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- PDB-1sgk: NUCLEOTIDE-FREE DIPHTHERIA TOXIN -

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Basic information

Entry
Database: PDB / ID: 1sgk
TitleNUCLEOTIDE-FREE DIPHTHERIA TOXIN
ComponentsDIPHTHERIA TOXIN (DIMERIC)
KeywordsTOXIN / ADP-RIBOSYLATION / TRANSFERASE / GLYCOSYLTRANSFERASE / NAD / ADP-RIBOSYL TRANSFERASE
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 speciesCorynephage beta (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBell, C.E. / Eisenberg, D.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of nucleotide-free diphtheria toxin.
Authors: Bell, C.E. / Eisenberg, D.
#1: Journal: Biochemistry / Year: 1996
Title: Crystal Structure of Diphtheria Toxin Bound to Nicotinamide Adenine Dinucleotide
Authors: Bell, C.E. / Eisenberg, D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Domain Swapping: Entangling Alliances between Proteins
Authors: Bennett, M.J. / Choe, S. / Eisenberg, D.
#3: Journal: Protein Sci. / Year: 1994
Title: Refined Structure of Monomeric Diphtheria Toxin at 2.3 A Resolution
Authors: Bennett, M.J. / Eisenberg, D.
#4: 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.
#5: 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
DepositionSep 12, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN (DIMERIC)


Theoretical massNumber of molelcules
Total (without water)58,4111
Polymers58,4111
Non-polymers00
Water6,431357
1
A: DIPHTHERIA TOXIN (DIMERIC)

A: DIPHTHERIA TOXIN (DIMERIC)


Theoretical massNumber of molelcules
Total (without water)116,8232
Polymers116,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area8350 Å2
ΔGint-26 kcal/mol
Surface area41190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.200, 91.200, 65.300
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DIPHTHERIA TOXIN (DIMERIC) / DT


Mass: 58411.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PURCHASED FROM CONNAUGHT LABORATORIES / Source: (natural) Corynephage beta (virus) / Genus: Lambda-like viruses
References: UniProt: P00588, NAD+-diphthamide ADP-ribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 46 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP, 12 % PEG8000, 0.43M NACL, 0.043M TRIS, PH 7.5, vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG80001reservoir
20.43 M1reservoirNaCl
30.043 MTris1reservoir
425 mg/mlDT1drop
514 %(w/v)PEG80001drop
60.5 M1dropNaCl
70.05 MTris1drop

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 26627 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 2.6 / % possible all: 92.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 74281
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
R-AXISdata collection
R-AXISdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DT-DIMER APUP COMPLEX (PDB ENTRY 1DDT)

1ddt


Resolution: 2.3→8 Å / Cross valid method: FREE R-FACTOR / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2565 10 %RANDOM
Rwork0.182 ---
obs0.182 25726 96.2 %-
Displacement parametersBiso mean: 38.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 0 357 4378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
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
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.351 325 81.5 %
Rwork0.2874 2729 -
obs--9.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 23161
Solvent computation
*PLUS
Displacement parameters
*PLUS

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