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- PDB-9ba3: High-resolution crystal structure of the ligand binding domain of... -

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Basic information

Entry
Database: PDB / ID: 9ba3
TitleHigh-resolution crystal 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 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
B: Chemotaxis protein
C: Chemotaxis protein
D: Chemotaxis protein
E: Chemotaxis protein
F: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,49212
Polymers194,5856
Non-polymers9076
Water10,269570
1
A: Chemotaxis protein
B: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1644
Polymers64,8622
Non-polymers3022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Chemotaxis protein
D: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1644
Polymers64,8622
Non-polymers3022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Chemotaxis protein
F: Chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1644
Polymers64,8622
Non-polymers3022
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.346, 104.496, 145.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_2ens_1(chain "B" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_3ens_1(chain "C" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_4ens_1(chain "D" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_5ens_1(chain "E" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_6ens_1(chain "F" and (resid 50 through 82 or resid 84 through 158 or resid 160 through 204))
d_1ens_2chain "H"
d_2ens_2chain "I"
d_3ens_2chain "J"
d_4ens_2chain "K"
d_5ens_2chain "L"
d_6ens_2chain "M"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LEULEUGLUGLUAA50 - 8221 - 53
d_12ens_1TRPTRPTYRTYRAA84 - 15855 - 129
d_13ens_1LEULEUSERSERAA160 - 204131 - 175
d_21ens_1LEULEUGLUGLUBB50 - 8221 - 53
d_22ens_1TRPTRPTYRTYRBB84 - 15855 - 129
d_23ens_1LEULEUSERSERBB160 - 204131 - 175
d_31ens_1LEULEUGLUGLUCC50 - 8221 - 53
d_32ens_1TRPTRPTYRTYRCC84 - 15855 - 129
d_33ens_1LEULEUSERSERCC160 - 204131 - 175
d_41ens_1LEULEUGLUGLUDD50 - 8221 - 53
d_42ens_1TRPTRPTYRTYRDD84 - 15855 - 129
d_43ens_1LEULEUSERSERDD160 - 204131 - 175
d_51ens_1LEULEUGLUGLUEE50 - 8221 - 53
d_52ens_1TRPTRPTYRTYREE84 - 15855 - 129
d_53ens_1LEULEUSERSEREE160 - 204131 - 175
d_61ens_1LEULEUGLUGLUFF50 - 8221 - 53
d_62ens_1TRPTRPTYRTYRFF84 - 15855 - 129
d_63ens_1LEULEUSERSERFF160 - 204131 - 175
d_11ens_2GUNGUNGUNGUNEK401
d_21ens_2GUNGUNGUNGUNCI401
d_31ens_2GUNGUNGUNGUNBH401
d_41ens_2GUNGUNGUNGUNDJ401
d_51ens_2GUNGUNGUNGUNAG401
d_61ens_2GUNGUNGUNGUNFL401

