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- PDB-2l4c: Solution Structure of the b domain of Human ERp27 -

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Basic information

Entry
Database: PDB / ID: 2l4c
TitleSolution Structure of the b domain of Human ERp27
ComponentsEndoplasmic reticulum resident protein 27
KeywordsPEPTIDE BINDING PROTEIN / ERp27 / PDI / b domain / Endoplasmic reticulum
Function / homology
Function and homology information


response to unfolded protein / response to endoplasmic reticulum stress / protein folding / endoplasmic reticulum lumen / endoplasmic reticulum
Similarity search - Function
Thioredoxin-like domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endoplasmic reticulum resident protein 27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsAmin, N.T. / Wallis, K. / Rowe, M.L. / Kelly, G. / Frenkiel, T.A. / Williamson, R.A. / Howard, M.J. / Freedman, R.B.
CitationJournal: To be Published
Title: Solution structure and dynamics of the b domain of human ERp27
Authors: Amin, N.T. / Wallis, K. / Rowe, M.L. / Kelly, G. / Frenkiel, T.A. / Williamson, R.A. / Howard, M.J. / Freedman, R.B.
History
DepositionOct 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Endoplasmic reticulum resident protein 27


Theoretical massNumber of molelcules
Total (without water)13,8111
Polymers13,8111
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)50 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Endoplasmic reticulum resident protein 27 / ER protein 27 / ERp27


Mass: 13811.459 Da / Num. of mol.: 1 / Fragment: B domain (UNP Residues 26-141)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERP27, C12orf46, UNQ781/PRO1575 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS / References: UniProt: Q96DN0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D HN(COCA)CB
1413D HSQC-TOCSY
1513D (H)CCH-TOCSY
1612D aromatic 1H-13C HSQC
1712D aromatic 13C-edited NOESY
1812D 1H-1H TOCSY
1912D 1H-1H NOESY
11013D 1H-15N NOESY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 25 mM sodium phosphate, 100 mM sodium chloride, 1-1.5 mM [U-99% 13C; U-99% 15N] ERp27 b domain, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
25 mMsodium phosphate-11
100 mMsodium chloride-21
mMERp27 b domain-3[U-99% 13C; U-99% 15N]1-1.51
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.1Linge, O'Donoghue and Nilgeschemical shift assignment
TALOSCornilescu, Delaglio and Baxrefinement
CCPN_AnalysisCCPNpeak picking
CCPN_AnalysisCCPNdata analysis
CCPN_AnalysisCCPNchemical shift assignment
ProcheckNMRLaskowski and MacArthurvalidation
ProcheckNMRLaskowski and MacArthurdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1939 / NOE intraresidue total count: 296 / NOE long range total count: 206 / NOE medium range total count: 146 / NOE sequential total count: 232 / Hydrogen bond constraints total count: 84 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 58
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 50

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