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- PDB-5jje: Structure of the SRII/HtrII Complex in I212121 space group ("U" shape) -

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Basic information

Entry
Database: PDB / ID: 5jje
TitleStructure of the SRII/HtrII Complex in I212121 space group ("U" shape)
Components
  • Sensory rhodopsin II transducer
  • Sensory rhodopsin-2
KeywordsSIGNALING PROTEIN / sensory rhodopsin II / transducer / membrane protein complex
Function / homology
Function and homology information


photoreceptor activity / phototransduction / transmembrane signaling receptor activity / chemotaxis / lysozyme activity / monoatomic ion channel activity / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / 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 ...Htr2, transmembrane domain / Htr2 transmembrane domain / Helix hairpin bin / 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 / Bacterial rhodopsins retinal binding site. / HAMP domain profile. / HAMP domain / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
EICOSANE / RETINAL / Sensory rhodopsin-2 / Sensory rhodopsin II transducer
Similarity search - Component
Biological speciesNatronomonas pharaonis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIshchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. ...Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. / Engelhard, M. / Bueldt, G. / Gordeliy, V.
Funding support Russian Federation, France, 2items
OrganizationGrant numberCountry
Russian Science Foundation14-14-00995 Russian Federation
French National Research AgencyANR-10-INSB-05-02 France
CitationJournal: Sci Rep / Year: 2017
Title: New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex.
Authors: Ishchenko, A. / Round, E. / Borshchevskiy, V. / Grudinin, S. / Gushchin, I. / Klare, J.P. / Remeeva, A. / Polovinkin, V. / Utrobin, P. / Balandin, T. / Engelhard, M. / Buldt, G. / Gordeliy, V.
History
DepositionApr 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,72716
Polymers43,7592
Non-polymers3,96714
Water1,00956
1
A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules

A: Sensory rhodopsin-2
B: Sensory rhodopsin II transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,45332
Polymers87,5184
Non-polymers7,93528
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556-x+1/2,y,-z+11
Buried area14940 Å2
ΔGint-5 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.642, 113.661, 125.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II


Mass: 26534.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host: Escherichia coli (E. coli) / References: UniProt: P42196
#2: Protein Sensory rhodopsin II transducer / HTR-II / Methyl-accepting phototaxis protein II / MPP-II


Mass: 17224.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronomonas pharaonis (archaea) / Gene: htr2, htrII / Production host: Escherichia coli (E. coli) / References: UniProt: P42259

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 69 molecules

#3: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#5: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 1 M Na/K phosphate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→28.1348 Å / Num. obs: 28430 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.393

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1h2s

1h2s


Resolution: 1.9→28.1348 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2183 1438 5.06 %
Rwork0.1966 --
obs0.1978 28420 99.41 %
Refinement stepCycle: LAST / Resolution: 1.9→28.1348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 171 56 2317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112294
X-RAY DIFFRACTIONf_angle_d1.2333080
X-RAY DIFFRACTIONf_dihedral_angle_d15.407823
X-RAY DIFFRACTIONf_chiral_restr0.279369
X-RAY DIFFRACTIONf_plane_restr0.006359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.35591460.31782681X-RAY DIFFRACTION100
1.9679-2.04670.32861490.2712655X-RAY DIFFRACTION100
2.0467-2.13980.24621440.21932670X-RAY DIFFRACTION100
2.1398-2.25260.22641450.19372688X-RAY DIFFRACTION100
2.2526-2.39360.21511280.17572693X-RAY DIFFRACTION100
2.3936-2.57830.20041520.1742673X-RAY DIFFRACTION100
2.5783-2.83760.21791460.16712698X-RAY DIFFRACTION100
2.8376-3.24760.19191450.18562708X-RAY DIFFRACTION100
3.2476-4.08970.22531320.18332758X-RAY DIFFRACTION100
4.0897-28.13480.20331510.20842758X-RAY DIFFRACTION96

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