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- PDB-5z4b: GB1 structure determination in living eukaryotic cells by in-cell... -

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Basic information

Entry
Database: PDB / ID: 5z4b
TitleGB1 structure determination in living eukaryotic cells by in-cell NMR spectroscopy
ComponentsProtein LG
KeywordsIMMUNE SYSTEM / PROTEIN
Function / homologyProtein L, Ig light chain-binding / Protein L b1 domain / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Protein LG
Function and homology information
Biological speciesFinegoldia magna (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTanaka, T. / Teppei, I. / Kamoshida, H. / Mishima, M. / Shirakawa, M. / Guentert, P. / Ito, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST; JPMJCR13M3 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Authors: Tanaka, T. / Ikeya, T. / Kamoshida, H. / Suemoto, Y. / Mishima, M. / Shirakawa, M. / Guntert, P. / Ito, Y.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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: Protein LG


Theoretical massNumber of molelcules
Total (without water)6,2591
Polymers6,2591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein Protein LG


Mass: 6258.835 Da / Num. of mol.: 1 / Fragment: IgG_binding_B domain,B1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q53291

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CO)CA
161isotropic13D CBCA(CO)NH
171isotropic13D HBHA(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 uM [U-100% 15N] GB1, 90% H2O/10% D2OGB1_sample90% H2O/10% D2O
solution250 uM [U-100% 13C; U-100% 15N] GB1, 90% H2O/10% D2OGB1_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 uMGB1[U-100% 15N]1
50 uMGB1[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 0 Not defined / Pressure: AMBIENT atm / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
Analysis2.4.2CCPNchemical shift assignment
TopSpin3Bruker Biospincollection
Azara2.8.1Boucherprocessing
TALOS-N4.12Cornilescu, Delaglio and Baxdata analysis
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOL2.6Koradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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