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Yorodumi- PDB-7ml9: The Mpp75Aa1.1 beta-pore-forming protein from Brevibacillus later... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ml9 | ||||||
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Title | The Mpp75Aa1.1 beta-pore-forming protein from Brevibacillus laterosporus | ||||||
Components | Insecticidal protein | ||||||
Keywords | TOXIN / beta-pore-forming protein | ||||||
Function / homology | Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / ACETATE ION / SAMARIUM (III) ION / Insecticidal protein Function and homology information | ||||||
Biological species | Brevibacillus laterosporus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å | ||||||
Authors | Rydel, T.J. / Zheng, M. / Evdokimov, A. | ||||||
Citation | Journal: Plos One / Year: 2021 Title: Structural and functional characterization of Mpp75Aa1.1, a putative beta-pore forming protein from Brevibacillus laterosporus active against the western corn rootworm. Authors: Kouadio, J.L. / Duff, S. / Aikins, M. / Zheng, M. / Rydel, T. / Chen, D. / Bretsnyder, E. / Xia, C. / Zhang, J. / Milligan, J. / Evdokimov, A. / Nageotte, J. / Yin, Y. / Moar, W. / Giddings, ...Authors: Kouadio, J.L. / Duff, S. / Aikins, M. / Zheng, M. / Rydel, T. / Chen, D. / Bretsnyder, E. / Xia, C. / Zhang, J. / Milligan, J. / Evdokimov, A. / Nageotte, J. / Yin, Y. / Moar, W. / Giddings, K. / Park, Y. / Jerga, A. / Haas, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ml9.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ml9.ent.gz | 56.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ml9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ml9_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 7ml9_full_validation.pdf.gz | 450.6 KB | Display | |
Data in XML | 7ml9_validation.xml.gz | 15 KB | Display | |
Data in CIF | 7ml9_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7ml9 ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7ml9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35862.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus laterosporus (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli Rosetta2 DE3 / References: UniProt: A0A249JQG5 |
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-Non-polymers , 5 types, 212 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 69.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: Structure-quality crystals were obtained using the Wizard34 reagent A2 (30% 2-methyl-2,4-pentanediol, 0.1 M sodium acetate buffer-pH 4.6, 0.2M calcium chloride) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→39.69 Å / Num. obs: 45222 / % possible obs: 98.4 % / Redundancy: 13.2 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.162 / Net I/σ(I): 42.9 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 2066 / Χ2: 0.56 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.94→39.69 Å / SU ML: 0.2104 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6309 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 31.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→39.69 Å
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Refine LS restraints |
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LS refinement shell |
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