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- PDB-4d8m: Crystal structure of Bacillus thuringiensis Cry5B nematocidal toxin -

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Basic information

Entry
Database: PDB / ID: 4d8m
TitleCrystal structure of Bacillus thuringiensis Cry5B nematocidal toxin
ComponentsPesticidal crystal protein cry5Ba
KeywordsLIPID BINDING PROTEIN / glycolipid binding / Structural Genomics / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


sporulation resulting in formation of a cellular spore / : / toxin activity
Similarity search - Function
Vitelline Membrane Outer Layer Protein I, subunit A - #40 / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, N-terminal domain / 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 ...Vitelline Membrane Outer Layer Protein I, subunit A - #40 / Pesticidal crystal protein Cry, domain V / Insecticidal delta-endotoxin CryIA(c) domain 5 / Pesticidal crystal protein, N-terminal domain / 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
Pesticidal crystal protein Cry5Ba
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFan, H. / Hu, Y. / Aroian, R.V. / Ghosh, P. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Biochemistry / Year: 2012
Title: Structure and Glycolipid Binding Properties of the Nematicidal Protein Cry5B.
Authors: Hui, F. / Scheib, U. / Hu, Y. / Sommer, R.J. / Aroian, R.V. / Ghosh, P.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pesticidal crystal protein cry5Ba


Theoretical massNumber of molelcules
Total (without water)66,0881
Polymers66,0881
Non-polymers00
Water8,665481
1
A: Pesticidal crystal protein cry5Ba

A: Pesticidal crystal protein cry5Ba

A: Pesticidal crystal protein cry5Ba


Theoretical massNumber of molelcules
Total (without water)198,2643
Polymers198,2643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area11320 Å2
ΔGint-43 kcal/mol
Surface area68130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.528, 115.528, 110.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-720-

HOH

21A-778-

HOH

31A-832-

HOH

41A-1130-

HOH

51A-1136-

HOH

61A-1150-

HOH

71A-1152-

HOH

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Components

#1: Protein Pesticidal crystal protein cry5Ba / 140 kDa crystal protein / Crystaline entomocidal protoxin / Insecticidal delta-endotoxin CryVB(a)


Mass: 66088.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Gene: cry5Ba, cryVB(a) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45712
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.2 M sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9793
SYNCHROTRONALS 5.0.220.97865
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.978651
ReflectionResolution: 2.3→50 Å / Num. all: 37593 / Num. obs: 37218 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.3-2.341,299.9
2.34-2.381,299.9
2.38-2.431,299.9
2.43-2.481,299.9
2.48-2.531,299.9
2.53-2.591,299.9
2.59-2.661,2100
2.66-2.731,2100
2.73-2.811,2100
2.81-2.91,2100
2.9-31,2100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.894 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1856 4.99 %random
Rwork0.1726 ---
all0.2319 37243 --
obs0.1749 37191 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.271 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2711 Å2-0 Å2-0 Å2
2--3.2711 Å20 Å2
3----6.5422 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4624 0 0 481 5105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084728
X-RAY DIFFRACTIONf_angle_d1.1326431
X-RAY DIFFRACTIONf_dihedral_angle_d14.7351729
X-RAY DIFFRACTIONf_chiral_restr0.079717
X-RAY DIFFRACTIONf_plane_restr0.005850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38070.26121740.20343531X-RAY DIFFRACTION100
2.3807-2.4760.26131650.1923498X-RAY DIFFRACTION100
2.476-2.58870.24421850.19073536X-RAY DIFFRACTION100
2.5887-2.72510.3042070.19873511X-RAY DIFFRACTION100
2.7251-2.89580.24021740.18163548X-RAY DIFFRACTION100
2.8958-3.11930.23282040.18363520X-RAY DIFFRACTION100
3.1193-3.4330.22091880.16863511X-RAY DIFFRACTION100
3.433-3.92940.18871700.15663565X-RAY DIFFRACTION100
3.9294-4.94920.18211950.1393532X-RAY DIFFRACTION100
4.9492-39.90030.18171940.16893583X-RAY DIFFRACTION99

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