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.130305847618, -0.0384781050463, -0.990726915708), (-0.0282590434285, -0.998984823066, 0.0350820430975), (-0.991071043135, 0.0234255995748, -0.131260918569)-2.98970209917, -35.9166587606, -2.35084519527
2given(-0.771460125874, 0.00296278532161, -0.636270772619), (-0.0216264974927, -0.999533466473, 0.0215671974662), (-0.635910031995, 0.0303985411408, 0.77116428853)-17.4911221365, -18.7684721482, -19.449278234
3given(0.530865859847, -0.0692372779559, 0.844622778635), (0.0210175826687, 0.997426051172, 0.0685531448058), (-0.847195195966, -0.0186405950888, 0.530954638503)-15.0255143966, 17.5895517952, -20.1331381876
4given(-0.920255447286, 0.025261985695, 0.390501912695), (-0.0393241202326, -0.998832568691, -0.0280555393858), (0.389337289901, -0.0411744071122, 0.920174517628)-37.5843249182, -0.919505539609, -10.6922579988
5given(-0.463203849361, -0.0764825709168, 0.882945417499), (0.00415864261741, 0.996070747045, 0.0884633967961), (-0.886242009627, 0.0446484403656, -0.461065740589)-38.1802437235, 35.7528073954, -12.2189399508
6given(0.564399158724, 0.0872649395237, -0.820876616771), (-0.0928050885531, 0.994800377209, 0.0419455008793), (0.820268739603, 0.052507521702, 0.569563126435)-3.55517065497, -21.8541324506, 16.7461100069
7given(-0.400271904758, -0.0252227105834, -0.916049243836), (-0.0881146870829, 0.996048748346, 0.0110766799903), (0.912150318852, 0.0851510762712, -0.400912820983)-26.8300207211, -39.2635332036, 28.3666492741
8given(-0.218884295253, 0.0658196956783, 0.973528342141), (0.0522716730687, -0.99549864872, 0.0790576535851), (0.974349699793, 0.0681924340129, 0.214458514537)-13.4432753851, 19.8446457823, 18.7957488915
9given(-0.94794944119, -0.0913637856213, 0.305031991148), (0.0949543800894, -0.995476869529, -0.00307700104088), (0.303933418118, 0.0260472822096, 0.952337133814)-33.1528526328, 3.48406698082, 20.5744610551
10given(0.727868615196, 0.146722148814, 0.66983571871), (0.106080011434, -0.989173922924, 0.101400105433), (0.67746166695, -0.00274977362279, -0.735552940691)-3.71199669448, 40.6291268257, 5.85617905465

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Components

#1: Protein
Chemotaxis protein / Htc10


Mass: 32430.799 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C5H5N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 200 mM (NH4)2SO4, 100 mM sodium cacodylate trihydrate pH 6.5, 30% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→89.35 Å / Num. obs: 80249 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.032 / Rrim(I) all: 0.099 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4521 / CC1/2: 0.759 / Rpim(I) all: 0.441 / Rrim(I) all: 1.383

