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- PDB-9qih: Structure of response regulator LvrC from Leptospira -

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Basic information

Entry
Database: PDB / ID: 9qih
TitleStructure of response regulator LvrC from Leptospira
ComponentsSenB
KeywordsSIGNALING PROTEIN / Anti-sigma factor / response regulator / Leptospirosis / gene regulation / histidine kinase
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Histidine kinase-like ATPase domain / : / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / SenB
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsAgustoni, E. / Hiller, S. / Buschiazzo, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Novartis FreeNovation Switzerland
CitationJournal: To Be Published
Title: Leptospira virulence factor LvrB unveils the activation mechanism of Rec-controlled histidine kinases
Authors: Agustoni, E. / Buschiazzo, A. / Hiller, S.
History
DepositionMar 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SenB
B: SenB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7727
Polymers68,6312
Non-polymers1,1415
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-65 kcal/mol
Surface area26440 Å2
Unit cell
Length a, b, c (Å)70.289, 85.210, 111.271
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 (eV)
d_1ens_1(chain "A" and (resid 2 through 13 or resid 15...
d_2ens_1(chain "B" and (resid 2 through 13 or resid 15...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRGLUGLUAA2 - 132 - 13
d_12ILEILEALAALAAA15 - 3515 - 35
d_13GLUGLUTHRTHRAA37 - 13637 - 136
d_14SERSERMETMETAA138 - 159138 - 159
d_15SERSERILEILEAA161 - 221161 - 221
d_16GLUGLULYSLYSAA223 - 295223 - 295
d_17ADPADPADPADPAD402
d_21THRTHRGLUGLUBB2 - 132 - 13
d_22ILEILEALAALABB15 - 3515 - 35
d_23GLUGLUTHRTHRBB37 - 13637 - 136
d_24SERSERMETMETBB138 - 159138 - 159
d_25SERSERILEILEBB161 - 221161 - 221
d_26GLUGLULYSLYSBB223 - 295223 - 295
d_27ADPADPADPADPBF401

NCS oper: (Code: givenMatrix: (-0.993877217595, -0.109351519186, -0.0158215548601), (-0.108614737689, 0.940667917701, 0.32147582703), (-0.0202710410024, 0.321225954524, -0.946785599297)Vector: 0. ...NCS oper: (Code: given
Matrix: (-0.993877217595, -0.109351519186, -0.0158215548601), (-0.108614737689, 0.940667917701, 0.32147582703), (-0.0202710410024, 0.321225954524, -0.946785599297)
Vector: 0.650281936882, 7.08226607124, -41.5085663822)

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Components

#1: Protein SenB


Mass: 34315.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: senB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9APH2
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium HEPES, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.6→34.63 Å / Num. obs: 105097 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 47.34 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.056 / Rrim(I) all: 0.131 / Χ2: 0.97 / Net I/σ(I): 8.2
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2545 / Rpim(I) all: 0.379 / Rrim(I) all: 0.888 / Χ2: 1.08 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→34.01 Å / SU ML: 0.3906 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 26.8144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2525 1980 5.06 %
Rwork0.2034 37115 -
obs0.2058 39095 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.23 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 71 137 4893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354885
X-RAY DIFFRACTIONf_angle_d0.70686616
X-RAY DIFFRACTIONf_chiral_restr0.0466759
X-RAY DIFFRACTIONf_plane_restr0.0047840
X-RAY DIFFRACTIONf_dihedral_angle_d15.3381850
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.40911936717 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.35441420.34152640X-RAY DIFFRACTION98.58
2.67-2.740.40821530.32082640X-RAY DIFFRACTION98.17
2.74-2.820.33991590.30422613X-RAY DIFFRACTION97.85
2.82-2.910.38711320.29292688X-RAY DIFFRACTION98.43
2.91-3.010.34161610.27922589X-RAY DIFFRACTION98
3.01-3.130.30431490.2742631X-RAY DIFFRACTION97.78
3.13-3.280.30121450.25552627X-RAY DIFFRACTION97.88
3.28-3.450.26721410.21632654X-RAY DIFFRACTION98.9
3.45-3.660.2524960.19592739X-RAY DIFFRACTION99.33
3.66-3.950.20091320.18812662X-RAY DIFFRACTION99.11
3.95-4.340.21691300.16542675X-RAY DIFFRACTION99.15
4.34-4.970.21741560.15192661X-RAY DIFFRACTION98.7
4.97-6.250.20771580.17592588X-RAY DIFFRACTION97.38
6.26-34.010.1921260.14982708X-RAY DIFFRACTION99.82
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)
16.52636458704-0.3344345753962.49849878443.797119735022.185165916476.291569301110.15986314830.306300120493-0.9400954508420.1513643073750.240813773188-0.3230232021620.1947454157750.559258017187-0.2676428572330.402445206048-0.0272157365113-0.0539758410660.368596279169-0.01632446182620.43051398691715.8494895107-1.01224955613-46.5519839959
24.242201617373.218043070810.1028144293844.53562605939-2.314154264712.74549613119-0.0857480175282-0.311820626316-0.325317986092-0.1418483982680.7070536680060.2584051595980.645380934416-0.113885141034-0.2939275620851.13758639229-0.1292058853220.1185933243411.023008804140.2001492623420.85055207352713.80602161431.86366211625-14.281258192
35.63456774571.2431499592-0.5756811030421.53814169131-1.091226800273.096111093290.2878783732670.4857325422160.6490064225610.118221835898-0.09122603670460.132872971504-0.1074695070650.121025504667-0.1666795366730.3391012661660.04034341954080.0625069213750.3939515260290.09500342858880.391044956115-17.2360314258.79175139687-11.3315312872
45.41204571217-0.01198436007931.61500525914.710320987670.896403681063.284287134410.0475886687818-0.407307726286-0.1740866410460.138815131559-0.0448500995730.131863188747-0.184944566943-0.0615969251110.01889977038030.365727664221-0.06911534915490.01507920969820.398698942568-0.02813461772820.285893632482-15.0286774464-11.05170607562.11607296823
56.147361037564.29817548173-5.314346141594.44809909419-2.227198839256.28422554217-0.351219602330.881435107819-0.70481951449-0.791657896114-0.749797366443-1.000774994390.4353330812910.2374615186850.5838584045610.5974815218410.1860640610760.02056807275721.026072553-0.002358103970090.840983719535-11.8802349021.56294017628-27.1400493689
65.17645695836-1.13755132508-2.072722694561.53576017969-0.21327552673.073473752570.0233747855204-0.196750117689-0.0191622300576-0.005634926109390.09901579898050.112846161775-0.0896172214763-0.123417004344-0.1159059060830.325171000714-0.0365103581707-0.00170142162750.4776480683320.1055476551210.32925568606116.970432150514.1733416026-27.8239649672
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 2:123AA2 - 1231 - 122
22chain A and resid 124:132AA124 - 132123 - 131
33chain A and resid 133:403AA - C133 - 403132
44chain B and resid 1:123BD1 - 1231 - 123
55chain B and resid 124:132BD124 - 132124 - 132
66chain B and resid 133:301BD - E133 - 301133

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