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- PDB-5ub0: Solution NMR Structure of NERD-C, a natively folded tetramutant o... -

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Basic information

Entry
Database: PDB / ID: 5ub0
TitleSolution NMR Structure of NERD-C, a natively folded tetramutant of the B1 domain of streptococcal protein G (GB1)
ComponentsImmunoglobulin G-binding protein G
KeywordsDE NOVO PROTEIN / dynamics / computational design / conformational exchange / immunoglobulin-binding
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. ...IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesStreptococcus sp. GX7805 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDamry, A.M. / Davey, J.A. / Goto, N.K. / Chica, R.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-386662-2011 Canada
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Rational design of proteins that exchange on functional timescales.
Authors: Davey, J.A. / Damry, A.M. / Goto, N.K. / Chica, R.A.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jun 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 1.6May 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:
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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,1661
Polymers6,1661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10010 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 6165.795 Da / Num. of mol.: 1 / Fragment: UNP residues 373-427 / Mutation: Y3F/L7I/F30L/V39I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. GX7805 (bacteria) / Gene: spg / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D 1H-15N NOESY
123isotropic23D 1H-13C NOESY aliphatic
133isotropic23D 1H-13C NOESY aromatic
142isotropic23D HN(CA)CB
152isotropic23D CBCA(CO)NH
172isotropic23D HNCO
163isotropic23D CCH-TOCSY
193isotropic23D (H)CCH-TOCSY
183isotropic23D (H)CCH-COSY
1121isotropic22D 1H-15N HSQC
1113isotropic22D 1H-13C HSQC
1102isotropic22D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O, 10% D2O15N_Sample90% H2O/10% D2O
solution21.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 90% H2O/10% D2O13C/15N_Sample_H2O90% H2O/10% D2O
solution31.0 mM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100% D2O13C/15N_Sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein (GB1)[U-98% 15N]1
10 mMsodium phosphatenatural abundance1
1.0 mMprotein (GB1)[U-99% 13C; U-98% 15N]2
10 mMsodium phosphatenatural abundance2
1.0 mMprotein (GB1)[U-99% 13C; U-98% 15N]3
10 mMsodium phosphatenatural abundance3
Sample conditionsIonic strength: 10 mM sodium phosphate mM / Label: conditions / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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