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- PDB-1sr4: Crystal Structure of the Haemophilus ducreyi cytolethal distendin... -

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Basic information

Entry
Database: PDB / ID: 1sr4
TitleCrystal Structure of the Haemophilus ducreyi cytolethal distending toxin
Components
  • Cytolethal distending toxin subunit A
  • cytolethal distending toxin protein B
  • cytolethal distending toxin protein C
KeywordsTOXIN / bacterial / Haemophilus ducreyi / virulence / DNA Damage / genotoxin / cytotoxins / Cell Cycle / Apoptosis / lectin / Deoxyribonuclease I
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
BROMIDE ION / Cytolethal distending toxin subunit A / Cytolethal distending toxin protein B / Cytochrome C oxidase subunit I
Similarity search - Component
Biological speciesHaemophilus ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsNesic, D. / Hsu, Y. / Stebbins, C.E.
CitationJournal: Nature / Year: 2004
Title: Assembly and Function of a Bacterial Genotoxin
Authors: Nesic, D. / Hsu, Y. / Stebbins, C.E.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Cytolethal distending toxin subunit A
B: cytolethal distending toxin protein B
C: cytolethal distending toxin protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,32029
Polymers70,2433
Non-polymers2,07826
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-43 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.652, 75.653, 121.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytolethal distending toxin subunit A / CDT A


Mass: 22873.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: CDTA, HD0902 / Production host: Escherichia coli (E. coli) / References: UniProt: O06522
#2: Protein cytolethal distending toxin protein B / CDT B


Mass: 28989.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O06523
#3: Protein cytolethal distending toxin protein C / CDT C


Mass: 18379.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O06524
#4: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-25% PEG MME 5000, 25-30% glycerol, 0.1M imidazole, 2mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 113.1 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.92 Å
RadiationMonochromator: Monochromator: Double crystal monochromator with fixed exit geometry; Bragg angle range is 7.55 degrees - 28 degrees; sagitally focusing Si(111) crystals, high precision rotary energy ...Monochromator: Monochromator: Double crystal monochromator with fixed exit geometry; Bragg angle range is 7.55 degrees - 28 degrees; sagitally focusing Si(111) crystals, high precision rotary energy scale; operates in high vacuum; located 9.6 meters from the source. Mirror: For harmonics rejection and vertical focusing (0.08 mm FWHM); flat cylindrically bent mirror; independent choice of mirror angle and focal length; located 11 meters from the source
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. all: 45190 / Num. obs: 45190 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 98.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2→99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2232 5 %Random
Rwork0.182 ---
all0.182 45402 --
obs0.182 44954 --
Refinement stepCycle: LAST / Resolution: 2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 26 477 5039

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