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- PDB-4ae0: Crystal structure of diphtheria toxin mutant CRM197 -

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Basic information

Entry
Database: PDB / ID: 4ae0
TitleCrystal structure of diphtheria toxin mutant CRM197
ComponentsDIPHTHERIA TOXIN
KeywordsTOXIN
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Uptake and function of diphtheria toxin / protein transmembrane transporter activity / nucleotidyltransferase activity / toxin activity / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / 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 ...Diphtheria toxin, translocation domain / Diphtheria toxin, receptor-binding domain / 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 / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Globin-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCORYNEBACTERIUM DIPHTHERIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsMalito, E. / Spraggon, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for Lack of Toxicity of the Diphtheria Toxin Mutant Crm197.
Authors: Malito, E. / Bursulaya, B. / Chen, C. / Surdo, P.L. / Picchianti, M. / Balducci, E. / Biancucci, M. / Brock, A. / Berti, F. / Bottomley, M.J. / Nissum, M. / Costantino, P. / Rappuoli, R. / Spraggon, G.
History
DepositionJan 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN


Theoretical massNumber of molelcules
Total (without water)58,4831
Polymers58,4831
Non-polymers00
Water3,045169
1
A: DIPHTHERIA TOXIN

A: DIPHTHERIA TOXIN


Theoretical massNumber of molelcules
Total (without water)116,9672
Polymers116,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7190 Å2
ΔGint-23.7 kcal/mol
Surface area40480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.841, 91.388, 63.838
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2054-

HOH

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Components

#1: Protein DIPHTHERIA TOXIN / / DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN ...DT / NAD(+)--DIPHTHAMIDE ADP-RIBOSYLTRANSFERASE / DIPHTHERIA TOXIN FRAGMENT A / DIPHTHERIA TOXIN FRAGMENT B / CRM197


Mass: 58483.422 Da / Num. of mol.: 1 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) CORYNEBACTERIUM DIPHTHERIAE (bacteria)
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLY 53 TO GLU
Sequence detailsCOORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE ...COORDINATES USE STANDARD RESIDUE NUMBERING FOR CONSISTENCY WITH PREVIOUS WORK RESULTING IN THE NATURAL GLY TO GLU MUTATION AT POSITION 52 INSTEAD OF 53. RESIDUES 1-32 IN THE UNIPROT SEQUENCE ARE THE SIGNAL PEPTIDE.

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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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 9 / Details: 1.9 M AMMONIUM SULFATE, 100 MM BICINE [PH 9.0]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39541 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.3 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SGK

1sgk


Resolution: 1.996→41.335 Å / SU ML: 0.29 / σ(F): 0.21 / Phase error: 28.36 / Stereochemistry target values: ML
Details: RESIDUES 1-4, 38-49, 188-200, 349-352, AND 517-519, ARE DISORDERED. DISORDERED SIDE CHAINS WERE MODELED UP TO THE BACKBONE CBETA ATOMS, AND RESIDUE NAMES WERE KEPT CONSISTENT WITH SEQUENCE OF THE PROTEIN.
RfactorNum. reflection% reflection
Rfree0.2411 1837 5 %
Rwork0.2096 --
obs0.2112 36533 88.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.666 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1--8.2649 Å20 Å2-9.5035 Å2
2--15.4835 Å20 Å2
3----7.2187 Å2
Refinement stepCycle: LAST / Resolution: 1.996→41.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3664 0 0 169 3833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073735
X-RAY DIFFRACTIONf_angle_d0.9615082
X-RAY DIFFRACTIONf_dihedral_angle_d12.2711287
X-RAY DIFFRACTIONf_chiral_restr0.067590
X-RAY DIFFRACTIONf_plane_restr0.004664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9958-2.06710.305960.26992137X-RAY DIFFRACTION55
2.0671-2.14990.30651630.24662985X-RAY DIFFRACTION77
2.1499-2.24770.28051730.22383318X-RAY DIFFRACTION85
2.2477-2.36620.24331760.21233463X-RAY DIFFRACTION89
2.3662-2.51450.28431860.21493605X-RAY DIFFRACTION92
2.5145-2.70860.25862040.21353735X-RAY DIFFRACTION95
2.7086-2.98110.27351900.21753829X-RAY DIFFRACTION97
2.9811-3.41230.24352120.22023870X-RAY DIFFRACTION99
3.4123-4.29840.21222110.18853906X-RAY DIFFRACTION99
4.2984-41.34370.22162260.19273848X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -15.9226 Å / Origin y: 24.0845 Å / Origin z: 27.364 Å
111213212223313233
T0.279 Å2-0.0234 Å20.0243 Å2-0.3515 Å20.0245 Å2--0.262 Å2
L1.137 °20.177 °2-0.0665 °2-1.0249 °20.1043 °2--0.4686 °2
S-0.1805 Å °0.1049 Å °0.0038 Å °-0.1289 Å °0.1524 Å °0.1927 Å °-0.0506 Å °-0.1535 Å °0.0253 Å °
Refinement TLS groupSelection details: ALL

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