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- PDB-2k1o: NMR Structure of Helicobacter pylori JHP0511 (HP0564). -

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Basic information

Entry
Database: PDB / ID: 2k1o
TitleNMR Structure of Helicobacter pylori JHP0511 (HP0564).
ComponentsPutative
KeywordsGENE REGULATION / Helicobacter pylori / repressor / transcriptional regulator / DNA-binding / ribbon-helix-helix / HP0564 / JHP0511 / UNKNOWN FUNCTION
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
RHH transcriptional regulator CopG / Transcriptional regulator, RHH-like, CopG / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, energy minimization
AuthorsBorin, B.N. / Krezel, A.M.
CitationJournal: Proteins / Year: 2008
Title: Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator.
Authors: Borin, B.N. / Krezel, A.M.
History
DepositionMar 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 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: Putative
B: Putative


Theoretical massNumber of molelcules
Total (without water)15,6042
Polymers15,6042
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 / 50structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative


Mass: 7801.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99 / Gene: JHP0511 / Plasmid: pETBNK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZLR7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1312D 1H-1H NOESY
1433D CBCA(CO)NH
1533D C(CO)NH
1633D H(CCO)NH
1733D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM JHP0511, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-15N] JHP0511, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-13C; U-15N] JHP0511, 50 mM potassium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMJHP05111
50 mMpotassium phosphate1
1 mMJHP0511[U-15N]2
50 mMpotassium phosphate2
1 mMJHP0511[U-13C; U-15N]3
50 mMpotassium phosphate3
Sample conditionsIonic strength: 50 / pH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospinprocessing
SparkyGoddardpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
ProcheckNMRLaskowski and MacArthurdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, energy minimization / Software ordinal: 1
Details: CYANA calculations, 25000 steps, 10000 steps of conjugate gradient energy minimization using AMBER
NMR constraintsNOE constraints total: 797 / NOE intraresidue total count: 222 / NOE long range total count: 221 / NOE medium range total count: 134 / NOE sequential total count: 220 / Hydrogen bond constraints total count: 88
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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