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- PDB-1je3: Solution Structure of EC005 from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1je3
TitleSolution Structure of EC005 from Escherichia coli
ComponentsHYPOTHETICAL 8.6 KDA PROTEIN IN AMYA-FLIE INTERGENIC REGION
KeywordsSTRUCTURAL GENOMICS / mixed alpha-beta structure
Function / homology
Function and homology information


DNA damage response
Similarity search - Function
: / TusA-like domain / Uncharacterized protein family UPF0033 signature. / TusA-like domain / Sulfurtransferase TusA / TusA-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative sulfur carrier protein YedF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsYee, A. / Gutierrez, P. / Kozlov, G. / Denisov, A. / Gehring, K. / Arrowsmith, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: An NMR approach to structural proteomics.
Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.H. / Cort, J.R. / Kozlov, G. / ...Authors: Yee, A. / Chang, X. / Pineda-Lucena, A. / Wu, B. / Semesi, A. / Le, B. / Ramelot, T. / Lee, G.M. / Bhattacharyya, S. / Gutierrez, P. / Denisov, A. / Lee, C.H. / Cort, J.R. / Kozlov, G. / Liao, J. / Finak, G. / Chen, L. / Wishart, D. / Lee, W. / McIntosh, L.P. / Gehring, K. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: HYPOTHETICAL 8.6 KDA PROTEIN IN AMYA-FLIE INTERGENIC REGION


Theoretical massNumber of molelcules
Total (without water)10,8181
Polymers10,8181
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HYPOTHETICAL 8.6 KDA PROTEIN IN AMYA-FLIE INTERGENIC REGION / EC005


Mass: 10818.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YEDF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P0AA31

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1332D NOESY
1442D NOESY
NMR detailsText: The structure was determined using standard triple-resonance NMR experiments.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM EC005 U-15N; 50mM phosphate buffer; 0.15 M NaCl; 1 mM DTT; 1 mM NaN3.90% H2O/10% D2O
22mM EC005 U-15N, 13C; 50mM phosphate buffer; 0.15 M NaCl; 1 mM 2mM EC005 U-15N; 50mM phosphate buffer; 0.15 M NaCl; 1 mM DTT; 1 mM NaN3.DTT; 1 mM NaN3.100% D2O
32mM EC005 Unlabeled; 50mM phosphate buffer; 0.15 M NaCl; 1 mM DTT; 1 mM NaN3.90% H2O/10% D2O
42mM EC005 Unlabeled; 50mM phosphate buffer; 0.15 M NaCl; 1 mM DTT; 1 mM NaN3.100% D2O
Sample conditionsIonic strength: 0.3 M / pH: 7.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1brukercollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wutrichdata analysis
CNS0.9Brungerrefinement
ARIA0.9Nilgesstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures were based on 619 non-redundant NOE-derived distance constraints, 85 dihedral angle restraints and 32 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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