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- PDB-6owr: NMR solution structure of YfiD -

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Basic information

Entry
Database: PDB / ID: 6owr
TitleNMR solution structure of YfiD
ComponentsAutonomous glycyl radical cofactor
KeywordsPROTEIN BINDING / Glycyl radical enzyme / Cofactor repair
Function / homology
Function and homology information


formate C-acetyltransferase activity / threonine catabolic process / acyltransferase activity / lyase activity / cytoplasm / cytosol
Similarity search - Function
Autonomous glycyl radical cofactor GrcA / Formate C-acetyltransferase glycine radical, conserved site / Glycine radical domain signature. / Glycine radical / Glycine radical domain / Glycine radical domain profile.
Similarity search - Domain/homology
Autonomous glycyl radical cofactor / Autonomous glycyl radical cofactor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsBowman, S.E.J. / Drennan, C.L.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM129882 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM099257 United States
National Science Foundation (NSF, United States)1122374 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2019
Title: Solution structure and biochemical characterization of a spare part protein that restores activity to an oxygen-damaged glycyl radical enzyme.
Authors: Bowman, S.E.J. / Backman, L.R.F. / Bjork, R.E. / Andorfer, M.C. / Yori, S. / Caruso, A. / Stultz, C.M. / Drennan, C.L.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
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: Autonomous glycyl radical cofactor


Theoretical massNumber of molelcules
Total (without water)14,2861
Polymers14,2861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, circular dichroism
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Autonomous glycyl radical cofactor


Mass: 14286.153 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YfiD / Plasmid: p-CAL-n-EK / Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: E2QQ39, UniProt: P68066*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
162isotropic12D 1H-15N HSQC
131isotropic23D 1H-15N NOESY
141isotropic23D 1H-15N TOCSY
152isotropic13D HNCA
172isotropic13D HN(CA)CB
182isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-15N] YfiD, 18 mM HEPES, 2.7 mM ammonium sulfate, 10 % v/v D2O, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21.3 mM [U-100% 13C; U-100% 15N] YfiD, 18 mM HEPES, 2.7 mM ammonium sulfate, 10 % v/v D2O, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMYfiD[U-15N]1
18 mMHEPESnatural abundance1
2.7 mMammonium sulfatenatural abundance1
10 % v/vD2Onatural abundance1
1.3 mMYfiD[U-100% 13C; U-100% 15N]2
18 mMHEPESnatural abundance2
2.7 mMammonium sulfatenatural abundance2
10 % v/vD2Onatural abundance2
Sample conditionsIonic strength: 2.7 mM / Label: conditions_all / pH: 7.2 / Pressure: 760 mmHg / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA8001cryogenic triple resonance probe
FBML CMR 600 EFBMLCMR 600 E6002

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddardstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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