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- PDB-9h99: Native structure of the full-length pesticidal protein Cry1Ca18 a... -

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Basic information

Entry
Database: PDB / ID: 9h99
TitleNative structure of the full-length pesticidal protein Cry1Ca18 at pH7, 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: 1.8 Å
AuthorsBest, H.L. / Williamson, L.J. / Rizkallah, P.J. / Galchenkova, M. / 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: Structure of Cry1Ca18 pesticidal protein at pH 7
Authors: Best, H.L. / Williamson, L.J. / Rizkallah, P.J. / Galchenkova, M. / Oberthur, D. / Crickmore, N. / Berry, C.
History
DepositionOct 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: 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)134,9573
Polymers134,8521
Non-polymers1052
Water14,574809
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area48810 Å2
Unit cell
Length a, b, c (Å)88.160, 88.160, 266.430
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-2086-

HOH

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Components

#1: Protein Crystaline entomocidal protoxin


Mass: 134851.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thuringiensis (bacteria) / References: UniProt: Q6YNB8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.01 Å3/Da / Density % sol: 38.69 %
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: Y
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: 1.8→36.19 Å / Num. obs: 98288 / % possible obs: 100 % / Redundancy: 207.97 % / CC1/2: 0.9965445 / CC star: 0.9991343 / Net I/σ(I): 13.75
Reflection shellResolution: 1.8→1.82 Å / Mean I/σ(I) obs: 2.77 / Num. unique obs: 6425 / CC1/2: 0.79 / CC star: 0.94 / Χ2: 40.03 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
CrystFELdata scaling
PHASERphasing
CrystFELdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→36.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.077 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22169 4841 4.9 %RANDOM
Rwork0.18157 ---
obs0.18353 93379 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.56 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.8→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8493 0 2 809 9304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128707
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168105
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.82411841
X-RAY DIFFRACTIONr_angle_other_deg0.6131.76118600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86351056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.482573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.574101426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022149
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_it0.4580.174233
X-RAY DIFFRACTIONr_mcbond_other0.4580.174233
X-RAY DIFFRACTIONr_mcangle_it0.8070.35286
X-RAY DIFFRACTIONr_mcangle_other0.8070.35287
X-RAY DIFFRACTIONr_scbond_it0.8240.2574474
X-RAY DIFFRACTIONr_scbond_other0.8220.2574473
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3510.4376556
X-RAY DIFFRACTIONr_long_range_B_refined4.8534.579629
X-RAY DIFFRACTIONr_long_range_B_other4.8073.179482
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 348 -
Rwork0.252 6763 -
obs--100 %
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)
13.17020.7630.47580.59340.26930.40380.01640.123-0.1371-0.0780.0239-0.02550.01740.0075-0.04030.1823-0.0003-0.01960.1301-0.00940.013735.33744.86819.2
24.84131.7921-0.71351.3648-0.41771.01450.0813-0.0461-0.1805-0.0245-0.0347-0.0164-0.0461-0.0664-0.04660.15640.0281-0.02020.11930.00670.016745.80559.10328.658
31.66630.2668-0.09161.49690.11220.81470.01220.110.1681-0.16120.0173-0.0948-0.14370.107-0.02950.1484-0.00860.0030.1270.0140.029259.04770.86926.756
42.43650.70050.06231.49940.29341.65950.015-0.3589-0.16430.2594-0.05140.14670.1332-0.07290.03640.1739-0.0130.00320.22560.02750.050137.68250.34547.789
51.4784-0.70390.11544.9051-0.93982.47530.11010.19940.1611-0.3406-0.04520.1376-0.09180.0605-0.06490.1690.0051-0.01570.1806-0.01150.038415.08829.51858.634
60.81340.00110.23253.38631.36281.33050.0081-0.0316-0.0258-0.0021-0.01950.03330.0541-0.00850.01140.110.0038-0.00150.13450.00180.001226.62216.22979.63
70.81612.0641-0.10435.4192-0.33180.0668-0.194-0.013-0.1801-0.6096-0.0456-0.8759-0.07710.08340.23960.731-0.1096-0.0410.66550.17921.03830.12441.08970.192
80.02720.0020.31270.01040.20116.80620.02990.0027-0.0403-0.0003-0.01380.02250.4093-0.3217-0.01610.2553-0.0131-0.00340.2283-0.00140.141430.046-3.675100.542
93.09820.3651-0.15511.9166-0.47242.5759-0.08650.10250.1282-0.02840.0484-0.0064-0.0008-0.03580.03810.1336-0.01130.00090.1037-0.01440.012541.916.851128.533
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 254
2X-RAY DIFFRACTION2A255 - 274
3X-RAY DIFFRACTION3A275 - 455
4X-RAY DIFFRACTION4A456 - 618
5X-RAY DIFFRACTION5A619 - 690
6X-RAY DIFFRACTION6A691 - 787
7X-RAY DIFFRACTION6A832 - 880
8X-RAY DIFFRACTION7A788 - 831
9X-RAY DIFFRACTION8A881 - 984
10X-RAY DIFFRACTION9A985 - 1189

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