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- PDB-7fdp: Crystal structure of PirB insecticidal protein from Photorhabdus ... -

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Basic information

Entry
Database: PDB / ID: 7fdp
TitleCrystal structure of PirB insecticidal protein from Photorhabdus akhurstii
ComponentsInsecticidal protein
KeywordsTOXIN / Insecticidal protein / two-domain / PirB
Function / homologyPesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / Insecticidal protein
Function and homology information
Biological speciesPhotorhabdus akhurstii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPrashar, A. / Kinkar, O. / Kumar, A. / Hire, R.S. / Makde, R.D.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2023
Title: Crystal structures of PirA and PirB toxins from Photorhabdus akhurstii subsp. akhurstii K-1
Authors: Prashar, A. / Kinkar, O.U. / Kumar, A. / Hadapad, A.B. / Makde, R.D. / Hire, R.S.
History
DepositionJul 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insecticidal protein
B: Insecticidal protein


Theoretical massNumber of molelcules
Total (without water)92,6862
Polymers92,6862
Non-polymers00
Water11,530640
1
A: Insecticidal protein


Theoretical massNumber of molelcules
Total (without water)46,3431
Polymers46,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Insecticidal protein


Theoretical massNumber of molelcules
Total (without water)46,3431
Polymers46,3431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.802, 89.274, 124.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Insecticidal protein


Mass: 46343.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus akhurstii (bacteria) / Gene: pirB / Plasmid: pST50Tr / Details (production host): pET3a-based / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: G5DBH4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.2
Details: 0.2 M sodium chloride, 0.1 M phosphate-Citrate buffer pH 4.2, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2019 / Details: Mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→47.62 Å / Num. obs: 48762 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.68 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.059 / Rrim(I) all: 0.159 / Χ2: 1.01 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-47.626.30.06725.47340.9950.0290.0731.0899.4
2.1-2.166.70.6322.938590.8240.2610.6850.8998.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.18.2_3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X0U

3x0u


Resolution: 2.1→36.52 Å / SU ML: 0.2367 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 2436 5 %
Rwork0.1917 46248 -
obs0.1937 48684 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 0 640 6896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236372
X-RAY DIFFRACTIONf_angle_d0.52418635
X-RAY DIFFRACTIONf_chiral_restr0.0405975
X-RAY DIFFRACTIONf_plane_restr0.00321118
X-RAY DIFFRACTIONf_dihedral_angle_d11.4736875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.28721430.22722587X-RAY DIFFRACTION97.78
2.14-2.190.29821360.2272732X-RAY DIFFRACTION99.97
2.19-2.240.29781340.23712690X-RAY DIFFRACTION100
2.24-2.30.26961490.23292671X-RAY DIFFRACTION100
2.3-2.360.25561300.22322699X-RAY DIFFRACTION100
2.36-2.430.31550.21642675X-RAY DIFFRACTION99.93
2.43-2.510.27781400.22022711X-RAY DIFFRACTION100
2.51-2.60.26051690.21792673X-RAY DIFFRACTION100
2.6-2.70.27631590.21372688X-RAY DIFFRACTION100
2.7-2.820.2271180.21292729X-RAY DIFFRACTION99.96
2.82-2.970.24721490.21262719X-RAY DIFFRACTION99.97
2.97-3.160.241210.20982728X-RAY DIFFRACTION99.96
3.16-3.40.26261440.19652737X-RAY DIFFRACTION99.9
3.4-3.740.21071410.18262753X-RAY DIFFRACTION99.97
3.74-4.280.18061610.15712738X-RAY DIFFRACTION99.83
4.28-5.390.16291310.14272796X-RAY DIFFRACTION99.93
5.39-36.520.19581560.16092922X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 25.511748404 Å / Origin y: -8.72025553449 Å / Origin z: 24.6222936792 Å
111213212223313233
T0.189284785011 Å2-0.00158609796293 Å20.00633547716034 Å2-0.202104463622 Å2-0.000794903609023 Å2--0.178204516668 Å2
L0.137231028668 °2-0.0204965636061 °2-0.0206391961468 °2-0.343361579989 °2-0.0474728977848 °2--0.260300434002 °2
S0.0205456453079 Å °0.00234269853701 Å °-0.00702348847929 Å °-0.0123809022248 Å °0.00275086097212 Å °-0.0080162291864 Å °-0.0344731596541 Å °-0.0269956423034 Å °-0.0240749447945 Å °
Refinement TLS groupSelection details: all

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