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→84.9 Å / SU ML: 0.303 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 4034 5.03 %
Rwork0.2107 76093 -
obs0.2121 80127 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.07 Å2
Refinement stepCycle: LAST / Resolution: 2.1→84.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7537 0 66 570 8173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00397797
X-RAY DIFFRACTIONf_angle_d0.64610618
X-RAY DIFFRACTIONf_chiral_restr0.04451125
X-RAY DIFFRACTIONf_plane_restr0.00731430
X-RAY DIFFRACTIONf_dihedral_angle_d14.68592842
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.33501704499
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.28942877677
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.00018545407
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.762427657312
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.966129061449
ens_2d_2KEX-RAY DIFFRACTIONTorsion NCS0.00152894833028
ens_2d_3KEX-RAY DIFFRACTIONTorsion NCS0.0021261711637
ens_2d_4KEX-RAY DIFFRACTIONTorsion NCS0.00205552231435
ens_2d_5KEX-RAY DIFFRACTIONTorsion NCS0.00149261494245
ens_2d_6KEX-RAY DIFFRACTIONTorsion NCS0.00198083256432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.40671420.35532589X-RAY DIFFRACTION99.71
2.12-2.150.38361420.34982585X-RAY DIFFRACTION99.82
2.15-2.180.39531200.33632649X-RAY DIFFRACTION99.96
2.18-2.210.32951400.30192548X-RAY DIFFRACTION99.96
2.21-2.240.31181240.31552604X-RAY DIFFRACTION99.96
2.24-2.270.31751490.29232579X-RAY DIFFRACTION99.96
2.27-2.30.34541530.29972601X-RAY DIFFRACTION99.96
2.3-2.340.30911220.28952606X-RAY DIFFRACTION99.96
2.34-2.380.32971520.28342572X-RAY DIFFRACTION99.96
2.38-2.420.35791470.27652608X-RAY DIFFRACTION99.96
2.42-2.460.29241260.27012591X-RAY DIFFRACTION99.96
2.46-2.510.33591220.25992609X-RAY DIFFRACTION99.96
2.51-2.560.33671120.26262645X-RAY DIFFRACTION99.96
2.56-2.620.35941470.26762593X-RAY DIFFRACTION100
2.62-2.680.25981410.25752608X-RAY DIFFRACTION100
2.68-2.740.3221150.25952636X-RAY DIFFRACTION99.96
2.74-2.820.29241420.23592592X-RAY DIFFRACTION100
2.82-2.90.29641420.23492635X-RAY DIFFRACTION100
2.9-2.990.2481370.23372627X-RAY DIFFRACTION100
2.99-3.10.27421390.21842599X-RAY DIFFRACTION100
3.1-3.230.25451400.20622619X-RAY DIFFRACTION99.93
3.23-3.370.22771450.20712624X-RAY DIFFRACTION99.96
3.37-3.550.20481260.18332659X-RAY DIFFRACTION100
3.55-3.770.20551610.17182615X-RAY DIFFRACTION100
3.77-4.060.1931350.16712679X-RAY DIFFRACTION100
4.06-4.470.15361400.15122643X-RAY DIFFRACTION100
4.47-5.120.16651440.14812678X-RAY DIFFRACTION99.96
5.12-6.450.21091470.17942712X-RAY DIFFRACTION100
6.45-84.90.19181820.19322788X-RAY DIFFRACTION99.3
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.531572872030.667169061283-0.0105323907454.68078323119-0.2141927584733.67160092567-0.0971986430573-0.03732583801010.1630548287960.06100117015030.00464541699653-0.280239976638-0.2939507185090.1198503558350.09990648807360.1867433165690.00380282770308-0.04848128191710.221207044181-0.03949544398090.2563313558868.803-4.196-6.544
22.706721063540.262587874437-0.4643024358593.183506388010.7772727567044.01162447278-0.137822249714-0.0397816689056-0.155223106326-0.12103959759-0.0490035553805-0.03044146943670.3479446717110.2167107805060.1526300382240.2587233102530.06114487716520.02460316595230.219562214180.02617701552970.2415751919264.703-32.159-10.2
33.496340527280.3018134374130.5770155815563.806469512460.3684610198663.733176454430.1071556822510.262765035432-0.208958367269-0.0871539643910.01939407420780.06355651475340.427128854864-0.0104692917202-0.09129036113060.277950779592-0.014350626674-0.04535846711080.22322438572-0.01035369094050.251161454308-20.13-14.849-29.995
42.453548413920.1754597109570.04693214984322.81204791905-1.608751022664.93603769549-0.08852164888710.1285548832740.0829330163997-0.122501810950.0813652273279-0.0555172875051-0.2837791667760.01222449483020.0248012340950.202912751083-0.01219353878370.02239601265650.2106671933450.006279636554070.264831163143-15.4513.063-30.816
52.613197135811.21936904643-0.08257004523164.1002371661-0.7237488198593.333058451290.1502487893010.0459757166167-0.047361570529-0.150683832536-0.04984552940510.2299095917230.260755409894-0.148986906615-0.02215751897940.1958239049780.0109863756308-0.04173334055770.2290728522840.01546924267410.232034358018-48.3533.058-12.866
64.28325923979-0.892042912566-0.2003387598213.76672695237-1.108151346313.271898943350.0585724030546-0.02853068503680.409585818586-0.00917462319904-0.07776226014190.244473882124-0.4681148067-0.2442144188040.04693356985630.3199057725150.0120384251725-0.05912453350610.229896642026-0.03043746056220.320643750703-47.35631.01-17.341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 49:179 )A49 - 179
2X-RAY DIFFRACTION2( CHAIN B AND RESID 50:179 )B50 - 179
3X-RAY DIFFRACTION3( CHAIN C AND RESID 50:179 )C50 - 179
4X-RAY DIFFRACTION4( CHAIN D AND RESID 49:176 )D49 - 176
5X-RAY DIFFRACTION5( CHAIN E AND RESID 49:176 )E49 - 176
6X-RAY DIFFRACTION6( CHAIN F AND RESID 50:177 )F50 - 177

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