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- PDB-1ryk: Solution NMR Structure Protein yjbJ from Escherichia coli. Northe... -

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Basic information

Entry
Database: PDB / ID: 1ryk
TitleSolution NMR Structure Protein yjbJ from Escherichia coli. Northeast Structural Genomics Consortium Target ET93; Ontario Centre for Structural Proteomics target EC0298_1_69;
ComponentsProtein yjbJ
Keywordsstructural genomics / unknown function / Alpha protein / Protein Structure Initiative / OCSP / NESG / PSI / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


cell pole / cytosol
Similarity search - Function
YjbJ / CsbD-like domain / Stress response protein YjbJ / YjbJ superfamily / : / CsbD-like / Protein Yjbj; Chain: A; / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UPF0337 protein YjbJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, restrained molecular dynamic simulations
AuthorsPineda-Lucena, A. / Liao, J. / Wu, B. / Yee, A. / Cort, J.R. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2002
Title: An NMR approach to structural proteomics.
Authors: Pineda-Lucena, A. / Liao, J. / Wu, B. / Yee, A. / Cort, J.R. / Kennedy, M.A. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 24, 2004ID: 1JYG
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein yjbJ


Theoretical massNumber of molelcules
Total (without water)8,3391
Polymers8,3391
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 Protein yjbJ


Mass: 8339.261 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YJBJ, B4045, Z5644, ECS5028, SF4160, S3571 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P68206

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113d 13c-separated NOESY
1213d 15n-separated NOESY

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1delaglio, fprocessing
DYANA1.5gunter, p.structure solution
CNS1refinement
RefinementMethod: torsion angle dynamics, simulated annealing, restrained molecular dynamic simulations
Software ordinal: 1
Details: 2036 noe-derived distance constraints, 101 dihedral angle constraints, 62 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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