[English] 日本語
![](img/lk-miru.gif)
- PDB-7qx7: mosquitocidal Cry11Aa-F17Y determined at pH 7 from naturally-occu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7qx7 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | mosquitocidal Cry11Aa-F17Y determined at pH 7 from naturally-occurring nanocrystals by Serial femtosecond crystallography | |||||||||||||||||||||
![]() | Pesticidal crystal protein Cry11Aa | |||||||||||||||||||||
![]() | TOXIN / naturally-occurring crystals mosquitocidal toxin serial femtosecond crystallography | |||||||||||||||||||||
Function / homology | Pesticidal crystal protein / symbiont-mediated killing of host cell / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / sporulation resulting in formation of a cellular spore / toxin activity / Pesticidal crystal protein Cry11Aa![]() | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||||||||
![]() | De Zitter, E. / Tetreau, G. / Andreeva, E.A. / Coquelle, N. / Colletier, J.-P. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: De novo determination of mosquitocidal Cry11Aa and Cry11Ba structures from naturally-occurring nanocrystals. Authors: Tetreau, G. / Sawaya, M.R. / De Zitter, E. / Andreeva, E.A. / Banneville, A.S. / Schibrowsky, N.A. / Coquelle, N. / Brewster, A.S. / Grunbein, M.L. / Kovacs, G.N. / Hunter, M.S. / Kloos, M. ...Authors: Tetreau, G. / Sawaya, M.R. / De Zitter, E. / Andreeva, E.A. / Banneville, A.S. / Schibrowsky, N.A. / Coquelle, N. / Brewster, A.S. / Grunbein, M.L. / Kovacs, G.N. / Hunter, M.S. / Kloos, M. / Sierra, R.G. / Schiro, G. / Qiao, P. / Stricker, M. / Bideshi, D. / Young, I.D. / Zala, N. / Engilberge, S. / Gorel, A. / Signor, L. / Teulon, J.M. / Hilpert, M. / Foucar, L. / Bielecki, J. / Bean, R. / de Wijn, R. / Sato, T. / Kirkwood, H. / Letrun, R. / Batyuk, A. / Snigireva, I. / Fenel, D. / Schubert, R. / Canfield, E.J. / Alba, M.M. / Laporte, F. / Despres, L. / Bacia, M. / Roux, A. / Chapelle, C. / Riobe, F. / Maury, O. / Ling, W.L. / Boutet, S. / Mancuso, A. / Gutsche, I. / Girard, E. / Barends, T.R.M. / Pellequer, J.L. / Park, H.W. / Laganowsky, A.D. / Rodriguez, J. / Burghammer, M. / Shoeman, R.L. / Doak, R.B. / Weik, M. / Sauter, N.K. / Federici, B. / Cascio, D. / Schlichting, I. / Colletier, J.P. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 125.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 95.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7qx4C ![]() 7qx5C ![]() 7qx6C ![]() 7qydC ![]() 7r1eC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 72423.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cry11Aa, cryD, cryIVd, cryXIA(a) / Plasmid: pWF53 Production host: ![]() ![]() Strain (production host): 4Q7 / References: UniProt: P21256 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % |
---|---|
Crystal grow | Temperature: 300 K / Method: in cell / pH: 7 Details: In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid. |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: AGIPD / Detector: PIXEL / Date: Sep 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.33 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→23.17 Å / Num. obs: 10990 / % possible obs: 99.6 % / Redundancy: 265.7 % / CC1/2: 0.96 / R split: 0.197 / Net I/σ(I): 6.31 |
Reflection shell | Resolution: 3.4→3.48 Å / Num. unique obs: 707 / CC1/2: 0.31 / R split: 0.802 |
Serial crystallography measurement | Focal spot size: 1.3 µm2 / Pulse photon energy: 9.3 keV |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: Pure water / Description: GVDN / Power by: gas Preparation: crystals rinsed and kept in water after sucrose gradient purification |
Serial crystallography data reduction | Frames indexed: 28227 / Frames total: 3150500 / Lattices indexed: 1 |
-Phasing
Phasing | Method: ![]() | ||||||
---|---|---|---|---|---|---|---|
Phasing MR |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: D_1292119069 Resolution: 3.4→23.17 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.59 Å2 / Biso mean: 54.4002 Å2 / Biso min: 41.7 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→23.17 Å
| ||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
|