONED AS HOPPMAL RESIDUES 135-273, CUT WITH TEV, THEN TREATED WITH LIMITING AMOUNTS OF ...PROTEIN WAS CLONED AS HOPPMAL RESIDUES 135-273, CUT WITH TEV, THEN TREATED WITH LIMITING AMOUNTS OF THERMOLYSI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris pH 6.5 plus 1.5M Ammonium Sulphate. 0.03 mg/ml chymotrypsin was added to the protein prior to adding crystallization liquor. Crystals were cryoprotected with Paratone-N oil , ...Details: 0.1M Bis-Tris pH 6.5 plus 1.5M Ammonium Sulphate. 0.03 mg/ml chymotrypsin was added to the protein prior to adding crystallization liquor. Crystals were cryoprotected with Paratone-N oil , VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009 / Details: mirrors |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→25.682 Å / Num. all: 11562 / Num. obs: 11555 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 42.133 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.501 / % possible all: 100 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.325 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→25.682 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.4761 Å / Origin y: -4.9353 Å / Origin z: 13.9018 Å
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Refinement TLS group | Selection details: (chain A and resid 140:217) |