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- PDB-7o4w: Crystal structure of diphtheria toxin mutant CRM197 with a disulp... -

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Basic information

Entry
Database: PDB / ID: 7o4w
TitleCrystal structure of diphtheria toxin mutant CRM197 with a disulphide bond replaced by a Cys-Acetone-Cys bridge
ComponentsDiphtheria toxin
KeywordsTOXIN / Diphtheria toxin / mutant / disulphide bridge / modified disulphide bridge / acetone.
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space
Similarity search - Function
Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain
Similarity search - Domain/homology
1-hydroxypropan-2-one / ACETATE ION / TRIETHYLENE GLYCOL / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03002061079 Å
AuthorsVeggi, D. / Dello Iacono, L.
CitationJournal: Chem Sci / Year: 2022
Title: Retaining the structural integrity of disulfide bonds in diphtheria toxoid carrier protein is crucial for the effectiveness of glycoconjugate vaccine candidates.
Authors: Carboni, F. / Kitowski, A. / Sorieul, C. / Veggi, D. / Marques, M.C. / Oldrini, D. / Balducci, E. / Brogioni, B. / Del Bino, L. / Corrado, A. / Angiolini, F. / Dello Iacono, L. / Margarit, I. ...Authors: Carboni, F. / Kitowski, A. / Sorieul, C. / Veggi, D. / Marques, M.C. / Oldrini, D. / Balducci, E. / Brogioni, B. / Del Bino, L. / Corrado, A. / Angiolini, F. / Dello Iacono, L. / Margarit, I. / Romano, M.R. / Bernardes, G.J.L. / Adamo, R.
History
DepositionApr 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1038
Polymers58,4831
Non-polymers6207
Water2,396133
1
A: Diphtheria toxin
hetero molecules

A: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,20616
Polymers116,9672
Non-polymers1,23914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_567x,x-y+1,-z+21
Buried area11750 Å2
ΔGint15 kcal/mol
Surface area41440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.996, 97.996, 98.267
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-827-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Diphtheria toxin /


Mass: 58483.422 Da / Num. of mol.: 1 / Mutation: G52E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5PY51

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-4Y8 / 1-hydroxypropan-2-one / Hydroxyacetone


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M magnesium acetate, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.03→49 Å / Num. obs: 35072 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 49.9066061092 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.22
Reflection shellResolution: 2.03→2.103 Å / Rmerge(I) obs: 1.225 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3440 / CC1/2: 0.711

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AE0

4ae0


Resolution: 2.03002061079→48.99795 Å / SU ML: 0.310560222709 / Cross valid method: FREE R-VALUE / σ(F): 1.35509021097 / Phase error: 28.3917685748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237125486782 1716 4.89767959586 %
Rwork0.204160409163 33321 -
obs0.205820694042 35037 99.9771722072 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.5854607343 Å2
Refinement stepCycle: LAST / Resolution: 2.03002061079→48.99795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 40 133 4113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01972393594244054
X-RAY DIFFRACTIONf_angle_d1.211150096245481
X-RAY DIFFRACTIONf_chiral_restr0.0754226678536623
X-RAY DIFFRACTIONf_plane_restr0.00765616160093707
X-RAY DIFFRACTIONf_dihedral_angle_d19.58358441891460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03002061079-2.08980.3488320865311360.3131649740412784X-RAY DIFFRACTION99.9657651489
2.0898-2.15720.3383437287841390.291259828452756X-RAY DIFFRACTION100
2.1572-2.23430.3242310155691120.2685814463492807X-RAY DIFFRACTION100
2.2343-2.32380.3132942903211520.2535004235042717X-RAY DIFFRACTION100
2.3238-2.42950.2857562017121410.2495803366782755X-RAY DIFFRACTION99.9654815326
2.4295-2.55760.2997592848271510.2468974289092750X-RAY DIFFRACTION100
2.5576-2.71780.3012473708621460.2438802485612781X-RAY DIFFRACTION100
2.7178-2.92770.307599525331270.2511389350732775X-RAY DIFFRACTION100
2.9277-3.22220.2739702532221720.2342330847222754X-RAY DIFFRACTION100
3.2222-3.68840.2270513904491400.2046754971972771X-RAY DIFFRACTION99.9656593407
3.6884-4.64640.1754207588831420.1595462806662819X-RAY DIFFRACTION100
4.6464-48.997950.207994494971580.1754431664152852X-RAY DIFFRACTION99.8672859987

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