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- PDB-1zhc: Solution structure of HP1242 from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 1zhc
TitleSolution structure of HP1242 from Helicobacter pylori
Componentshypothetical protein HP1242
KeywordsUNKNOWN FUNCTION / a-helical protein
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #50 / Protein of unknown function DUF465 / DUF465 superfamily / Protein of unknown function (DUF465) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / DUF465 domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsKang, S.J. / Park, S.J. / Jung, S.J. / Lee, B.J.
CitationJournal: Proteins / Year: 2005
Title: Solution structure of HP1242 from Helicobacter pylori
Authors: Kang, S.J. / Park, S.J. / Jung, S.J. / Lee, B.J.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein HP1242


Theoretical massNumber of molelcules
Total (without water)9,1301
Polymers9,1301
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 acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein hypothetical protein HP1242 / conserved hypothetical protein


Mass: 9130.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP1242 / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O25839

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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
131HNHA
1412D NOESY

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Sample preparation

DetailsContents: U-15N, 13C; 50mM phosphate buffer, 100mM NaCl, 1mM EDTA, pH 6.8; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mm NaCl / pH: 6.8 / Pressure: ambient / Temperature: 303 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
NMRPipe2Delaglioprocessing
NMRView5Johnsondata analysis
CNS1.1Brungerstructure solution
CNS1.1refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1040 restraints, 911 are NOE-derived distance constraints, 129 dihedral angle restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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