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

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Basic information

Entry
Database: PDB / ID: 5gtt
TitleCrystal structure of C. perfringens iota-like enterotoxin CPILE-a
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
Binary enterotoxin of Clostridium perfringens component a
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.011 Å
AuthorsToniti, W. / Yoshida, T. / Tsurumura, T. / Irikura, D. / Tsuge, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research, MEXT of Japan15K08289 Japan
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
DepositionAug 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: Binary enterotoxin of Clostridium perfringens component a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7963
Polymers47,6711
Non-polymers1242
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint7 kcal/mol
Surface area19610 Å2
Unit cell
Length a, b, c (Å)70.338, 100.665, 126.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 47.58 %
Crystal growTemperature: 277.15 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: Sep 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 29584 / % possible obs: 98.3 % / Redundancy: 6.7 % / Net I/σ(I): 31.2
Reflection shellResolution: 2.01→2.04 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.88 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.011→21.832 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.38
RfactorNum. reflection% reflection
Rfree0.2286 1996 6.75 %
Rwork0.1757 --
obs0.1793 29557 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2.011→21.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 8 249 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073399
X-RAY DIFFRACTIONf_angle_d1.0844591
X-RAY DIFFRACTIONf_dihedral_angle_d13.4481278
X-RAY DIFFRACTIONf_chiral_restr0.042512
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0109-2.06110.27431220.27881688X-RAY DIFFRACTION86
2.0611-2.11680.28041340.2541842X-RAY DIFFRACTION93
2.1168-2.1790.29931400.23291927X-RAY DIFFRACTION97
2.179-2.24930.27171410.21441973X-RAY DIFFRACTION99
2.2493-2.32960.30621430.20581975X-RAY DIFFRACTION100
2.3296-2.42280.25351450.1991986X-RAY DIFFRACTION100
2.4228-2.53290.27681420.19431969X-RAY DIFFRACTION100
2.5329-2.66620.24121450.18582005X-RAY DIFFRACTION100
2.6662-2.83290.24151450.19071996X-RAY DIFFRACTION100
2.8329-3.05110.2361460.18542005X-RAY DIFFRACTION100
3.0511-3.35720.23811450.18232007X-RAY DIFFRACTION100
3.3572-3.84070.24681470.16012021X-RAY DIFFRACTION100
3.8407-4.83020.15621480.13762038X-RAY DIFFRACTION100
4.8302-21.83330.21281530.15262129X-RAY DIFFRACTION100
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)
13.1407-0.9284-0.38221.9915-0.26682.2544-0.07250.51750.6717-0.13290.0341-0.0329-0.3132-0.01720.02170.2462-0.0854-0.09690.44520.08840.3978-15.8955-7.9962-22.3528
21.4632-0.1888-0.46283.0891-1.38832.252-0.0249-0.0160.0429-0.13460.08510.33890.121-0.3326-0.03570.1974-0.0154-0.04760.4183-0.02610.2485-20.299-21.3504-10.2719
33.6328-0.3419-0.12711.0822-0.28761.8087-0.06240.0847-0.0017-0.1151-0.0347-0.22850.23530.40870.09720.26330.0429-0.00090.4653-0.00610.15712.5194-28.7466-13.8319
41.8166-0.20670.21811.3046-0.3342.308-0.03460.4505-0.2093-0.2792-0.01520.0190.26210.17380.05030.25370.02170.01270.4472-0.06440.20752.2565-31.74-20.3515
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 196 )
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 285 )
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 419 )

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