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- PDB-5hd2: The crystal structure of SeMet-Cry51Aa2-L11M -

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Basic information

Entry
Database: PDB / ID: 5hd2
TitleThe crystal structure of SeMet-Cry51Aa2-L11M
ComponentsParasporal crystal protein
KeywordsTOXIN / Cry51Aa2 / Bt / Cry
Function / homologyAerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Parasporal crystal protein
Function and homology information
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.276 Å
AuthorsRydel, T.J. / Sturman, E.J. / Moshiri, F.
CitationJournal: Nat Commun / Year: 2016
Title: A transgenic approach for controlling Lygus in cotton.
Authors: Gowda, A. / Rydel, T.J. / Wollacott, A.M. / Brown, R.S. / Akbar, W. / Clark, T.L. / Flasinski, S. / Nageotte, J.R. / Read, A.C. / Shi, X. / Werner, B.J. / Pleau, M.J. / Baum, J.A.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 1.3Oct 30, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parasporal crystal protein


Theoretical massNumber of molelcules
Total (without water)34,3561
Polymers34,3561
Non-polymers00
Water84747
1
A: Parasporal crystal protein

A: Parasporal crystal protein


Theoretical massNumber of molelcules
Total (without water)68,7122
Polymers68,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4060 Å2
ΔGint-15 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.567, 55.567, 208.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Parasporal crystal protein


Mass: 34356.023 Da / Num. of mol.: 1 / Mutation: L11M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Plasmid: pET28a + pRARE2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: E9KBU4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 % / Description: Bipyramidal.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Starting protein solution was 5.5 mg/ml protein in 25 mM sodium carbonate buffer-pH 10.5. The reservoir solution was 500 ul of 2.0 M sodium chloride and 50 mM HEPES-pH 7.5 buffer. ...Details: Starting protein solution was 5.5 mg/ml protein in 25 mM sodium carbonate buffer-pH 10.5. The reservoir solution was 500 ul of 2.0 M sodium chloride and 50 mM HEPES-pH 7.5 buffer. Bipyramidal crystals resulted from 2 ul drops, using 0.7 ul protein solution and 1.3 ul well solution.
PH range: ~7.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: The structure was initially solved using four wavelengths of SeMet MAD data to 2.8 A resolution. The structure was extended to 2.27 A using data collected at 2.27 A resolution ...Ambient temp details: The structure was initially solved using four wavelengths of SeMet MAD data to 2.8 A resolution. The structure was extended to 2.27 A using data collected at 2.27 A resolution on the SER-CAT 22-ID line.
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 12, 2007
Details: 115 data frames were collected using 3 second exposures, with an oscillation angle of 1 degree, and a crystal-to-detector distance of 200 mm.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→53.7 Å / Num. all: 15236 / Num. obs: 15236 / % possible obs: 95.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 17.4
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 1.75 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVE2.08phasing
RefinementMethod to determine structure: MAD / Resolution: 2.276→53.7 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.299 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29458 766 5 %RANDOM
Rwork0.23523 ---
obs0.23813 14531 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.305 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--1.24 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.276→53.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 47 2437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9293358
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.35325.534103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.26815382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.028154
X-RAY DIFFRACTIONr_chiral_restr0.1260.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211856
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_it1.0471.51536
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91722525
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0013916
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6744.5833
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: 2.276→2.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 65 -
Rwork0.262 1037 -
obs--95.25 %

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