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- PDB-2kq4: Atomic resolution protein structure determination by three-dimens... -

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Basic information

Entry
Database: PDB / ID: 2kq4
TitleAtomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / GB1 / TEDOR / Solid-State / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted / THERMOSTABLE
Function / homology
Function and homology information


IgG binding / cell wall / : / 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 ...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)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailslowest energy, model 4
AuthorsNieuwkoop, A.J. / Wylie, B.J. / Franks, W. / Shah, G.J. / Rienstra, C.M.
CitationJournal: J.Chem.Phys. / Year: 2009
Title: Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy
Authors: Nieuwkoop, A.J. / Wylie, B.J. / Franks, W.T. / Shah, G.J. / Rienstra, C.M.
History
DepositionOct 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Data collection / Database references
Category: 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

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the lowest energy
RepresentativeModel #4lowest 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: UNP residues 303 to 357 / 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D TEDOR
1223D TEDOR

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Sample preparation

Details
Solution-IDContentsSolvent system
130 mg 1,3-13C glycerol, U 15N entity-1, 50 v/v MPTG-2, solidsolid
230 mg 2-13C glycerol, U 15N entity-3, 50 v/v MPTG-4, solidsolid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
30 mg/mLprotein1,3-13C glycerol, U 15N1
50 v/vMPTG-21
30 mg/mLprotein2-13C glycerol, U 15N2
50 v/vMPTG-42
Sample conditionsPressure: ambient / Temperature units: 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
NameVersionDeveloperClassification
X-PLOR NIH2.21Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
Details: DG sub-embed was used from initial extend geometry, Two steps of simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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