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- PDB-5wu0: Crystal structure of C. perfringens iota-like enterotoxin CPILE-a... -

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Basic information

Entry
Database: PDB / ID: 5wu0
TitleCrystal structure of C. perfringens iota-like enterotoxin CPILE-a with NADH
ComponentsBinary enterotoxin of Clostridium perfringens component a
KeywordsTOXIN / bacterial toxin / actin / CPILE-a / ADP-ribosylation
Function / homology
Function and homology information


nucleotide binding / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Binary enterotoxin of Clostridium perfringens component a
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsToniti, W. / Yoshida, T. / Tsurumura, T. / Irikura, D. / Tsuge, H.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure and structure-based mutagenesis of actin-specific ADP-ribosylating toxin CPILE-a as novel enterotoxin
Authors: Toniti, W. / Yoshida, T. / Tsurumura, T. / Irikura, D. / Monma, C. / Kamata, Y. / Tsuge, H.
History
DepositionDec 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Binary enterotoxin of Clostridium perfringens component a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3372
Polymers47,6711
Non-polymers6651
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-8 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.583, 101.631, 125.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-729-

HOH

31A-731-

HOH

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Components

#1: Protein Binary enterotoxin of Clostridium perfringens component a / CPILE-a


Mass: 47671.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: W5052 / Gene: becA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: X5I2D7
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.37 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Tris HCl, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.251→50 Å / Num. obs: 21170 / % possible obs: 98.4 % / Redundancy: 6 % / Net I/σ(I): 41.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GTT

5gtt


Resolution: 2.251→20.499 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.57
RfactorNum. reflection% reflection
Rfree0.2479 1012 4.79 %
Rwork0.1756 --
obs0.1789 21127 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.251→20.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 44 131 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083458
X-RAY DIFFRACTIONf_angle_d1.1234683
X-RAY DIFFRACTIONf_dihedral_angle_d17.0161305
X-RAY DIFFRACTIONf_chiral_restr0.044523
X-RAY DIFFRACTIONf_plane_restr0.004595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2515-2.370.33691320.24762591X-RAY DIFFRACTION89
2.37-2.51830.30451420.23262872X-RAY DIFFRACTION98
2.5183-2.71230.31231620.23232817X-RAY DIFFRACTION98
2.7123-2.98450.32511290.22282899X-RAY DIFFRACTION99
2.9845-3.41460.28431390.20142931X-RAY DIFFRACTION99
3.4146-4.29560.22051520.14812938X-RAY DIFFRACTION99
4.2956-20.49970.17881560.1293067X-RAY DIFFRACTION99
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)
11.6376-0.1503-0.10041.5559-0.91872.3373-0.13030.11150.22290.00910.05260.102-0.2283-0.19820.07250.2515-0.0075-0.06820.3626-0.06460.273-18.0517-16.0612-15.0451
25.8167-0.90241.06464.1021-0.23442.81750.00430.2869-0.2095-0.07380.062-0.51310.25020.6124-0.06880.2333-0.00420.0350.49010.04070.228520.8004-31.5999-14.8616
33.31130.11611.32751.75160.21613.3740.02650.2258-0.0924-0.1749-0.10750.07290.20220.12410.09080.20630.04160.02150.3719-0.01910.23612.4498-31.7732-20.1266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 419 )

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