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- PDB-7ml9: The Mpp75Aa1.1 beta-pore-forming protein from Brevibacillus later... -

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Basic information

Entry
Database: PDB / ID: 7ml9
TitleThe Mpp75Aa1.1 beta-pore-forming protein from Brevibacillus laterosporus
ComponentsInsecticidal protein
KeywordsTOXIN / beta-pore-forming protein
Function / homologyAerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / ACETATE ION / SAMARIUM (III) ION / Insecticidal protein
Function and homology information
Biological speciesBrevibacillus laterosporus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsRydel, T.J. / Zheng, M. / Evdokimov, A.
CitationJournal: 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
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.2Oct 27, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insecticidal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4949
Polymers35,8631
Non-polymers6318
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.791, 69.791, 241.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Insecticidal 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 ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sm
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.97 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2475 2278 5.04 %
Rwork0.2193 42944 -
obs0.2207 45222 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.02 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 23 204 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722393
X-RAY DIFFRACTIONf_angle_d0.83013247
X-RAY DIFFRACTIONf_chiral_restr0.0546354
X-RAY DIFFRACTIONf_plane_restr0.0047428
X-RAY DIFFRACTIONf_dihedral_angle_d12.2281333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.31251540.28662576X-RAY DIFFRACTION99.13
1.98-2.030.33331470.27012612X-RAY DIFFRACTION99.96
2.03-2.080.2981430.26512640X-RAY DIFFRACTION100
2.08-2.140.26081230.25312645X-RAY DIFFRACTION99.96
2.14-2.20.27291350.24762652X-RAY DIFFRACTION100
2.2-2.270.26721420.24812643X-RAY DIFFRACTION99.96
2.27-2.350.30641290.25032670X-RAY DIFFRACTION100
2.35-2.450.28291200.24662648X-RAY DIFFRACTION99.96
2.45-2.560.29411550.24792678X-RAY DIFFRACTION100
2.56-2.690.28591460.2462660X-RAY DIFFRACTION99.96
2.69-2.860.26711490.24262652X-RAY DIFFRACTION99.96
2.86-3.080.26191640.23352683X-RAY DIFFRACTION99.96
3.08-3.390.24361290.21632730X-RAY DIFFRACTION99.97
3.39-3.880.21591490.19182734X-RAY DIFFRACTION99.93
3.88-4.890.21631500.16882760X-RAY DIFFRACTION99.9
4.89-39.690.19351430.2032961X-RAY DIFFRACTION99.3

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