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- PDB-3svi: 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: 3svi | ||||||
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Title | Structure of the Pto-binding domain of HopPmaL generated by limited thermolysin digestion | ||||||
![]() | Type III effector HopAB2 | ||||||
![]() | SIGNALING PROTEIN / type III effector / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helical bundle | ||||||
Function / homology | Monooxygenase - #110 / Effector protein HopAB, Pto-binding domain / Monooxygenase / Up-down Bundle / Mainly Alpha / Type III effector HopAB2![]() | ||||||
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 | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 35.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 440 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lf3C ![]() 2lf6C ![]() 3tjyC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 9581.355 Da / Num. of mol.: 1 / Fragment: sequence database residues 72-156 Source method: isolated from a genetically manipulated source Details: protein was cut with TEV, then treated with limiting amounts of thermolysin during crystallization Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes ph7.5, 0.1M NaCl, 1.6M Ammonium Sulphate, 0.2 mg/ml thermolysin was added to the protein mixture. Paratone-N oil was used for cryoprotection, 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: 1.75→25.615 Å / Num. obs: 9824 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 43.429 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.9 / Num. unique all: 477 / Rsym value: 0.428 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.16 Å2 / ksol: 0.379 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→25.615 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -14.7794 Å / Origin y: -3.9139 Å / Origin z: 13.8576 Å
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Refinement TLS group | Selection details: (chain A and resid 139:217) |