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- PDB-4jox: Crystal structure of cry34Ab1 protein at 2.15 A resolution -

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Basic information

Entry
Database: PDB / ID: 4jox
TitleCrystal structure of cry34Ab1 protein at 2.15 A resolution
Components13.6 kDa insecticidal crystal protein
KeywordsTOXIN / beta-sandwich
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / sporulation resulting in formation of a cellular spore / toxin activity
Similarity search - Function
Mutm (Fpg) Protein; Chain: A, domain 2 - #50 / Hemolysin, aegerolysin type / Aegerolysin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Insecticidal crystal protein Cry34Ab1
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.15 Å
AuthorsYang, C. / Pflugrath, J.W. / Kelker, M.S. / Evan, S.L. / Narva, K.E.
CitationJournal: To be Published
Title: Structural and biophysical characterization of Cry34Ab1 and Cry35Ab1.
Authors: Kelker, M.S. / Berry, C. / Evans, S.L. / Pai, R. / McCaskill, D. / Pflugrath, J.W. / Wade, M. / Wess, T.J. / Baker, M.D. / Yang, C. / Narva, K.E. / McCaskill, D.G. / Wang, N.X. / Russell, J.C.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 13.6 kDa insecticidal crystal protein


Theoretical massNumber of molelcules
Total (without water)13,6181
Polymers13,6181
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.561, 100.561, 56.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 13.6 kDa insecticidal crystal protein


Mass: 13617.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q939T0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 289 K / Method: liquid diffusion / pH: 4.4
Details: 25% (V/V) PEG400, 50mM sodium acetate, pH 4.4, LIQUID DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 299280 / Num. obs: 14955 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 19.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 17.7
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MLPHAREphasing
REFMAC5refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.15→12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.05 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27912 787 9.8 %RANDOM
Rwork0.23398 ---
obs0.23829 7271 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 0 72 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021933
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9061263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7153116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05115153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.3398
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.5124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6660.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.091.5574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8842925
X-RAY DIFFRACTIONr_scbond_it2.9563359
X-RAY DIFFRACTIONr_scangle_it4.6574.5338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.204 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 51
Rwork0.289 513
Refinement TLS params.Method: refined / Origin x: -8.452 Å / Origin y: 22.2251 Å / Origin z: -10.0253 Å
111213212223313233
T0.0337 Å2-0.0044 Å2-0.0456 Å2-0.0917 Å20.0638 Å2--0.0985 Å2
L3.1304 °2-0.1074 °22.379 °2-3.0553 °21.4036 °2--5.7499 °2
S0.1791 Å °-0.0113 Å °-0.2287 Å °-0.0706 Å °0.0881 Å °0.0291 Å °0.1968 Å °-0.4598 Å °-0.2672 Å °

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