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- PDB-4arx: Lepidoptera-specific toxin Cry1Ac from Bacillus thuringiensis ssp... -

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Basic information

Entry
Database: PDB / ID: 4arx
TitleLepidoptera-specific toxin Cry1Ac from Bacillus thuringiensis ssp. kurstaki HD-73
ComponentsPESTICIDAL CRYSTAL PROTEIN CRY1AC
KeywordsTOXIN / MEMBRANE PORE-FORMING TOXIN / INSECTICIDAL PROTEIN LEPIDOPTERAN SPECIFICITY / RECEPTOR BINDING SITE
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
: / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / Pesticidal crystal protein, central domain / delta endotoxin / Pesticidal crystal protein, central domain superfamily / Pesticidal crystal protein, C-terminal ...: / Cry1Ac, domain VII / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, central domain / Pesticidal crystal protein, N-terminal domain / 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 / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Delta-Endotoxin; domain 1 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,3-DIAMINOPROPANE / Pesticidal crystal protein Cry1Ac
Similarity search - Component
Biological speciesBACILLUS THURINGIENSIS SEROVAR KURSTAKI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDerbyshire, D.J. / Carroll, J. / Ellar, D.J. / Li, J.
Citation
Journal: To be Published
Title: Structural Basis of Galnac-Dependent Receptor Recognition by B. Thuringiensis Toxin Cry1Ac
Authors: Derbyshire, D.J. / Carroll, J. / Ellar, D.J. / Li, J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization of the Bacillus Thuringiensis Toxin Cry1Ac and its Complex with the Receptor Ligand N-Aceryl-D-Galactosamine
Authors: Derbyshire, D.J. / Ellar, D.J. / Li, J.
History
DepositionApr 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PESTICIDAL CRYSTAL PROTEIN CRY1AC
B: PESTICIDAL CRYSTAL PROTEIN CRY1AC
C: PESTICIDAL CRYSTAL PROTEIN CRY1AC
D: PESTICIDAL CRYSTAL PROTEIN CRY1AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,3639
Polymers259,9744
Non-polymers3895
Water12,989721
1
A: PESTICIDAL CRYSTAL PROTEIN CRY1AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1423
Polymers64,9931
Non-polymers1482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PESTICIDAL CRYSTAL PROTEIN CRY1AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1423
Polymers64,9931
Non-polymers1482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PESTICIDAL CRYSTAL PROTEIN CRY1AC


Theoretical massNumber of molelcules
Total (without water)64,9931
Polymers64,9931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PESTICIDAL CRYSTAL PROTEIN CRY1AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0862
Polymers64,9931
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.808, 112.975, 123.299
Angle α, β, γ (deg.)113.11, 91.52, 100.51
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA32 - 6072 - 577
21GLYGLYBB32 - 6072 - 577
12GLYGLYAA32 - 6072 - 577
22GLYGLYCC32 - 6072 - 577
13TYRTYRAA33 - 6073 - 577
23TYRTYRDD33 - 6073 - 577
14GLYGLYBB32 - 6072 - 577
24GLYGLYCC32 - 6072 - 577
15TYRTYRBB33 - 6073 - 577
25TYRTYRDD33 - 6073 - 577
16TYRTYRCC33 - 6073 - 577
26TYRTYRDD33 - 6073 - 577

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.9958, 0.05312, 0.07401), (0.045, -0.9932, 0.1074), (0.07921, -0.1036, -0.9915)1.416, 12.83, 85.97
2given(0.9961, 0.06099, 0.06348), (-0.05478, 0.9939, -0.09536), (-0.06891, 0.09151, 0.9934)27.44, -23.31, 56.53
3given(0.9965, -0.05359, 0.06442), (-0.05614, -0.9977, 0.03854), (0.0622, -0.04202, -0.9972)26.3, 38.78, 27.04

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Components

#1: Protein
PESTICIDAL CRYSTAL PROTEIN CRY1AC / 133 KDA CRYSTAL PROTEIN / CRYSTALINE ENTOMOCIDAL PROTOXIN / INSECTICIDAL DELTA-ENDOTOXIN CRYIA(C)


Mass: 64993.480 Da / Num. of mol.: 4
Fragment: ACTIVATED TOXIN OBTAINED BY TRYPSIN CLEAVAGE, RESIDUES 31-609
Source method: isolated from a natural source
Source: (natural) BACILLUS THURINGIENSIS SEROVAR KURSTAKI (bacteria)
Variant: HD-73 / References: UniProt: P05068
#2: Chemical
ChemComp-13D / 1,3-DIAMINOPROPANE / 1,3-Diaminopropane


Mass: 74.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H10N2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,3-DIAMINOPROPANE (13D): USING 1,3-DIAMINOPROPANE AS BUFFER DURING PURIFICATION PREVENTED ...1,3-DIAMINOPROPANE (13D): USING 1,3-DIAMINOPROPANE AS BUFFER DURING PURIFICATION PREVENTED AGGREGATION OF CRY1AC.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Description: FROZEN CRYSTALS WERE ANNEALED BY THAWING IN THE CRYO -PROTECTANT SOLUTION AND RE-FROZEN IN THE VAPOUR OF LIQUID N2.
Crystal growMethod: microdialysis / pH: 9.8
Details: MICRODIALYSIS AGAINST 65-69 MM PIPERAZINE PH 9.8, 25-29 MM NABR, 21-25% GLYCEROL, 9% MPD, 1% PEG350MME. FOR DETAILS SEE REFERNCE 1 IN REMARK 1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.4
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 19, 1997 / Details: MONOCHROMATOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.34→43.19 Å / Num. obs: 95755 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 29.267 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3.7 / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CIY

1ciy


Resolution: 2.35→112.51 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.302 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOCAL NCS RESTRAINTS WERE DEFINED AUTOMATICALLY. JELLY BODY RESTRAINTS AGAINST EXCESSIVE POSITION SHIFTS WERE APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21772 4815 5 %RANDOM
Rwork0.18382 ---
obs0.18552 90938 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.553 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0.27 Å20.41 Å2
2---1.1 Å2-0.74 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 2.35→112.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18358 0 26 721 19105
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01918859
X-RAY DIFFRACTIONr_bond_other_d0.0050.0212709
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.93325692
X-RAY DIFFRACTIONr_angle_other_deg1.049330587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81452305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98223.067952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.243152854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.46315168
X-RAY DIFFRACTIONr_chiral_restr0.0690.22793
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02121415
X-RAY DIFFRACTIONr_gen_planes_other0.0040.024313
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A225770.05
12B225770.05
21A225730.05
22C225730.05
31A225870.04
32D225870.04
41B226220.04
42C226220.04
51B224960.05
52D224960.05
61C225040.04
62D225040.04
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 299 -
Rwork0.22 5418 -
obs--74.24 %

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