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- PDB-2n9l: 1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1 -

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Basic information

Entry
Database: PDB / ID: 2n9l
Title1H, 13C, and 15N Chemical Shift Assignments for in-cell GB1
ComponentsImmunoglobulin G-binding protein G
KeywordsIMMUNE SYSTEM / in-cell NMR / QME data processing / FLYA automatic assignment / Bayesian
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 / mimimization
Model detailslowest energy, model1
AuthorsIkeya, T. / Hanashima, T. / Hosoya, S. / Shimazaki, M. / Ikeda, S. / Mishima, M. / Guentert, P. / Ito, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Improved in-cell structure determination of proteins at near-physiological concentration
Authors: Ikeya, T. / Hanashima, T. / Hosoya, S. / Shimazaki, M. / Ikeda, S. / Mishima, M. / Guentert, P. / Ito, Y.
History
DepositionNov 30, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 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)6,2591
Polymers6,2591
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)20 / 1416structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 6258.835 Da / Num. of mol.: 1 / Fragment: UNP residues 303-357
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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D HCACO
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D (H)CCH-COSY
11413D HN(CO)CA

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Sample preparation

DetailsContents: 250 uM [U-100% 13C; U-100% 15N] Protein G B1-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 250 uM / Component: Protein G B1-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.31 / pH: 7 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure solution
Azara2.8.1Boucherprocessing
ANSIG3.3Kraulischemical shift assignment
MOLMOL2.6Koradi, Billeter and Wuthrichstructure solution
TALOS1Cornilescu, Delaglio and Baxdata analysis
TopSpin3.1Bruker Biospincollection
OPALrefinement
RefinementMethod: mimimization / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 53 / Protein psi angle constraints total count: 53
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1416 / Conformers submitted total number: 20 / Representative conformer: 1

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