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- PDB-2l6b: NRC consensus ankyrin repeat protein solution structure -

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Basic information

Entry
Database: PDB / ID: 2l6b
TitleNRC consensus ankyrin repeat protein solution structure
ComponentsNR1C
KeywordsDE NOVO PROTEIN / NRC / ankyrin / consensus / repeat protein / ising model
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 5
AuthorsAksel, T. / Majumdar, A. / Barrick, D.
CitationJournal: Structure / Year: 2011
Title: The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding.
Authors: Aksel, T. / Majumdar, A. / Barrick, D.
History
DepositionNov 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NR1C


Theoretical massNumber of molelcules
Total (without water)12,3491
Polymers12,3491
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 / 80back calculated data agree with experimental NOESY spectrum
RepresentativeModel #5closest to the average

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Components

#1: Protein NR1C


Mass: 12348.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli)

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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 CBCA(CO)NH
1313D HN(CA)CB
1413D HBHA(CO)NH
1513D HNCO
1613D HNHA
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY
11013D H(CCO)NH
11112D 1H-15N HSQC

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Sample preparation

DetailsContents: 25 mM sodium phosphate, 25 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMsodium phosphate-11
25 mMsodium chloride-21
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
163 6.5 ambient 298 K
263 6.5 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
UNIO2.0.1Dr. Torsten Herrmannchemical shift assignment
UNIO2.0.1Dr. Torsten Herrmannstructure solution
CARA1.8.4Kurt W thrichchemical shift assignment
CARA1.8.4Kurt W thrichdata analysis
X-PLOR NIH2.24Schwieters, Kuszewski, Tjandra and Clorerefinement
ModelFree4.2Palmerdata analysis
NMRPipe5.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics, DGSA-distance geometry simulated annealing
Software ordinal: 1
Details: UNIO+CYANA used together for initial structure determination, XPLOR-NIH used for final refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 80 / Conformers submitted total number: 20

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