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- PDB-6njf: Solution NMR Structure of DANCER3-F34A, a rigid and natively fold... -

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Basic information

Entry
Database: PDB / ID: 6njf
TitleSolution NMR Structure of DANCER3-F34A, a rigid and natively folded single mutant of the dynamic protein DANCER-3
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 / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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 / GA-like domain / GA-like domain / Ubiquitin-like (UB roll) - #10 / 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. group G (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDamry, A.M. / Mayer, M.M. / Goto, N.K. / Chica, R.A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04831 Canada
Citation
Journal: Commun Biol / Year: 2019
Title: Origin of conformational dynamics in a globular protein.
Authors: Damry, A.M. / Mayer, M.M. / Broom, A. / Goto, N.K. / Chica, R.A.
#1: Journal: Biorxiv / Year: 2019
Title: Origin of Conformational Dynamics in a Globular Protein
Authors: Damry, A.M. / Mayer, M.M. / Broom, A. / Goto, N.K. / Chica, R.A.
History
DepositionJan 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Revision 1.2Dec 18, 2019Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: citation / database_2 / pdbx_database_status
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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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)7,2311
Polymers7,2311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3980 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7230.964 Da / Num. of mol.: 1 / Fragment: residues 373-427 / Mutation: Y3F, V7I, V39L, V54I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
123isotropic13D 1H-13C NOESY aliphatic
133isotropic13D 1H-13C NOESY aromatic
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
162isotropic13D HNCO
173isotropic13D CCH-TOCSY
183isotropic13D (H)CCH-TOCSY
193isotropic13D (H)CCH-COSY
1101isotropic13D 1H-15N TOCSY
1111isotropic12D 1H-15N HSQC
1122isotropic12D 1H-13C HSQC
1133isotropic12D 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: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / 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
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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