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- PDB-6dsl: Consensus engineered intein (Cat) with atypical split site -

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Basic information

Entry
Database: PDB / ID: 6dsl
TitleConsensus engineered intein (Cat) with atypical split site
Components
  • Consensus engineered intein CatC
  • Consensus engineered intein CatN
KeywordsSPLICING / Intein Protein / Trans Splicing / Consensus Engineering / Protein Engineering
Biological speciesEnterobacteria phage T7 (virus)
MethodSOLUTION NMR / molecular dynamics
AuthorsSekar, G. / Stevens, A.J. / Muir, T.W. / Cowburn, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM086868 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: An Atypical Mechanism of Split Intein Molecular Recognition and Folding.
Authors: Stevens, A.J. / Sekar, G. / Gramespacher, J.A. / Cowburn, D. / Muir, T.W.
History
DepositionJun 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Consensus engineered intein CatN
B: Consensus engineered intein CatC


Theoretical massNumber of molelcules
Total (without water)17,2952
Polymers17,2952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2730 Å2
ΔGint-20 kcal/mol
Surface area8270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Consensus engineered intein CatN


Mass: 3775.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Protein Consensus engineered intein CatC


Mass: 13520.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / 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-IDSample stateSpectrometer-IDType
111isotropic23D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic23D 1H-15N NOESY
181isotropic33D HNCA
171isotropic33D HN(CA)CB
161isotropic33D CBCA(CO)NH
151isotropic13D HNCO
141isotropic13D HN(CA)CO
191isotropic23D (H)CCH-TOCSY
1101isotropic13D (H)CC(CO)NH

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-99% 13C; U-99% 15N] CatN, 300 uM [U-99% 13C; U-99% 15N] CatC, 50 mM sodium phosphate, 100 mM sodium chloride, 2 mM TCEP, 90% H2O/10% D2O
Details: 15N, 13C labeled CatN-CatC complex / Label: CatN-CatC Complex / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMCatN[U-99% 13C; U-99% 15N]1
300 uMCatC[U-99% 13C; U-99% 15N]1
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mMTCEPnatural abundance1
Sample conditionsIonic strength: 150 mM / Label: CatN-CatC Complex / pH: 6.8 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCE IIIBrukerAVANCE III9002
Bruker AVANCE IIIBrukerAVANCE III8003

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Processing

NMR software
NameDeveloperClassification
AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 20

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