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- PDB-2kwd: Supramolecular Protein Structure Determination by Site-Specific L... -

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Basic information

Entry
Database: PDB / ID: 2kwd
TitleSupramolecular Protein Structure Determination by Site-Specific Long-Range Intermolecular Solid State NMR Spectroscopy
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / GB1 / Crystal Packing / Solid-State / Quaternary Structure / TEDOR
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 / simulated annealing
Model detailslowest energy, model 2
AuthorsNieuwkoop, A.J. / Rienstra, C.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Supramolecular protein structure determination by site-specific long-range intermolecular solid state NMR spectroscopy.
Authors: Nieuwkoop, A.J. / Rienstra, C.M.
History
DepositionApr 5, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein G
B: Immunoglobulin G-binding protein G
C: Immunoglobulin G-binding protein G
D: Immunoglobulin G-binding protein G
E: Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)31,1445
Polymers31,1445
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 600structures 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.: 5 / 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) / Strain (production host): BL21 / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR / Details: Crystal Packing of GB1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 15N-13C TEDOR
1212D 15N-13C TEDOR
1332D 15N-13C TEDOR
NMR detailsText: 11.111 kHz MAS

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mg [U-1,3-13C-glycerol; U-100% 15N] GB1-1, solidsolid
250 % [U-1,3-13C-glycerol] GB1-2, 50 % [U-99% 15N] GB1-3, solidsolid
320 mg [U-2-13C-glycerol; U-100% 15N] GB1-4, solidsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mg/mLGB1-1[U-1,3-13C-glycerol; U-100% 15N]1
50 %GB1-2[U-1,3-13C-glycerol]2
50 %GB1-3[U-99% 15N]2
20 mg/mLGB1-4[U-2-13C-glycerol; U-100% 15N]3
Sample conditionsPressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Varian Infinity Plus / Manufacturer: Varian / Model: Infinity Plus / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 10

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