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- PDB-6wpc: Crystal structure of Bacillus thuringiensis Cry1A.2 tryptic core ... -

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Basic information

Entry
Database: PDB / ID: 6wpc
TitleCrystal structure of Bacillus thuringiensis Cry1A.2 tryptic core variant
ComponentsCry1A.2
KeywordsTOXIN / Bacillus thuringiensis / B.t. / 3-domain Cry
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsRydel, T.J. / Evdokimov, A.
CitationJournal: Plos One / Year: 2021
Title: Bacillus thuringiensis chimeric proteins Cry1A.2 and Cry1B.2 to control soybean lepidopteran pests: New domain combinations enhance insecticidal spectrum of activity and novel receptor contributions.
Authors: Chen, D. / Moar, W.J. / Jerga, A. / Gowda, A. / Milligan, J.S. / Bretsynder, E.C. / Rydel, T.J. / Baum, J.A. / Semeao, A. / Fu, X. / Guzov, V. / Gabbert, K. / Head, G.P. / Haas, J.A.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cry1A.2
B: Cry1A.2
C: Cry1A.2
D: Cry1A.2


Theoretical massNumber of molelcules
Total (without water)265,3494
Polymers265,3494
Non-polymers00
Water1,18966
1
A: Cry1A.2


Theoretical massNumber of molelcules
Total (without water)66,3371
Polymers66,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cry1A.2


Theoretical massNumber of molelcules
Total (without water)66,3371
Polymers66,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cry1A.2


Theoretical massNumber of molelcules
Total (without water)66,3371
Polymers66,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cry1A.2


Theoretical massNumber of molelcules
Total (without water)66,3371
Polymers66,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.578, 225.820, 239.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

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
11GLYGLYSERSER(chain 'A' and (resid 53 through 305 or resid 307...AA53 - 3044 - 255
12GLYGLYPROPRO(chain 'A' and (resid 53 through 305 or resid 307...AA307 - 539258 - 490
13TYRTYRLEULEU(chain 'A' and (resid 53 through 305 or resid 307...AA544 - 639495 - 590
24GLYGLYSERSER(chain 'B' and (resid 53 through 305 or resid 307...BB53 - 3044 - 255
25GLYGLYPROPRO(chain 'B' and (resid 53 through 305 or resid 307...BB307 - 539258 - 490
26TYRTYRLEULEU(chain 'B' and (resid 53 through 305 or resid 307...BB544 - 639495 - 590
37GLYGLYSERSER(chain 'C' and (resid 53 through 305 or resid 307...CC53 - 3044 - 255
38GLYGLYPROPRO(chain 'C' and (resid 53 through 305 or resid 307...CC307 - 539258 - 490
39TYRTYRLEULEU(chain 'C' and (resid 53 through 305 or resid 307...CC544 - 639495 - 590
410GLYGLYSERSER(chain 'D' and (resid 53 through 305 or resid 307...DD53 - 3044 - 255
411GLYGLYPROPRO(chain 'D' and (resid 53 through 305 or resid 307...DD307 - 539258 - 490
412TYRTYRLEULEU(chain 'D' and (resid 53 through 305 or resid 307...DD544 - 639495 - 590

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Components

#1: Protein
Cry1A.2


Mass: 66337.359 Da / Num. of mol.: 4 / Mutation: Y140R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Bacillus thuringiensis (bacteria)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.84 Å3/Da / Density % sol: 60.04 % / Description: triangular & square plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Wizard 12 screen H7 (10% PEG8000, 0.1 M Tris, pH 7.0, 0.2 M magnesium 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: MARRESEARCH / Detector: CCD / Date: Mar 20, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→120 Å / Num. obs: 62795 / % possible obs: 95.1 % / Redundancy: 3.47 % / Biso Wilson estimate: 45.94 Å2 / Rmerge(I) obs: 0.182 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 1.33 / Num. unique obs: 1992 / % possible all: 60.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4ARX

4arx


Resolution: 2.99→46.12 Å / SU ML: 0.3469 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 3182 5.09 %
Rwork0.1976 59342 -
obs0.2008 62524 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.62 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18660 0 0 66 18726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012319140
X-RAY DIFFRACTIONf_angle_d1.555826035
X-RAY DIFFRACTIONf_chiral_restr0.10062843
X-RAY DIFFRACTIONf_plane_restr0.01053409
X-RAY DIFFRACTIONf_dihedral_angle_d10.15982639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.040.3969720.30191495X-RAY DIFFRACTION54.69
3.04-3.090.35281010.2941991X-RAY DIFFRACTION73.9
3.09-3.140.38221060.29212231X-RAY DIFFRACTION82.32
3.14-3.190.34831280.27152390X-RAY DIFFRACTION87.89
3.19-3.250.32731440.25572466X-RAY DIFFRACTION92.23
3.25-3.310.27971280.25722581X-RAY DIFFRACTION95.39
3.31-3.380.32041390.25482645X-RAY DIFFRACTION96.9
3.38-3.450.32761350.25372680X-RAY DIFFRACTION98.88
3.45-3.530.30791320.23682705X-RAY DIFFRACTION99.37
3.53-3.620.31911450.22752677X-RAY DIFFRACTION99.12
3.62-3.720.29451490.22162684X-RAY DIFFRACTION99.79
3.72-3.830.30961580.21142706X-RAY DIFFRACTION99.86
3.83-3.950.29281460.20542721X-RAY DIFFRACTION99.79
3.95-4.090.24011280.18952708X-RAY DIFFRACTION99.82
4.09-4.260.22841970.17412693X-RAY DIFFRACTION99.97
4.26-4.450.23291450.16412725X-RAY DIFFRACTION99.72
4.45-4.680.2041380.14922713X-RAY DIFFRACTION99.79
4.68-4.980.19581460.13722735X-RAY DIFFRACTION99.86
4.98-5.360.23391740.14562726X-RAY DIFFRACTION99.83
5.36-5.90.20571480.16482744X-RAY DIFFRACTION99.76
5.9-6.750.22861610.17152770X-RAY DIFFRACTION100
6.75-8.50.17741280.16922806X-RAY DIFFRACTION99.93
8.5-46.120.2151340.17362750X-RAY DIFFRACTION94.31

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