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- PDB-2rm8: The solution structure of phototactic transducer protein HtrII li... -

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Basic information

Entry
Database: PDB / ID: 2rm8
TitleThe solution structure of phototactic transducer protein HtrII linker region from Natronomonas pharaonis
ComponentsSensory rhodopsin II transducer
KeywordsSIGNALING PROTEIN / PROTEIN / Chemotaxis / Chromophore / Membrane / Methylation / Photoreceptor protein / Receptor / Sensory transduction / Transducer / Transmembrane
Function / homology
Function and homology information


photoreceptor activity / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1910 / Htr2, transmembrane domain / Htr2 transmembrane domain / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1910 / Htr2, transmembrane domain / Htr2 transmembrane domain / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodSOLUTION NMR / molecular dynamics
AuthorsHayashi, K. / Sudo, Y. / Jee, J. / Mishima, M. / Hara, H. / Kamo, N. / Kojima, C.
CitationJournal: Biochemistry / Year: 2007
Title: Structural Analysis of the Phototactic Transducer Protein HtrII Linker Region from Natronomonas pharaonis
Authors: Hayashi, K. / Sudo, Y. / Jee, J. / Mishima, M. / Hara, H. / Kamo, N. / Kojima, C.
History
DepositionOct 15, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / 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 / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensory rhodopsin II transducer


Theoretical massNumber of molelcules
Total (without water)7,9541
Polymers7,9541
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 Sensory rhodopsin II transducer / HTR-II / Methyl-accepting phototaxis protein II / MPP-II


Mass: 7953.507 Da / Num. of mol.: 1 / Fragment: Residues UNP 100-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htrII
Plasmid details: pHtrII(1-159) was expressed, and pHtrII(100-159) was obtained by trypsin digestion.
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: P42259

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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 HN(CA)CB
1313D HNCA
1413D HNCO
1513D HN(COCA)CB
1613D H(CCO)NH
1723D 1H-15N NOESY
1823D 1H-15N TOCSY
1913D H(CA)CONH
11013D (H)CCH-TOCSY
11122D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6-0.8mM [U-100% 13C; U-100% 15N] pHtrII(100-159), 10mM citric acid, 50mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.6-0.8mM [U-15N] pHtrII(100-159), 10mM citric acid, 50mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMpHtrII(100-159)[U-100% 13C; U-100% 15N]1
10 mMcitric acid1
50 mMpotassium chloride1
10 %D2O[U-2H]1
0.6 mMpHtrII(100-159)[U-15N]2
10 mMcitric acid2
50 mMpotassium chloride2
10 %D2O[U-2H]2
Sample conditionsIonic strength: 0.05 / pH: 5.0 / Pressure: ambient / Temperature: 277 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxcollection of dihedral angles
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 480 / NOE intraresidue total count: 209 / NOE long range total count: 0 / NOE medium range total count: 74 / NOE sequential total count: 197 / Hydrogen bond constraints total count: 9 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 22 / Protein psi angle constraints total count: 22
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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