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- PDB-2jsv: Dipole tensor-based refinement for atomic-resolution structure de... -

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Basic information

Entry
Database: PDB / ID: 2jsv
TitleDipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / SSNMR / GB1 / tensor refinement / Cell wall / IgG-binding protein / Peptidoglycan-anchor
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. 'group G' (bacteria)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing, simulated annealing
AuthorsFranks, W. / Wylie, B.J. / Frericks, H.L. / Nieuwkoop, A.J. / Mayrhofer, R. / Shah, G.J. / Graesser, D.T. / Rienstra, C.M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR
Authors: Franks, W.T. / Wylie, B.J. / Schmidt, H.L. / Nieuwkoop, A.J. / Mayrhofer, R.M. / Shah, G.J. / Graesser, D.T. / Rienstra, C.M.
History
DepositionJul 16, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)6,2291
Polymers6,2291
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 / 260structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6228.809 Da / Num. of mol.: 1 / Fragment: 2-1 repeat / Mutation: T2Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR / Details: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
114CC 2D DARR Mixing
125CC 2D DARR Mixing
132NN 2D PDSD Mixing
142HN-HN VEAN
151HN-NCA-HA VEAN
161NCACX, NCOCX 3D
173N(HH)C; C(HH)C
NMR detailsText: The precipitant was packed with excess mother liquor for data acquisition.

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Sample preparation

Details
Solution-IDContentsSolvent system
114 mg/mL [U-99% 13C; U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2OH2O
214 mg/mL [U-99% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2OH2O
314 mg/mL [U-100% 13C; U-100% 15N] protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2OH2O
414 mg/mL (1,3) 13C glycerol, U15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2OH2O
514 mg/mL 2 13C glycerol, Uniform 15N protein, (4R)-2-Metylpentane-2,4-Diol (50% v/v), Isopropyl alcohol (25% v/v), 25 mg/mL GB1 in 50 mM sodium phosphate buffered H2OH2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
14 mg/mLentity[U-99% 13C; U-99% 15N]1
1 v/visopropynol1
3 v/v(2,4)methyl-pentane-diol1
1 v/vsodium phosphate1
14 mg/mLentity[U-99% 15N]2
1 v/v(2,4)methyl-pentane-diol2
3 v/visopropynol2
1 v/vsodium phosphate2
14 mg/mLentity[U-100% 13C; U-100% 15N]3
3 v/visopropynol3
1 v/v(2,4)methyl-pentane-diol3
1 v/vsodium phosphate3
14 mg/mLentity(1,3) 13C glycerol, U15N4
3 v/visopropynol4
1 v/v(2,4)methyl-pentane-diol4
1 v/vsodium phosphate4
14 mg/mLentity2 13C glycerol, Uniform 15N5
3 v/visopropynol5
1 v/v(2,4)methyl-pentane-diol5
1 v/vsodium phosphate5
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 281 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian Infinity PlusVarianInfinity Plus6002
Varian Infinity PlusVarianInfinity Plus5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Mossdata analysis
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
Details: 50,000 steps at 2500 K, decreased over 25,000 steps to 1000 K, 1 fs step size, 70,000 steps from 1000K to 300 K, 1 fs step size
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 260 / Conformers submitted total number: 10

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