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- PDB-4rhz: Crystal structure of Cry23Aa1 and Cry37Aa1 binary protein complex -

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Basic information

Entry
Database: PDB / ID: 4rhz
TitleCrystal structure of Cry23Aa1 and Cry37Aa1 binary protein complex
Components
  • Cry23AA1
  • Cry37AA1
KeywordsTOXIN / aerolysin-family fold / C2-fold
Function / homologyInsecticidal delta endotoxin / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / metal ion binding / Crystal protein / Cry23
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å
AuthorsRydel, T.J. / Williams, J.M. / Brown, G.R. / Guzov, V.M. / Sturman, E.J. / Evdokimov, A.
CitationJournal: To be Published
Title: The Associated Bacillus thuringiensis Binary Protein Complex of Cry23Aa1 and Cry37Aa1: Crystal Structure, Insecticidal Data, and Pore Formation Modeling.
Authors: Rydel, T.J. / Sivasupramanian, S. / Williams, J.M. / Brown, G.R. / Fu, X. / Sturman, E.J. / Roberts, J.K. / Guzov, V.M. / Seale, J.W. / Moshiri, F.M. / Zheng, M. / Halls, C. / Evdokimov, A.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Assembly

Deposited unit
A: Cry23AA1
B: Cry37AA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5324
Polymers43,4272
Non-polymers1052
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-47 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.390, 126.390, 79.234
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cry23AA1


Mass: 29235.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: EG9328 / Gene: cryET33, cry23 / Production host: Bacillus thuringiensis (bacteria) / Strain (production host): EG10650 / References: UniProt: Q9KKG8
#2: Protein Cry37AA1


Mass: 14191.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: EG9328 / Gene: cryET34 / Production host: Bacillus thuringiensis (bacteria) / Strain (production host): EG10650 / References: UniProt: Q9KKG7
#3: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The protein sample was at a concentration of 2.1mg/mL in 25mM ethanolamine, and was prepared from chromatography fractions containing the co-eluted protein complex. For vapor diffusion ...Details: The protein sample was at a concentration of 2.1mg/mL in 25mM ethanolamine, and was prepared from chromatography fractions containing the co-eluted protein complex. For vapor diffusion crystallization, the precipitant solution was 2-6%(w/v) PEG8000 in 0.1M Tris-pH 8.5 buffer. A droplet using 2uL of protein and 2uL of precipitant solution was placed over a well containing 500 uL of precipitant solution. Crystals appeared within one week., VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→109 Å / Num. all: 30246 / Num. obs: 30216 / % possible obs: 99.9 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 49.1

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.35→49.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24549 1532 5.1 %RANDOM
Rwork0.19212 ---
obs0.19474 28652 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 2 209 3195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9424315
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20625.319141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89315486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.646158
X-RAY DIFFRACTIONr_chiral_restr0.1540.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212426
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.341.51950
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43323215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.39631187
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3164.51087
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
LS refinement shellResolution: 2.348→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 119 -
Rwork0.268 2107 -
obs--99.6 %

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