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- PDB-7rb4: Crystal structure of Peptono Toxin, a diphtheria toxin homolog, f... -

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Basic information

Entry
Database: PDB / ID: 7rb4
TitleCrystal structure of Peptono Toxin, a diphtheria toxin homolog, from Seinonella peptonophila
ComponentsDiphtheria toxin, C domain
KeywordsTOXIN / diphtheria toxin / DT / homolog / Seinonella peptonophila
Function / homology
Function and homology information


Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Diphtheria toxin, C domain
Similarity search - Component
Biological speciesSeinonella peptonophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsSugiman-Marangos, S.N. / Gill, S.K. / Melnyk, R.A.
CitationJournal: Commun Biol / Year: 2022
Title: Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold.
Authors: Sugiman-Marangos, S.N. / Gill, S.K. / Mansfield, M.J. / Orrell, K.E. / Doxey, A.C. / Melnyk, R.A.
History
DepositionJul 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin, C domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,74527
Polymers67,4451
Non-polymers3,30026
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.653, 82.456, 91.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Diphtheria toxin, C domain


Mass: 67445.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Seinonella peptonophila (bacteria) / Gene: SAMN05444392_1116 / Plasmid: Champion pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Nico(DE3) / References: UniProt: A0A1M4ZWA4
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 uL SPT (15.8 mg/mL in 20 mM Tris pH 8.0, 150 mM NaCl) and 1 uL mother liquor (100 mM potassium iodide, 22% PEG3350) dehydrated over 200 uL of mother liquor

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 2 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 6, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.185→59.291 Å / Num. obs: 28929 / % possible obs: 92.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 16.4
Reflection shellResolution: 2.185→2.192 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.587 / Num. unique obs: 168 / CC1/2: 0.663 / Rpim(I) all: 0.353 / Rrim(I) all: 0.69 / % possible all: 54

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Processing

Software
NameVersionClassification
autoPROC1.05data processing
autoPROC1.05data reduction
autoPROC1.05data scaling
PHENIX1.19.1_4122+SVNphasing
PHENIX1.19.1_4122+SVNrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.19→59.29 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.6688
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 1462 5.05 %
Rwork0.2012 27465 -
obs0.2024 28814 92.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.38 Å2
Refinement stepCycle: LAST / Resolution: 2.19→59.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 26 392 5080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184768
X-RAY DIFFRACTIONf_angle_d0.48856496
X-RAY DIFFRACTIONf_chiral_restr0.0425739
X-RAY DIFFRACTIONf_plane_restr0.0039844
X-RAY DIFFRACTIONf_dihedral_angle_d12.91581734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.260.3201790.27171724X-RAY DIFFRACTION59.04
2.26-2.350.2751920.26992258X-RAY DIFFRACTION75.73
2.35-2.460.3121630.26642771X-RAY DIFFRACTION95.79
2.46-2.590.27731760.24532834X-RAY DIFFRACTION97.63
2.59-2.750.25651290.2382950X-RAY DIFFRACTION99.23
2.75-2.970.28941380.24242916X-RAY DIFFRACTION99.06
2.97-3.260.23811510.21872945X-RAY DIFFRACTION99.36
3.26-3.740.24141660.18152966X-RAY DIFFRACTION99.87
3.74-4.710.18451750.15122987X-RAY DIFFRACTION99.97
4.71-59.290.15881930.16743114X-RAY DIFFRACTION99.88
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)
10.7349180701780.4773831371920.02211240185071.71483452404-0.08696136418450.7762046751580.0552762986913-0.135760014675-0.09183167534810.193490397068-0.0437383404844-0.0664152362459-0.00366168099007-0.077797379655-0.01257617745580.1713299937280.022318305047-0.01051131598940.2122966318410.006026835756320.1394759938515.396044679922.956184273865.7936605933
21.770180730190.682388921377-0.2104688144564.31974310570.4666258237753.03107380114-0.1332066427560.2801560576380.260477114926-0.2282783527450.07354420109590.064339528734-0.3771183412260.09080038840560.05340771272440.2198978431670.0162972011628-0.004874108921460.1546281331380.02306736709980.16509945392226.592720358158.076026975651.8906221417
30.7040494928890.923554384210.1417689837522.74624847060.5215350437510.830432317482-0.004064234843680.0569298078888-0.01739127887980.06122293580780.03675000417380.0322586744401-0.0183768356899-0.0324617427301-0.02617235665730.1213048819540.03266754523570.003684956913880.1771979754920.0004314873122550.12112662424420.310171087733.465197492850.1361542275
42.286631438211.540589934920.2210214429432.6342141498-0.5010091385242.38818758825-0.1882030969730.296457589028-0.0484590614793-0.3511063993530.1384973665470.0721781191555-0.0901622212239-0.09024110671210.03104299808610.1175814434810.03446437302870.01013957233610.203095556386-0.01772029172470.13853812703514.045184539425.077597566638.8946764932
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 271 )4 - 2711 - 268
22chain 'A' and (resid 272 through 365 )272 - 365269 - 362
33chain 'A' and (resid 366 through 536 )366 - 536363 - 533
44chain 'A' and (resid 537 through 606 )537 - 606534 - 603

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