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- PDB-1g7e: NMR STRUCTURE OF N-DOMAIN OF ERP29 PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1g7e
TitleNMR STRUCTURE OF N-DOMAIN OF ERP29 PROTEIN
ComponentsENDOPLASMIC RETICULUM PROTEIN ERP29
KeywordsCHAPERONE / alfa-beta structure / thioredoxin fold
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / negative regulation of protein secretion / smooth endoplasmic reticulum / response to endoplasmic reticulum stress / intracellular protein transport / melanosome / protein folding / protein-folding chaperone binding / positive regulation of protein phosphorylation ...regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein secretion / negative regulation of protein secretion / smooth endoplasmic reticulum / response to endoplasmic reticulum stress / intracellular protein transport / melanosome / protein folding / protein-folding chaperone binding / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of gene expression / cell surface / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Endoplasmic reticulum resident protein 29, C-terminal / ERp29, N-terminal / Endoplasmic reticulum resident protein 29 / Endoplasmic reticulum resident protein 29, C-terminal domain superfamily / Endoplasmic reticulum protein ERp29, C-terminal domain / ERp29, N-terminal domain / Endoplasmic reticulum targeting sequence. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsLiepinsh, E. / Mkrtchian, S. / Barishev, M. / Sharipo, M. / Ingelman-Sundberg, M. / Otting, G.
CitationJournal: Structure / Year: 2001
Title: Thioredoxin fold as homodimerization module in the putative chaperone ERp29: NMR structures of the domains and experimental model of the 51 kDa dimer.
Authors: Liepinsh, E. / Baryshev, M. / Sharipo, A. / Ingelman-Sundberg, M. / Otting, G. / Mkrtchian, S.
History
DepositionNov 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOPLASMIC RETICULUM PROTEIN ERP29


Theoretical massNumber of molelcules
Total (without water)13,8751
Polymers13,8751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy,target function
RepresentativeModel #17lowest energy. model #1 was best after dyana calculations, model #17 was best after opal refinement

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Components

#1: Protein ENDOPLASMIC RETICULUM PROTEIN ERP29


Mass: 13874.752 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P52555

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA, HNCO, HN(CO)CA
1213D 15N-separated NOESY
1313D 13C-separated NOESY
2422D NOESY, 2D TOCSY, 2D DQF COSY
1511H-15N HSQC, 1H-13C HSQC
NMR detailsText: The signal assignment was determined using triple-resonance NMR spectroscopy. The structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3mM N-domain ERp29 U-15N,13C90% H2O/10% D2O
20.3mM N-domain ERp2990% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.14.7ambient 308 K
20.14.7ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Varian UNITYPLUSVarianUNITYPLUS8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukercollection
PROSA3.6Guentertprocessing
XEASY970326Bartelsdata analysis
DYANA1.5Guentertstructure solution
OPAL2.6Luginbulrefinement
MOLMOL2.6.0Koradidata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The input for the final structure calculation of N-domain protein consisted of 1279 upper limit distance restraints and 358 dihedral angle restraints. 185 of the dihedral angle restraints ...Details: The input for the final structure calculation of N-domain protein consisted of 1279 upper limit distance restraints and 358 dihedral angle restraints. 185 of the dihedral angle restraints reflected coupling constant information, while 173 of them had been derived by HABAS from NOE and steric restraints alone.
NMR representativeSelection criteria: lowest energy. model #1 was best after dyana calculations, model #17 was best after opal refinement
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 50 / Conformers submitted total number: 20

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