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- PDB-4pkm: Crystal Structure of Bacillus thuringiensis Cry51Aa1 Protoxin at ... -

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Basic information

Entry
Database: PDB / ID: 4pkm
TitleCrystal Structure of Bacillus thuringiensis Cry51Aa1 Protoxin at 1.65 Angstroms Resolution
ComponentsCry51Aa1
KeywordsTOXIN / Bacterial Toxins / Cry Toxins / Pore-forming Toxins / Beta-pore-forming Toxins / Beetles / Insecticidal Toxins / Pro-toxins
Function / homologyAerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / GLYCINE / Cry51Aa1
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsXu, C. / Chinte, U. / Chen, L. / Yao, Q. / Zhou, D. / Meng, Y. / Li, L. / Rose, J. / Bi, L.J. / Yu, Z. ...Xu, C. / Chinte, U. / Chen, L. / Yao, Q. / Zhou, D. / Meng, Y. / Li, L. / Rose, J. / Bi, L.J. / Yu, Z. / Sun, M. / Wang, B.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2013CB127504 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of Cry51Aa1: A potential novel insecticidal aerolysin-type beta-pore-forming toxin from Bacillus thuringiensis.
Authors: Xu, C. / Chinte, U. / Chen, L. / Yao, Q. / Meng, Y. / Zhou, D. / Bi, L.J. / Rose, J. / Adang, M.J. / Wang, B.C. / Yu, Z. / Sun, M.
History
DepositionMay 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cry51Aa1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4206
Polymers34,0071
Non-polymers4135
Water7,350408
1
A: Cry51Aa1
hetero molecules

A: Cry51Aa1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84012
Polymers68,0142
Non-polymers82710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4990 Å2
ΔGint-47 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.703, 54.703, 209.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cry51Aa1


Mass: 34006.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Strain: F14-1 / Gene: cry51Aa1 / Plasmid: pHT304 / Production host: Bacillus thuringiensis (bacteria) / Strain (production host): BMB171 / References: UniProt: A7IZR5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3 / Details: ammonium sulfate, sodium acetate pH 3.0, PEG2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionRedundancy: 26.8 % / Number: 310493 / Rmerge(I) obs: 0.118 / Χ2: 1.11 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 11568 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.165010.0583.93423.4
4.896.1610.0832.61726.3
4.274.8910.0882.10626.7
3.884.2710.0971.26127.4
3.613.8810.1380.94627.6
3.393.6110.1690.80627.8
3.223.3910.2190.64228.2
3.083.2210.3270.5728.1
2.963.0810.470.53928.5
2.862.9610.6950.51728.3
2.772.8610.9390.50428.3
2.692.7710.48327.9
2.622.6910.54126.6
2.562.6210.47725.3
2.52.5610.47722.9
ReflectionResolution: 1.65→50 Å / Num. obs: 39741 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.114 / Χ2: 1.086 / Net I/av σ(I): 22.014 / Net I/σ(I): 7.4 / Num. measured all: 548719
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.7113.30.53638880.85799.8
1.71-1.7814.30.42238710.91100
1.78-1.8614.40.31538721.022100
1.86-1.9614.40.22639251.167100
1.96-2.0814.40.17739141.169100
2.08-2.2414.30.15239301.157100
2.24-2.4614.20.14239651.138100
2.46-2.8213.90.1339821.153100
2.82-3.5513.30.10440641.123100
3.55-5011.80.07743301.14699.6

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Phasing

PhasingMethod: SAD
Phasing MADD res high: -0 Å / D res low: 0 Å / FOM : 0 / Reflection: 0

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXphasing
Cootmodel building
HKL-2000data scaling
ARPmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→29.48 Å / FOM work R set: 0.8806 / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1989 1999 5.04 %
Rwork0.1812 37631 -
obs0.1821 39630 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.82 Å2 / Biso mean: 21.95 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.65→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 26 408 2796
Biso mean--32.98 31.65 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072442
X-RAY DIFFRACTIONf_angle_d1.063339
X-RAY DIFFRACTIONf_chiral_restr0.072388
X-RAY DIFFRACTIONf_plane_restr0.005427
X-RAY DIFFRACTIONf_dihedral_angle_d12.597860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.649-1.69030.25521370.22652580271799
1.6903-1.7360.21621390.215326312770100
1.736-1.7870.24591410.198726412782100
1.787-1.84470.23431410.191926432784100
1.8447-1.91060.21891400.182826372777100
1.9106-1.98710.21491410.186726502791100
1.9871-2.07750.21681400.184726632803100
2.0775-2.1870.19891420.182926742816100
2.187-2.3240.2021410.180726512792100
2.324-2.50330.22771440.191427102854100
2.5033-2.75510.18641440.19126992843100
2.7551-3.15340.20251440.183427162860100
3.1534-3.97140.1821480.164527792927100
3.9714-29.48460.17211570.170829573114100

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