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- PDB-2lum: Three-State Ensemble obtained from eNOEs of the Third Immunoglobu... -

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Basic information

Entry
Database: PDB / ID: 2lum
TitleThree-State Ensemble obtained from eNOEs of the Third Immunoglobulin Binding Domain of Protein G (GB3)
ComponentsImmunoglobulin G-binding protein G
KeywordsPROTEIN BINDING / correlated dynamics / NOE / eNOE / exact nuclear Overhauser effect / structure calculation / structure ensemble
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. 'group G' (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVogeli, B. / Kazemi, S. / Guntert, P. / Riek, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs.
Authors: Vogeli, B. / Kazemi, S. / Guntert, P. / Riek, R.
History
DepositionJun 18, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 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)6,2151
Polymers6,2151
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)60 / 100
RepresentativeModel #1lowest energy

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Components

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


Mass: 6214.848 Da / Num. of mol.: 1
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 (E. coli) / References: UniProt: P19909

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D [13C,15N]-resolved NOESY
1213D [15N]-resolved NOESY
1313D [15N]-resolved NOESY

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Sample preparation

DetailsContents: 4 mM [U-95% 13C; U-95% 15N] Third Immunoglobulin G-binding protein G, 50 mM potassium phosphate, 0.5 mg/mL sodium azide, 50 mM sodium chloride, 97% H2O/3% D2O
Solvent system: 97% H2O/3% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4 mMThird Immunoglobulin G-binding protein G-1[U-95% 13C; U-95% 15N]1
50 mMpotassium phosphate-21
0.5 mg/mLsodium azide-31
50 mMsodium chloride-41
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: THREE-STATE ENSEMBLE OBTAINED FROM ENOES OF THE THIRD IMMUNOGLOBULIN BINDING DOMAIN OF PROTEIN G (GB3). STATE A, B AND C ARE REPRESENTED BY THE MODELS 1-20, 21-40 AND 41-60, RESPECTIVELY. ...Details: THREE-STATE ENSEMBLE OBTAINED FROM ENOES OF THE THIRD IMMUNOGLOBULIN BINDING DOMAIN OF PROTEIN G (GB3). STATE A, B AND C ARE REPRESENTED BY THE MODELS 1-20, 21-40 AND 41-60, RESPECTIVELY. SIMULTANEOUSLY OPTIMIZED MODELS ARE N, N+20 AND N+40.
NMR constraintsNOE constraints total: 884 / NOE intraresidue total count: 277 / NOE long range total count: 241 / NOE medium range total count: 122 / NOE sequential total count: 244 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: lowest energy
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 60

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