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- PDB-6bi6: Solution NMR structure of uncharacterized protein YejG -

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Basic information

Entry
Database: PDB / ID: 6bi6
TitleSolution NMR structure of uncharacterized protein YejG
ComponentsUncharacterized protein YejG
KeywordsUNKNOWN FUNCTION / PF13989 / YejG
Function / homologyUncharacterised protein family YejG / YejG-like protein / Uncharacterized protein YejG
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics simulation, energy refinement
AuthorsMohanty, B. / Finn, T.J. / Macindoe, I. / Zhong, J. / Patrick, W.M. / Mackay, J.P.
CitationJournal: Proteins / Year: 2019
Title: The uncharacterized bacterial protein YejG has the same architecture as domain III of elongation factor G.
Authors: Mohanty, B. / Hanson-Manful, P. / Finn, T.J. / Chambers, C.R. / McKellar, J.L.O. / Macindoe, I. / Helder, S. / Setiyaputra, S. / Zhong, Y. / Mackay, J.P. / Patrick, W.M.
History
DepositionNov 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 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 1.4May 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: Uncharacterized protein YejG


Theoretical massNumber of molelcules
Total (without water)12,5571
Polymers12,5571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7870 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 40structures with lowest energy and acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein YejG


Mass: 12557.149 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: yejG, b2181, JW2169 / Plasmid: pGEX-6p
Details (production host): For production of GST-tagged YejG
Production host: Escherichia coli (E. coli) / References: UniProt: P0AD21

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D [15N,1H]-HSQC
121isotropic23D 15N-resolved [1H,1H]-NOESY
131isotropic23D 13Cali-resolved [1H,1H]-NOESY
141isotropic23D 13Caro-resolved [1H,1H]-NOESY
151isotropic22D [13Cali,1H]-HSQC (multiplicity edited)
161isotropic22D [13Caro,1H]-HSQC
171isotropic22D 1H-1H NOESY
181isotropic13D NUS HNCA
191isotropic13D NUS HN(CA)CB
1101isotropic13D NUS CBCA(CO)NH
1111isotropic13D NUS HN(CA)CO
1121isotropic13D NUS HNCO
1131isotropic13D NUS HBHA(CO)NH
1141isotropic13D NUS HNHA
1151isotropic13D NUS (H)CC(CO)NH
1161isotropic215N{1H}-NOE

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Sample preparation

DetailsType: solution
Contents: 600 uM [U-13C,15N] YejG, 20 mM Bi-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 90% H2O/10% D2O
Details: 600 uM [U-13C,15N]-labelled YejG 20 mM Bis-tris, 50 mM NaCl, 1 mM TCEP, 0.2 mM PMSF, 10% D2O; pH 6.5
Label: [U-13C,15N]-labelled YejG / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMYejG[U-13C,15N]1
20 mMBi-trisnatural abundance1
50 mMNaClnatural abundance1
1 mMTCEPnatural abundance1
0.2 mMPMSFnatural abundance1
Sample conditionsIonic strength: 50 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
OPALpKoradi, Billeter and Guntertrefinement
RefinementMethod: molecular dynamics simulation, energy refinement / Software ordinal: 7
Details: Koradi, R., Billeter, M. and Guntert, P. Point-centered domain decomposition for parallel molecular dynamics simulation
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with lowest energy and acceptable covalent geometry
Conformers calculated total number: 40 / Conformers submitted total number: 15

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