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- PDB-4ow6: Crystal structure of Diphtheria Toxin at acidic pH -

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Basic information

Entry
Database: PDB / ID: 4ow6
TitleCrystal structure of Diphtheria Toxin at acidic pH
ComponentsDiphtheria toxin
KeywordsTOXIN / TRANSFERASE / Diphtheria toxin translocation / membrane insertion / bicelles / membrane channels
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / glycosyltransferase activity
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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsLeka, O. / Vallese, F. / Pirazzini, M. / Berto, P. / Montecucco, C. / Zanotti, G.
CitationJournal: Febs J. / Year: 2014
Title: Diphtheria toxin conformational switching at acidic pH.
Authors: Leka, O. / Vallese, F. / Pirazzini, M. / Berto, P. / Montecucco, C. / Zanotti, G.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)116,8232
Polymers116,8232
Non-polymers00
Water0
1
A: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)58,4111
Polymers58,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)58,4111
Polymers58,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.440, 141.280, 176.020
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 Diphtheria toxin /


Mass: 58411.359 Da / Num. of mol.: 2 / Fragment: UNP residues 26-560 / Source method: isolated from a natural source / Source: (natural) Corynebacterium diphtheriae (bacteria) / Strain: C7 (beta)
References: UniProt: H2GU79, NAD+-diphthamide ADP-ribosyltransferase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 31, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.8→47.44 Å / Num. all: 30102 / Num. obs: 30102 / % possible obs: 94.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.8→45.135 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3216 1452 5.12 %
Rwork0.238 --
obs0.2421 28350 94.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 0 0 0 7374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017522
X-RAY DIFFRACTIONf_angle_d1.50710192
X-RAY DIFFRACTIONf_dihedral_angle_d15.7222714
X-RAY DIFFRACTIONf_chiral_restr0.0591153
X-RAY DIFFRACTIONf_plane_restr0.0081323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.34231500.29022711X-RAY DIFFRACTION98
2.9001-3.01620.35391550.26152717X-RAY DIFFRACTION97
3.0162-3.15340.33181570.24942758X-RAY DIFFRACTION98
3.1534-3.31960.35561300.24352745X-RAY DIFFRACTION98
3.3196-3.52750.38741490.25442304X-RAY DIFFRACTION83
3.5275-3.79970.35211310.29392391X-RAY DIFFRACTION85
3.7997-4.18190.37411180.24262458X-RAY DIFFRACTION86
4.1819-4.78640.241460.18282869X-RAY DIFFRACTION99
4.7864-6.02810.30171600.21872883X-RAY DIFFRACTION100
6.0281-45.14060.29011560.2333062X-RAY DIFFRACTION100

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