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- PDB-1tox: DIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD -

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Basic information

Entry
Database: PDB / ID: 1tox
TitleDIPHTHERIA TOXIN DIMER COMPLEXED WITH NAD
ComponentsDIPHTHERIA TOXIN (DIMERIC)
KeywordsTOXIN / ADP-RIBOSYLATION / GLUCOSYLTRANSFERASE / TRANSFERASE / NAD
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Diphtheria toxin
Similarity search - Component
Biological speciesCorynephage beta (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBell, C.E. / Eisenberg, D.
Citation
Journal: Biochemistry / Year: 1996
Title: Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide.
Authors: Bell, C.E. / Eisenberg, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Domain Swapping: Entangling Alliances between Proteins
Authors: Bennett, M.J. / Choe, S. / Eisenberg, D.
#2: Journal: Protein Sci. / Year: 1994
Title: Refined Structure of Monomeric Diphtheria Toxin at 2.3 A Resolution
Authors: Bennett, M.J. / Eisenberg, D.
#3: Journal: Protein Sci. / Year: 1994
Title: Refined Structure of Dimeric Diphtheria Toxin at 2.0 A Resolution
Authors: Bennett, M.J. / Choe, S. / Eisenberg, D.
#4: Journal: Nature / Year: 1992
Title: The Crystal Structure of Diphtheria Toxin
Authors: Choe, S. / Bennett, M.J. / Fujii, G. / Curmi, P.M. / Kantardjieff, K.A. / Collier, R.J. / Eisenberg, D.
History
DepositionOct 6, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN (DIMERIC)
B: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1504
Polymers116,8232
Non-polymers1,3272
Water5,441302
1
A: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules

A: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1504
Polymers116,8232
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area9720 Å2
ΔGint-39 kcal/mol
Surface area40270 Å2
MethodPISA, PQS
2
B: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0752
Polymers58,4111
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules

B: DIPHTHERIA TOXIN (DIMERIC)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1504
Polymers116,8232
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)105.000, 89.500, 130.100
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999945, -0.006208, 0.00843), (0.00634, 0.999857, -0.015694), (-0.008331, 0.015747, 0.999841)
Vector: 3.92825, -8.59869, -64.28194)

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Components

#1: Protein DIPHTHERIA TOXIN (DIMERIC) / DT


Mass: 58411.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: NAD FROM YEAST, CRYSTALLINE FORM, PURCHASED FROM SIGMA (N 1636)
Source: (natural) Corynephage beta (virus) / Genus: Lambda-like viruses
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 46 %
Description: DATA COLLECTION USING LIQUID NITROGEN COOLED NITROGEN VAPOR
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mldimeric DT1drop
210 mMTris-HCl1drop
30.2 mMEDTA1drop
411.2 %PEG80001drop
50.4 M1dropNaCl
60.43 MTris-HCl1reservoir
712.0 %PEG80001reservoir
80.43 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 22, 1994 / Details: MIRRORS (MSC)
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→65 Å / Num. obs: 48977 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Num. measured all: 157244 / Biso Wilson estimate: 28.6 Å2
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 87.4 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
R-AXISdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.307 -10 %
Rwork0.227 --
obs0.227 48300 92.6 %
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7905 0 88 302 8295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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