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- PDB-9b9x: Crystal structure of the ligand binding domain of the Halomonas t... -

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Basic information

Entry
Database: PDB / ID: 9b9x
TitleCrystal structure of the ligand binding domain of the Halomonas titanicae chemoreceptor Htc10 in complex with hypoxanthine
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
HYPOXANTHINE / Chemotaxis protein
Similarity search - Component
Biological speciesHalomonas titanicae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.63 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

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Assembly

Deposited unit
A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7542
Polymers32,6181
Non-polymers1361
Water00
1
A: Chemotaxis protein
hetero molecules

A: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5094
Polymers65,2372
Non-polymers2722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2850 Å2
ΔGint-2 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.856, 175.856, 88.611
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-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O / 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: 4.07 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1 M (NH4)2SO4

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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: 3.63→76.59 Å / Num. obs: 6047 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 109.69 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.066 / Rrim(I) all: 0.224 / Net I/σ(I): 10.3
Reflection shellResolution: 3.63→3.98 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1429 / CC1/2: 0.802 / Rpim(I) all: 0.345 / Rrim(I) all: 1.175 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.63→57.75 Å / SU ML: 0.342 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.7762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2943 324 5.37 %
Rwork0.2416 5714 -
obs0.2445 6038 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 116.91 Å2
Refinement stepCycle: LAST / Resolution: 3.63→57.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 10 0 1707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211742
X-RAY DIFFRACTIONf_angle_d0.51332366
X-RAY DIFFRACTIONf_chiral_restr0.0399257
X-RAY DIFFRACTIONf_plane_restr0.0036314
X-RAY DIFFRACTIONf_dihedral_angle_d12.6132627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.63-4.570.29831570.25082834X-RAY DIFFRACTION99.8
4.58-57.750.29191670.23682880X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: -1.706 Å / Origin y: 40.22 Å / Origin z: 37.532 Å
111213212223313233
T0.568582708191 Å2-0.119905551984 Å2-0.0235764819981 Å2-0.623903206809 Å20.241164330636 Å2--0.780378186308 Å2
L2.70433728736 °2-0.419686259239 °20.837127161942 °2-4.2813580229 °2-0.330223626242 °2--2.10972349398 °2
S0.203512656424 Å °0.143087230277 Å °0.303467909536 Å °0.0787576254644 Å °-0.467496175773 Å °-0.726249002015 Å °0.0404176507995 Å °0.338036424676 Å °0.215607691917 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 48:267 )

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