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- PDB-5ucf: Solution NMR-derived model of the minor species of DANCER-2, a dy... -

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Basic information

Entry
Database: PDB / ID: 5ucf
TitleSolution NMR-derived model of the minor species of DANCER-2, a dynamic and natively folded pentamutant 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 / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / 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 / M protein-type anchor domain / Ubiquitin-like (UB roll) - #10 / 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 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 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 1.3Nov 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 1.4Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.6Jun 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 1.7May 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: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2341
Polymers6,2341
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: 6233.827 Da / Num. of mol.: 1 / Fragment: UNP residues 373-427 / Mutation: Y3F/L5A/L7I/A34F/V39L
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
111isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY aliphatic
132isotropic13D 1H-13C NOESY aromatic
143isotropic13D HNCO
153isotropic13D HN(CA)CB
163isotropic13D CBCA(CO)NH
171isotropic13D 1H-15N TOCSY
182isotropic13D CCH-TOCSY
192isotropic13D (H)CCH-TOCSY
1102isotropic13D (H)CCH-COSY
1111isotropic12D 1H-15N HSQC
1123isotropic12D 1H-13C HSQC
1132isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1200 uM [U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O15N_Sample90% H2O/10% D2O
solution3200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 90% H2O/10% D2O13C/15N_Sample_H2O90% H2O/10% D2O
solution2200 uM [U-99% 13C; U-98% 15N] protein (GB1), 10 mM sodium phosphate, 100 uM EDTA, 0.02 % sodium azide, 100% D2O13C/15N_Sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMprotein (GB1)[U-98% 15N]1
10 mMsodium phosphatenatural abundance1
100 uMEDTAnatural abundance1
0.02 %sodium azidenatural abundance1
200 uMprotein (GB1)[U-99% 13C; U-98% 15N]3
10 mMsodium phosphatenatural abundance3
100 uMEDTAnatural abundance3
0.02 %sodium azidenatural abundance3
200 uMprotein (GB1)[U-99% 13C; U-98% 15N]2
10 mMsodium phosphatenatural abundance2
100 uMEDTAnatural abundance2
0.02 %sodium azidenatural abundance2
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: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 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
TopSpinBruker Biospincollection
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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