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- PDB-2h9z: Solution structure of hypothetical protein, HP0495 from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 2h9z
TitleSolution structure of hypothetical protein, HP0495 from Helicobacter pylori
ComponentsHypothetical protein HP0495
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / feredoxin-like (beta-alpha-beta-beta-alpha-beta)
Function / homologyUncharacterised protein family UPF0250, YbeD-like / YbeD-like domain superfamily / Protein of unknown function (DUF493) / ACT domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein HP_0495
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsSeo, M.D. / Park, S.J. / Kim, H.J. / Lee, B.J.
CitationJournal: Proteins / Year: 2007
Title: Solution structure of hypothetical protein, HP0495 (Y495_HELPY) from Helicobacter pylori.
Authors: Seo, M.D. / Park, S.J. / Kim, H.J. / Lee, B.J.
History
DepositionJun 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 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: Hypothetical protein HP0495


Theoretical massNumber of molelcules
Total (without water)10,2061
Polymers10,2061
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 least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Hypothetical protein HP0495


Mass: 10205.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O25237

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.2mM hp0495, U-15N, 13C; 50mM phosphate buffer NA, 150mM Sodium chloride, 1mM EDTA, 1mM BMD; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150mM salt / pH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brungerstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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