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- PDB-2quo: Crystal Structure of C terminal fragment of Clostridium perfringe... -

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Basic information

Entry
Database: PDB / ID: 2quo
TitleCrystal Structure of C terminal fragment of Clostridium perfringens enterotoxin
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / beta sandwich / claudin-4 binding domain / enterotoxin / therapeutic agent
Function / homologyJelly Rolls - #1050 / Clostridium enterotoxin / Clostridium enterotoxin / toxin activity / Jelly Rolls / Sandwich / extracellular region / Mainly Beta / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.75 Å
AuthorsBetts, L. / Van Itallie, C.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structure of the claudin-binding domain of Clostridium perfringens enterotoxin
Authors: Van Itallie, C.M. / Betts, L. / Smedley, J.G. / McClane, B.A. / Anderson, J.M.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jun 6, 2018Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat-labile enterotoxin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3682
Polymers14,2721
Non-polymers961
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.626, 49.041, 69.078
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heat-labile enterotoxin B chain


Mass: 14271.914 Da / Num. of mol.: 1 / Fragment: C-CPE, C-terminal fragment 194-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: F5603 / Gene: CPE / Plasmid: pMAL K4 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / References: UniProt: P01558
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, siting drop / pH: 8.3
Details: 0.8 M lithium sulfate monohydrate, 20% glycerol, Tris buffer, pH 8.3, vapor diffusion, siting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
ROTATING ANODERIGAKU RUH3R21.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2007 / Details: Osmic Confocal BLue optic
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1OsmicSINGLE WAVELENGTHMx-ray1
2OsmicSADMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 7.6 % / Av σ(I) over netI: 10.9 / Number: 98863 / Rmerge(I) obs: 0.127 / Χ2: 2.38 / D res high: 1.75 Å / D res low: 50 Å / Num. obs: 13042 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.775099.110.0864.137.7
2.993.7799.910.0993.4288.2
2.612.9910010.1352.9298.2
2.382.6110010.172.3318.2
2.22.3810010.2042.1348
2.072.210010.252.1217.9
1.972.0799.910.31.7327.8
1.891.9799.610.4011.5187.5
1.811.8999.610.531.2467
1.751.8196.410.5851.2855.3
ReflectionResolution: 1.75→50 Å / Num. all: 13039 / Num. obs: 13039 / % possible obs: 99.6 % / Observed criterion σ(I): 2.36 / Redundancy: 7.5 % / Biso Wilson estimate: 22.31 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Χ2: 1.285 / Net I/σ(I): 23.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.185 / Num. unique all: 1299 / Χ2: 1.192 / % possible all: 98.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
SHELXmodel building
REFMACrefinement
PDB_EXTRACT3data extraction
StructureStudiodata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.357 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.138 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 663 4.9 %RANDOM
Rwork0.197 ---
all0.19891 13412 --
obs0.19891 13412 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 5 202 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221042
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9511426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2485133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9925.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93115175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231153
X-RAY DIFFRACTIONr_chiral_restr0.0870.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02799
X-RAY DIFFRACTIONr_nbd_refined0.2110.2475
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.229
X-RAY DIFFRACTIONr_mcbond_it0.4711.5656
X-RAY DIFFRACTIONr_mcangle_it0.76721028
X-RAY DIFFRACTIONr_scbond_it1.2893452
X-RAY DIFFRACTIONr_scangle_it1.9544.5394
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 52 -
Rwork0.248 917 -
all-969 -
obs-917 99.28 %

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