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- PDB-2d42: Crystal structure analysis of a non-toxic crystal protein from Ba... -

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Basic information

Entry
Database: PDB / ID: 2d42
TitleCrystal structure analysis of a non-toxic crystal protein from Bacillus thuringiensis
Componentsnon-toxic crystal protein
KeywordsTOXIN / parasporin / bacterial toxin / beta-pore-forming toxin / parasporal inclusion / hinge-bending motion
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #380 / Proaerolysin, chain A, domain 3 / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Proaerolysin; Chain A, domain 3 / Nuclear Transport Factor 2; Chain: A, / Beta Complex / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsAkiba, T. / Higuchi, K. / Mizuki, E. / Ekino, K. / Shin, T. / Ohba, M. / Kanai, R. / Harata, K.
CitationJournal: Proteins / Year: 2006
Title: Nontoxic crystal protein from Bacillus thuringiensis demonstrates a remarkable structural similarity to beta-pore-forming toxins
Authors: Akiba, T. / Higuchi, K. / Mizuki, E. / Ekino, K. / Shin, T. / Ohba, M. / Kanai, R. / Harata, K.
History
DepositionOct 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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: non-toxic crystal protein
B: non-toxic crystal protein


Theoretical massNumber of molelcules
Total (without water)55,1312
Polymers55,1312
Non-polymers00
Water3,783210
1
A: non-toxic crystal protein


Theoretical massNumber of molelcules
Total (without water)27,5661
Polymers27,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: non-toxic crystal protein


Theoretical massNumber of molelcules
Total (without water)27,5661
Polymers27,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.380, 95.380, 130.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein non-toxic crystal protein


Mass: 27565.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacillus thuringiensis (bacteria) / Strain: A1470 (formerly called 89-T-34-22) / References: UniProt: Q6L5X8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 10%(v/v) 2-methyl-2,4-pentanediol, 50-100mM ammonium sulfate, 100mM sodium citrate, 1mM Na-EDTA, 1mM DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONPhoton Factory AR-NW12A21.0077, 1.0082, 1.0088, 0.992
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDJun 4, 2003mirrors
ADSC QUANTUM 2102CCDJun 4, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 double crystalSINGLE WAVELENGTHMx-ray1
2Si 111 double crystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.00771
31.00821
41.00881
50.9921
ReflectionResolution: 2.07→47.67 Å / Num. obs: 41642 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 20.4 Å2 / Rsym value: 0.054 / Net I/σ(I): 32.8
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 9.6 / Num. unique all: 6001 / Rsym value: 0.229 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.07→47.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2145829.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4200 10.1 %RANDOM
Rwork0.23 ---
obs0.23 41637 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.4809 Å2 / ksol: 0.380301 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.02 Å2-0.02 Å20 Å2
2---5.02 Å20 Å2
3---10.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.07→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 0 210 4100
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.07→2.2 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 710 10.3 %
Rwork0.261 6160 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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