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- PDB-2k6p: Solution Structure of hypothetical protein, HP1423 -

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Basic information

Entry
Database: PDB / ID: 2k6p
TitleSolution Structure of hypothetical protein, HP1423
ComponentsUncharacterized protein HP_1423
KeywordsUNKNOWN FUNCTION / hp1423 / alpha-L motif / RNA-binding
Function / homology
Function and homology information


RNA-binding protein, HP1423 type / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S4 RNA-binding domain profile. / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein HP_1423
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsKim, J. / Park, S. / Lee, K. / Son, W. / Sohn, N. / Lee, B.
CitationJournal: Proteins / Year: 2009
Title: Solution structure of hypothetical protein HP1423 (Y1423_HELPY) reveals the presence of alphaL motif related to RNA binding
Authors: Kim, J.H. / Park, S.J. / Lee, K.Y. / Son, W.S. / Sohn, N.Y. / Kwon, A.R. / Lee, B.J.
History
DepositionJul 15, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Uncharacterized protein HP_1423


Theoretical massNumber of molelcules
Total (without water)10,4721
Polymers10,4721
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein HP_1423


Mass: 10472.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1423 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O25966

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D HN(CA)CB
1613D HN(CO)CA
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D 1H-15N TOCSY
11213D H(CCO)NH

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Sample preparation

DetailsContents: 1-0.1mM [U-98% 15N] 15N, 1-0.5mM [U-98% 13C; U-98% 15N] 13C, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM15N[U-98% 15N]1
1 mM13C[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 0.3 / pH: 5.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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