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- PDB-1p9k: THE SOLUTION STRUCTURE OF YBCJ FROM E. COLI REVEALS A RECENTLY DI... -

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Basic information

Entry
Database: PDB / ID: 1p9k
TitleTHE SOLUTION STRUCTURE OF YBCJ FROM E. COLI REVEALS A RECENTLY DISCOVERED ALFAL MOTIF INVOLVED IN RNA-BINDING
Componentsorf, hypothetical protein
KeywordsRNA BINDING PROTEIN / alfaL motif / RNA-binding protein / E.coli / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


translation / RNA binding / cytosol
Similarity search - Function
RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S4 RNA-binding domain profile. / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein YbcJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsVolpon, L. / Lievre, C. / Osborne, M.J. / Gandhi, S. / Iannuzzi, P. / Larocque, R. / Matte, A. / Cygler, M. / Gehring, K. / Ekiel, I. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2003
Title: The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.
Authors: Volpon, L. / Lievre, C. / Osborne, M.J. / Gandhi, S. / Iannuzzi, P. / Larocque, R. / Cygler, M. / Gehring, K. / Ekiel, I.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionNov 25, 2003ID: 1O09
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: orf, hypothetical protein


Theoretical massNumber of molelcules
Total (without water)8,4171
Polymers8,4171
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 / 60structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #7closest to the average

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Components

#1: Protein orf, hypothetical protein


Mass: 8416.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ybcJ / Plasmid: pET20b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AAS7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131HNHA
1413D 15N-separated NOESY
152IPAP-HSQC
NMR detailsText: This structure was determined using standard 2D homonuclear and 3D heteronuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
14-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.890% H2O/10% D2O
24-7mM YbcJ U-15N,13C; 50mM phosphate buffer, 300mM NaCl, 15mM DTT, 1mM sodium azide, pH 6.8, 8mg/mL of Pf1 phage90% H2O/10% D2O
Sample conditionsIonic strength: 50mM Phosphate, 300mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.31Delsucprocessing
XwinNMR2.1Brukercollection
XEASY1.3.13Bartelsdata analysis
TALOS2003.027.13.05Baxrefinement
ARIA1.1Nilgesrefinement
CNS1.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1205 restraints, 1011 are NOE-derived distance constraints, 89 dihedral angle restraints, 54 distance restraints from hydrogen bonds (27 hydrogen bonds) ...Details: The structures are based on a total of 1205 restraints, 1011 are NOE-derived distance constraints, 89 dihedral angle restraints, 54 distance restraints from hydrogen bonds (27 hydrogen bonds), and 51 15N-1H residual dipolar couplings.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 60 / Conformers submitted total number: 20

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