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- PDB-2f2f: Crystal structure of cytolethal distending toxin (CDT) from Actin... -

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Basic information

Entry
Database: PDB / ID: 2f2f
TitleCrystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans
Components
  • Cytolethal distending toxin A
  • Cytolethal distending toxin B
  • cytolethal distending toxin C
KeywordsTOXIN / Cytolethal distending toxin / CDT / Actinobacillus actinomycetemcomitans / oligomerization / stability and toxic activity
Function / homology
Function and homology information


catalytic activity / cell outer membrane / toxin activity / carbohydrate binding
Similarity search - Function
Cytolethal distending toxin A/C / Cytolethal distending toxin A / Cytolethal distending toxin A/C domain / Cytolethal distending toxin B / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Lectin domain of ricin B chain profile. / Endonuclease/exonuclease/phosphatase superfamily ...Cytolethal distending toxin A/C / Cytolethal distending toxin A / Cytolethal distending toxin A/C domain / Cytolethal distending toxin B / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Lectin domain of ricin B chain profile. / Endonuclease/exonuclease/phosphatase superfamily / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 4-Layer Sandwich / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytolethal distending toxin subunit A / Cytochrome C oxidase subunit I / Cytolethal distending toxin
Similarity search - Component
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYamada, T. / Komoto, J. / Saiki, K. / Konishi, K. / Takusagawa, F.
CitationJournal: Protein Sci. / Year: 2006
Title: Variation of loop sequence alters stability of cytolethal distending toxin (CDT): crystal structure of CDT from Actinobacillus actinomycetemcomitans
Authors: Yamada, T. / Komoto, J. / Saiki, K. / Konishi, K. / Takusagawa, F.
History
DepositionNov 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AUTHOR STATES THAT SEQUENCE IN THE PDB FILE IS CORRECT ON THE BASIS OF ELECTRON DENSITY ...SEQUENCE AUTHOR STATES THAT SEQUENCE IN THE PDB FILE IS CORRECT ON THE BASIS OF ELECTRON DENSITY MAPS AND THE OTHER CDT SEQUENCES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytolethal distending toxin A
B: Cytolethal distending toxin B
C: cytolethal distending toxin C
D: Cytolethal distending toxin A
E: Cytolethal distending toxin B
F: cytolethal distending toxin C


Theoretical massNumber of molelcules
Total (without water)153,5866
Polymers153,5866
Non-polymers00
Water4,900272
1
A: Cytolethal distending toxin A
B: Cytolethal distending toxin B
C: cytolethal distending toxin C


Theoretical massNumber of molelcules
Total (without water)76,7933
Polymers76,7933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-35 kcal/mol
Surface area20820 Å2
MethodPISA
2
D: Cytolethal distending toxin A
E: Cytolethal distending toxin B
F: cytolethal distending toxin C


Theoretical massNumber of molelcules
Total (without water)76,7933
Polymers76,7933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-34 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.65, 117.46, 123.37
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsCDT is a heterotrimer, i.e., Subunit A, B, and C form a holotoxin, and Subunit D, E, and F form another holotoxin.

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Components

#1: Protein Cytolethal distending toxin A / CDT A


Mass: 24532.748 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: cdtA / Plasmid: A19-47CDT / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O87120
#2: Protein Cytolethal distending toxin B / CDT B


Mass: 31528.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: cdtB / Plasmid: A19-47CDT / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q7DK12
#3: Protein cytolethal distending toxin C / CDT C


Mass: 20731.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: cdtC / Plasmid: A19-47CDT / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q7DK11
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM MES, 10% MPD, 4% PEG-8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.08 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 66570 / Num. obs: 66570 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.5 Å / % possible all: 88

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Processing

Software
NameClassification
APSdata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SR4

1sr4


Resolution: 2.4→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 6746 RANDOM
Rwork0.221 --
all0.224 67570 -
obs0.224 66570 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8916 0 0 272 9188

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