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- PDB-1m7t: Solution Structure and Dynamics of the Human-Escherichia coli Thi... -

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Basic information

Entry
Database: PDB / ID: 1m7t
TitleSolution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability
ComponentsChimera of Human and E. coli thioredoxin
KeywordsELECTRON TRANSPORT / chimera / human / E. coli / dynamics / stability
Function / homology
Function and homology information


Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / positive regulation of DNA-directed DNA polymerase activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes ...Protein repair / cellular detoxification of hydrogen peroxide / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / positive regulation of DNA-directed DNA polymerase activity / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / positive regulation of DNA binding / DNA polymerase processivity factor activity / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / Purinergic signaling in leishmaniasis infection / activation of protein kinase B activity / cell redox homeostasis / TP53 Regulates Metabolic Genes / response to radiation / positive regulation of peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / oxidoreductase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin 1 / Thioredoxin
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodSOLUTION NMR / see publication
AuthorsDangi, B. / Dobrodumov, A.V. / Louis, J.M. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 2002
Title: Solution Structure and Dynamics of the Human-Escherichia coli Thioredoxin Chimera: Insights into Thermodynamic Stability
Authors: Dangi, B. / Dobrodumov, A.V. / Louis, J.M. / Gronenborn, A.M.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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: Chimera of Human and E. coli thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,6941
Polymers11,6941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100Back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #21closest to the average, minimized average structure

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Components

#1: Protein Chimera of Human and E. coli thioredoxin


Mass: 11693.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera consists of residues 1-66 from human, residues 67-107 from E. coli.
Source: (gene. exp.) Homo sapiens, Escherichia coli / Plasmid: pET 11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P10599, UniProt: P00274

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CB
13115N TOCSY-HSQC
141(H)CCH-TOCSY
151H(CCO)NH-TOCSY
161C(CO)NH-TOCSY

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Sample preparation

DetailsContents: 1 mM protein in 100 mM sodium phosphate buffer (pH 7.0), 20 M EDTA, 0.02% sodium azide, and 10% D2O.
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX7502
Bruker DMXBrukerDMX6003
Bruker DRXBrukerDRX8004

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Processing

NMR software
NameVersionClassification
DYANA1.5structure solution
XPLORrefinement
RefinementMethod: see publication / Software ordinal: 1
NMR representativeSelection criteria: closest to the average, minimized average structure
NMR ensembleConformer selection criteria: Back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the ...Conformer selection criteria: Back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 21

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