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- PDB-1g7d: NMR STRUCTURE OF ERP29 C-DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1g7d
TitleNMR STRUCTURE OF ERP29 C-DOMAIN
ComponentsENDOPLASMIC RETICULUM PROTEIN ERP29
KeywordsCHAPERONE / alpha helical protein
Function / homology
Function and homology information


regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / smooth endoplasmic reticulum / protein secretion / negative regulation of protein secretion / 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 / smooth endoplasmic reticulum / protein secretion / negative regulation of protein secretion / 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 protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / 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. / Thioredoxin-like superfamily ...Endoplasmic reticulum protein erp29 / Endoplasmic reticulum resident protein 29, C-terminal domain / 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. / Thioredoxin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 29
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsLiepinsh, E. / Mkrtchian, S. / Barishev, M. / Sharipo, A. / 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

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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)11,7871
Polymers11,7871
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)20 / 50structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein ENDOPLASMIC RETICULUM PROTEIN ERP29 /


Mass: 11787.470 Da / Num. of mol.: 1 / Fragment: C-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, DQF COSY
1513D HNHB
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
12mM C-domain ERp29 U-15N,13C90% H2O/10% D2O
22mM C-domain ERp2990% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1.1 4.7 ambient 308 K
2.1 4.7 ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.5Brukercollection
PROSA3.6Guentertprocessing
XEASY970326Bartelsdata analysis
DYANA1.5Guentertstructure solution
OPAL2.6Luginbulrefinement
MOLMOL2.6.0Koradidata analysis
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: The input for the final structure calculation of C-domain protein consisted of 1492 upper limit distance restraints and 340 measured HN-Ha, Ha-Hb, 15N-Hb coupling constants resulting in 328 ...Details: The input for the final structure calculation of C-domain protein consisted of 1492 upper limit distance restraints and 340 measured HN-Ha, Ha-Hb, 15N-Hb coupling constants resulting in 328 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
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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