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- PDB-3wa1: Crystal structure of BinB: A receptor binding component of the bi... -

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Basic information

Entry
Database: PDB / ID: 3wa1
TitleCrystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus
ComponentsBinB protein
KeywordsTOXIN / A-B TOXIN / BINARY TOXIN
Function / homologyInsecticidal Crystal Toxin, P42 / sporulation resulting in formation of a cellular spore / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / toxin activity / Mainly Beta / Binary larvicide subunit BinB / Binary larvicide subunit BinB
Function and homology information
Biological speciesLysinibacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSrisucharitpanit, K. / Yao, M. / Chimnaronk, S. / Promdonkoy, B. / Boonserm, P. / Tanaka, I.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of BinB: A receptor binding component of the binary toxin from Lysinibacillus sphaericus
Authors: Srisucharitpanit, K. / Yao, M. / Promdonkoy, B. / Chimnaronk, S. / Tanaka, I. / Boonserm, P.
History
DepositionApr 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references / Structure summary
Revision 1.2Oct 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_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BinB protein


Theoretical massNumber of molelcules
Total (without water)44,8001
Polymers44,8001
Non-polymers00
Water7,927440
1
A: BinB protein

A: BinB protein

A: BinB protein

A: BinB protein


Theoretical massNumber of molelcules
Total (without water)179,2014
Polymers179,2014
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area7890 Å2
ΔGint-21 kcal/mol
Surface area67660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.210, 95.210, 154.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21A-764-

HOH

31A-932-

HOH

41A-936-

HOH

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Components

#1: Protein BinB protein


Mass: 44800.152 Da / Num. of mol.: 1 / Fragment: ACTIVATE DOMAIN, UNP RESIDUES 19-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysinibacillus sphaericus (bacteria) / Strain: 2297 / Gene: binB / Plasmid: pET-28b(+)-BinB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q7B2I6, UniProt: P18568*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8
Details: 0.1M TRIS-HCL PH8.0, 0.2M LITHIUM SULFATE, 12% PEG 4000, VAPOR DIFFUSION, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 8, 2011
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→28.99 Å / Num. all: 42536 / Num. obs: 42536 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.12 / Net I/σ(I): 4.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6069 / Rsym value: 0.433 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
SHELXC/D/Emodel building
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→24.64 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.181 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2985 7 %RANDOM
Rwork0.174 ---
all0.174 42392 --
obs0.177 42392 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 0 440 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023237
X-RAY DIFFRACTIONr_angle_refined_deg2.1971.9614401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9055388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49824.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93615543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0221520
X-RAY DIFFRACTIONr_chiral_restr0.1880.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212511
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 178 -
Rwork0.197 2591 -
obs--99.78 %

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