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- PDB-1qvp: C terminal SH3-like domain from Diphtheria toxin Repressor residu... -

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Basic information

Entry
Database: PDB / ID: 1qvp
TitleC terminal SH3-like domain from Diphtheria toxin Repressor residues 144-226.
ComponentsDiphtheria toxin repressor
KeywordsDNA BINDING PROTEIN / REPRESSOR / DTXR / C-TERMINAL DOMAIN / PROKARYOTIC SH3 DOMAIN / TRANSCRIPTION REGULATION / PEPTIDE-BINDING / GENE REGULATION
Function / homology
Function and homology information


transition metal ion binding / SH3 domain binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Transcriptional repressor, C-terminal / SH3 type barrels. / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Diphtheria toxin repressor / Diphtheria toxin repressor
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsWylie, G.P. / Rangachari, V. / Bienkiewicz, E.A. / Marin, V. / Bhattacharya, N. / Love, J.F. / Murphy, J.R. / Logan, T.M.
CitationJournal: Biochemistry / Year: 2005
Title: Prolylpeptide binding by the prokaryotic SH3-like domain of the diphtheria toxin repressor: a regulatory switch.
Authors: Wylie, G.P. / Rangachari, V. / Bienkiewicz, E.A. / Marin, V. / Bhattacharya, N. / Love, J.F. / Murphy, J.R. / Logan, T.M.
History
DepositionAug 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin repressor


Theoretical massNumber of molelcules
Total (without water)9,6601
Polymers9,6601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 64structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Diphtheria toxin repressor / Iron-dependent diphtheria tox regulatory element / Tox regulatory factor


Mass: 9659.795 Da / Num. of mol.: 1 / Fragment: Residues 144-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: DTXR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21(DE3) / References: UniProt: P33120, UniProt: P0DJL7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HN(CA)CB
131CBCA(CO)NH
141HNCO
151H(C)(CO)NH-TOCSY
161HC(CO)NH-TOCSY
NMR detailsText: for listing of experiments run please see the primary citation

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM DtxR144-226 U-15N; 10mM Potassium Phosphate buffer pH6.590% H2O/10% D2O
21-2 mM DtxR144-226 U-15N and U-13C; 10mM Potassium Phosphate buffer pH6.590% H2O, 10% D2O; 100% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS7202

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerrefinement
CNS1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 64 / Conformers submitted total number: 13

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