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- PDB-9b9s: Crystal structure of the ligand binding domain of the Halomonas t... -

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Basic information

Entry
Database: PDB / ID: 9b9s
TitleCrystal structure of the ligand binding domain of the Halomonas titanicae chemoreceptor Htc10 in complex with guanine
ComponentsChemotaxis protein
KeywordsSIGNALING PROTEIN / Halomonas titanicae / chemoreceptor / guanine
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
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 (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
GUANINE / Chemotaxis protein
Similarity search - Component
Biological speciesHalomonas titanicae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsRamos Ricciuti, F.E. / Herrera Seitz, M.K. / Gasperotti, A.F. / Boyko, A. / Jung, K. / Bellinzoni, M. / Lisa, M.N. / Studdert, C.A.
Funding support Argentina, 2items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT2016-1629 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT2020-3814 Argentina
CitationJournal: Febs J. / Year: 2025
Title: The chemoreceptor controlling the Wsp-like transduction pathway in Halomonas titanicae KHS3 binds and responds to purine derivatives.
Authors: Ramos Ricciuti, F.E. / Soldano, A. / Herrera Seitz, M.K. / Gasperotti, A.F. / Boyko, A. / Jung, K. / Bellinzoni, M. / Lisa, M.N. / Studdert, C.A.
History
DepositionApr 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7702
Polymers32,6181
Non-polymers1511
Water00
1
A: Chemotaxis protein
hetero molecules

A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5394
Polymers65,2372
Non-polymers3022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2600 Å2
ΔGint-2 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.537, 178.537, 89.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Chemotaxis protein / Htc10


Mass: 32618.377 Da / Num. of mol.: 1 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas titanicae (bacteria) / Gene: RO22_21155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C3EFW7
#2: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: sodium acetate pH 4.6, 2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 3.6→77.38 Å / Num. obs: 6446 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 124.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.046 / Rrim(I) all: 0.132 / Net I/σ(I): 8.2
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1530 / CC1/2: 0.828 / Rpim(I) all: 0.307 / Rrim(I) all: 0.893 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→51.54 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2862 346 5.38 %
Rwork0.2525 6091 -
obs0.2544 6437 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.04 Å2
Refinement stepCycle: LAST / Resolution: 3.6→51.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 11 0 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251760
X-RAY DIFFRACTIONf_angle_d0.56222391
X-RAY DIFFRACTIONf_chiral_restr0.0395260
X-RAY DIFFRACTIONf_plane_restr0.0036318
X-RAY DIFFRACTIONf_dihedral_angle_d11.2265644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-4.540.29481650.29613021X-RAY DIFFRACTION100
4.54-51.540.28241810.23353070X-RAY DIFFRACTION99.79
Refinement TLS params.Method: refined / Origin x: 1.81247454188 Å / Origin y: 40.1951123091 Å / Origin z: 37.9664421052 Å
111213212223313233
T0.656866943793 Å2-0.0229479410741 Å2-0.0215665554207 Å2-0.697818098973 Å20.231669097366 Å2--0.825694103881 Å2
L3.30943191973 °20.284572690966 °20.480084564809 °2-0.743160966929 °20.24530112839 °2--0.972408294458 °2
S0.140345824682 Å °0.186383291746 Å °-0.416736186286 Å °0.0451325590881 Å °-0.24080340363 Å °-0.466714707195 Å °0.329407418796 Å °0.23510626784 Å °0.0740216460558 Å °
Refinement TLS groupSelection details: all

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