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- PDB-9j7x: Crystal structure of quintuple mutant C terminal fragment of Clos... -

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Basic information

Entry
Database: PDB / ID: 9j7x
TitleCrystal structure of quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)
ComponentsHeat-labile enterotoxin B chain
KeywordsTOXIN / claudin binger / C-CPE
Function / homologyClostridium enterotoxin / Clostridium enterotoxin / toxin activity / extracellular region / Heat-labile enterotoxin B chain
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAoyama, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)
Authors: Aoyama, H.
History
DepositionAug 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat-labile enterotoxin B chain


Theoretical massNumber of molelcules
Total (without water)16,9781
Polymers16,9781
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.590, 87.590, 63.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

21A-449-

HOH

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Components

#1: Protein Heat-labile enterotoxin B chain / Quintuple mutant C terminal fragment of Clostridium perfringens enterotoxin (C-CPEm19)


Mass: 16977.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cpe / Production host: Escherichia coli (E. coli) / References: UniProt: P01558
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.17 Å3/Da / Density % sol: 70.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: mixing 1 ml of protein solution at 9 mg/ml, 1 ml of reservoir solution containing 0.1 M sodium acetate pH 4.6 and 1.75 M ammonium sulfate, and allowing the drop to equilibrate against 1 ml ...Details: mixing 1 ml of protein solution at 9 mg/ml, 1 ml of reservoir solution containing 0.1 M sodium acetate pH 4.6 and 1.75 M ammonium sulfate, and allowing the drop to equilibrate against 1 ml of reservoir solution by the hanging drop method

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→63.81 Å / Num. obs: 19458 / % possible obs: 99.4 % / Redundancy: 11 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.027 / Rrim(I) all: 0.09 / Net I/σ(I): 15.8 / Num. measured all: 213236
Reflection shellResolution: 2→2.1 Å / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.903 / Num. measured all: 30827 / Num. unique obs: 2817 / CC1/2: 0.778 / Rpim(I) all: 0.283 / Rrim(I) all: 0.947 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.83 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 987 5.08 %
Rwork0.1955 --
obs0.1974 19432 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 0 49 1014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111010
X-RAY DIFFRACTIONf_angle_d1.1441380
X-RAY DIFFRACTIONf_dihedral_angle_d17.015364
X-RAY DIFFRACTIONf_chiral_restr0.076151
X-RAY DIFFRACTIONf_plane_restr0.009178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10.3111480.29382596X-RAY DIFFRACTION100
2.1-2.230.24471320.23292625X-RAY DIFFRACTION100
2.23-2.410.27611580.23822613X-RAY DIFFRACTION100
2.41-2.650.28541400.23392637X-RAY DIFFRACTION100
2.65-3.030.28381480.23672641X-RAY DIFFRACTION100
3.03-3.820.2661340.19752672X-RAY DIFFRACTION100
3.82-48.830.17341270.15442661X-RAY DIFFRACTION96

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