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- PDB-8hhe: Crystal structure of Cry5B from Bacillus thuringiensis at 4.5 A r... -

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Basic information

Entry
Database: PDB / ID: 8hhe
TitleCrystal structure of Cry5B from Bacillus thuringiensis at 4.5 A resolution
ComponentsCrystaline entomocidal protoxin
KeywordsTOXIN / Bacillus thuringiensis / Cry protein / nematicidal protein
Function / homology
Function and homology information


symbiont-mediated killing of host cell / sporulation resulting in formation of a cellular spore / toxin activity
Similarity search - Function
Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / 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 YBT-1518 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsLi, J. / Chan, M.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)GRF 14176017 Hong Kong
CitationJournal: Toxins / Year: 2022
Title: Insights from the Structure of an Active Form of Bacillus thuringiensis Cry5B.
Authors: Li, J. / Wang, L. / Kotaka, M. / Lee, M.M. / Chan, M.K.
History
DepositionNov 16, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crystaline entomocidal protoxin
B: Crystaline entomocidal protoxin


Theoretical massNumber of molelcules
Total (without water)181,2222
Polymers181,2222
Non-polymers00
Water00
1
A: Crystaline entomocidal protoxin

A: Crystaline entomocidal protoxin

A: Crystaline entomocidal protoxin

A: Crystaline entomocidal protoxin


Theoretical massNumber of molelcules
Total (without water)362,4434
Polymers362,4434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
2
B: Crystaline entomocidal protoxin

B: Crystaline entomocidal protoxin

B: Crystaline entomocidal protoxin

B: Crystaline entomocidal protoxin


Theoretical massNumber of molelcules
Total (without water)362,4434
Polymers362,4434
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z1
crystal symmetry operation4_445y-1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)114.401, 114.401, 263.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 27 through 82 or resid 88 through 698))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLNchain AAA27 - 69863 - 734
21SERSERPHEPHE(chain B and (resid 27 through 82 or resid 88 through 698))BB27 - 8263 - 118
22ALAALAGLNGLN(chain B and (resid 27 through 82 or resid 88 through 698))BB88 - 698124 - 734

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Components

#1: Protein Crystaline entomocidal protoxin


Mass: 90610.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis YBT-1518 (bacteria)
Gene: YBT1518_04070 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7SB31
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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 305 K / Method: vapor diffusion, sitting drop
Details: 2500 mM NaCl, 100 mM sodium cacodylate pH 6.5, and 200 mM Li2SO4
Temp details: 291K for two weeks then 305K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99984 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. obs: 10954 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.274 / Net I/σ(I): 2.2
Reflection shellResolution: 4.5→4.74 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 1560

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Processing

Software
NameVersionClassification
PHENIX1.18_3861refinement
CNSrefinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8M

4d8m


Resolution: 4.5→19.99 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 590 5.44 %
Rwork0.2376 10246 -
obs0.2405 10836 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197 Å2 / Biso mean: 107.0833 Å2 / Biso min: 55.57 Å2
Refinement stepCycle: final / Resolution: 4.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10254 0 0 0 10254
Num. residues----1293
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3858X-RAY DIFFRACTION3.158TORSIONAL
12B3858X-RAY DIFFRACTION3.158TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.5-4.950.3081590.243124742633100
4.95-5.650.30771430.254125172660100
5.65-7.060.32321480.271525602708100
7.07-19.990.24591400.20912695283599

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