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- PDB-2ztb: Crystal structure of the parasporin-2 Bacillus thuringiensis toxi... -

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Basic information

Entry
Database: PDB / ID: 2ztb
TitleCrystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells
ComponentsCrystal protein
KeywordsTOXIN / beta-hairpin
Function / homology
Function and homology information


Immunoglobulin-like - #3040 / Immunoglobulin-like - #4280 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A - #50 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis serovar dakota (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.38 Å
AuthorsAkiba, T.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells
Authors: Akiba, T. / Abe, Y. / Kitada, S. / Kusaka, Y. / Ito, A. / Ichimatsu, T. / Katayama, H. / Akao, T. / Higuchi, K. / Mizuki, E. / Ohba, M. / Kanai, R. / Harata, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization of parasporin-2, a Bacillus thuringiensis crystal protein with selective cytocidal activity against human cells
Authors: Akiba, T. / Abe, Y. / Kitada, S. / Kusaka, Y. / Ito, A. / Ichimatsu, T. / Katayama, H. / Akao, T. / Higuchi, K. / Mizuki, E. / Ohba, M. / Kanai, R. / Harata, K.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: A Bacillus thuringiensis crystal protein with selective cytocidal action to human cells
Authors: Ito, A. / Sasaguri, Y. / Kitada, S. / Kusaka, Y. / Kuwano, K. / Masutomi, K. / Mizuki, E. / Akao, T. / Ohba, M.
History
DepositionSep 29, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Crystal protein
B: Crystal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,06812
Polymers55,0752
Non-polymers99310
Water5,224290
1
A: Crystal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1667
Polymers27,5381
Non-polymers6286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Crystal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9025
Polymers27,5381
Non-polymers3654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.829, 136.829, 119.268
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Crystal protein


Mass: 27537.568 Da / Num. of mol.: 2
Fragment: the proteolytically activated form, UNP residues 52-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar dakota (bacteria)
Strain: A1547 / Plasmid: pET-23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7WZI1

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Non-polymers , 5 types, 300 molecules

#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Lu
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 5.85 Å3/Da / Density % sol: 78.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% (v/v) ethylene glycol, 8% (w/v) PEG 3350, 1mM TCEP, 50mM HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.3403, 1.3408, 1.3460
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2004
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.34031
21.34081
31.3461
ReflectionResolution: 2.38→29.75 Å / Num. obs: 50770 / % possible obs: 99.9 % / Redundancy: 11 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 26.2
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 4.2 / Num. unique all: 7356 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.38→29.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.442 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.165 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22212 5121 10.1 %RANDOM
Rwork0.19064 ---
obs0.19377 45647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.421 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.38→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 32 290 4128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9465328
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12924160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4191520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21526
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22703
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6151.52520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07624062
X-RAY DIFFRACTIONr_scbond_it1.64331550
X-RAY DIFFRACTIONr_scangle_it2.6054.51266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.441 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.335 389
Rwork0.276 3314
obs-3703
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
114.5486-4.2846-0.43911.7757-0.03950.0687-0.1948-0.75920.40450.05290.1427-0.20770.14350.10250.0521-0.26120.0522-0.02290.035-0.0492-0.31627.15157.1525.089
22.4027-2.4067-0.22145.02410.25080.6165-0.07780.0729-0.00650.0747-0.07940.08060.038-0.2110.1572-0.24230.02450.0083-0.21580.0183-0.307651.17323.80711.706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 298
2X-RAY DIFFRACTION2B51 - 298

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