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- PDB-9qxq: native structure of full-length pesticidal protein Cry1Ca18 at pH... -

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Basic information

Entry
Database: PDB / ID: 9qxq
Titlenative structure of full-length pesticidal protein Cry1Ca18 at pH9, from crystals formed in vivo
ComponentsCrystaline entomocidal protoxin
KeywordsTOXIN / bacterial toxin
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity / signaling receptor binding
Similarity search - Function
: / Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal ...: / Pesticidal crystal protein Cry1Aa, domain IV / : / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal / delta endotoxin / Pesticidal crystal protein / Pesticidal crystal protein, N-terminal / Pesticidal crystal protein, N-terminal domain superfamily / delta endotoxin, N-terminal domain / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Crystaline entomocidal protoxin
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBest, H.L. / Williamson, L.J. / Rizkallah, P.J. / Oberthur, D. / Crickmore, N. / Berry, C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002774/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
CitationJournal: To Be Published
Title: native structure of full-length pesticidal protein Cry1Ca18 at pH9, from crystals formed in vivo
Authors: Best, H.L. / Williamson, L.J. / Rizkallah, P.J. / Oberthur, D. / Crickmore, N. / Berry, C.
History
DepositionApr 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Crystaline entomocidal protoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,9593
Polymers134,8541
Non-polymers1052
Water12,899716
1
A: Crystaline entomocidal protoxin
hetero molecules

A: Crystaline entomocidal protoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,9196
Polymers269,7082
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area7720 Å2
ΔGint-59 kcal/mol
Surface area91430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.800, 88.800, 267.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

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Components

#1: Protein Crystaline entomocidal protoxin


Mass: 134853.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thuringiensis (bacteria) / References: UniProt: Q9L877
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 298 K / Method: in cell / pH: 9 / Details: Naturally grown

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.33 Å
DetectorType: AGIPD / Detector: PIXEL / Date: May 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.33 Å / Relative weight: 1
ReflectionResolution: 1.65→26.91 Å / Num. obs: 122789 / % possible obs: 100 % / Redundancy: 1379 % / Biso Wilson estimate: 17.8 Å2 / CC1/2: 0.9986875 / CC star: 0.9996716 / Net I/σ(I): 23.214064
Reflection shellResolution: 1.65→1.69 Å / Mean I/σ(I) obs: 0.44 / Num. unique obs: 8223 / CC1/2: 0.18 / CC star: 0.55 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFELdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→26.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.864 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2064 6387 5 %RANDOM
Rwork0.17762 ---
obs0.17906 122231 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.476 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.16 Å2
Refinement stepCycle: 1 / Resolution: 1.65→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8519 0 2 716 9237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129040
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168417
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.82612331
X-RAY DIFFRACTIONr_angle_other_deg0.6311.76619308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89751121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.933580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.968101491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022260
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8670.5824403
X-RAY DIFFRACTIONr_mcbond_other0.8670.5824403
X-RAY DIFFRACTIONr_mcangle_it1.521.0355551
X-RAY DIFFRACTIONr_mcangle_other1.521.0365552
X-RAY DIFFRACTIONr_scbond_it1.3930.7484637
X-RAY DIFFRACTIONr_scbond_other1.3920.7474635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3061.316781
X-RAY DIFFRACTIONr_long_range_B_refined6.5659.289922
X-RAY DIFFRACTIONr_long_range_B_other6.4627.829789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 429 -
Rwork0.425 8223 -
obs--92.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6946-0.924-0.34162.39160.62460.28140.05240.07920.0294-0.078-0.0196-0.1164-0.00160.0074-0.03280.17020.0031-0.00420.1873-0.02260.021-47.7438.943-46.985
21.2979-0.5149-0.20241.99350.03830.84080.01520.09150.0538-0.0905-0.01430.1883-0.0544-0.1596-0.00080.1593-0.0064-0.00840.1636-0.01130.0288-72.94758.304-39.506
32.1646-0.1908-0.2742.11180.03672.0576-0.0576-0.3417-0.26930.40710.008-0.0670.08820.13780.04960.32780.0371-0.0140.19180.00050.0672-51.26638.273-19.182
43.35390.23810.25553.05110.51564.639-0.04240.3997-0.081-0.340.10440.4675-0.0936-0.477-0.0620.2306-0.04150.00370.2676-0.00960.0986-30.83415.358-8.216
53.77380.4267-1.5241.73480.37141.7435-0.01990.15510.1284-0.07420.01970.1443-0.0428-0.12810.00020.1719-0.01020.01850.135-0.00390.0186-20.1526.98211.94
60.00840.0104-0.00470.0490.4936.9881-0.02510.013-0.0321-0.01540.0391-0.04210.28160.468-0.0140.24520.01610.01810.2977-0.01390.1683.67829.87134.209
72.496-0.52490.10162.64050.0392.45870.09170.05110.0007-0.091-0.05460.10680.0045-0.0415-0.0370.12830.01510.01740.14560.00550.0087-6.67942.18761.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 295
2X-RAY DIFFRACTION2A296 - 457
3X-RAY DIFFRACTION3A458 - 614
4X-RAY DIFFRACTION4A615 - 690
5X-RAY DIFFRACTION5A691 - 880
6X-RAY DIFFRACTION6A881 - 984
7X-RAY DIFFRACTION7A985 - 1189

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