PDB-9ql9: CA domain of LvrB from Leptospira in its apo form

ID or keywords:

Entry

Database: PDB / ID: 9ql9

Title

CA domain of LvrB from Leptospira in its apo form

Components

histidine kinase

Keywords

SIGNALING PROTEIN / Leptospirosis / histidine kinase / response regulator

Function / homology

Function and homology information

phosphorelay sensor kinase activity / histidine kinase / signal transduction / ATP binding / metal ion binding
Similarity search - Function

Biological species

Leptospira interrogans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Hiller, S. / Agustoni, E. / Buschiazzo, A.

Funding support

Switzerland, 1items

Citation

Journal: To Be Published
Title: Leptospira virulence factor LvrB unveils the activation mechanism of Rec-controlled histidine kinases
Authors: Hiller, S. / Agustoni, E. / Buschiazzo, A.

History

Deposition	Mar 20, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 8, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ql9.cif.gz	168.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9ql9.ent.gz	110.9 KB	Display	PDB format
PDBx/mmJSON format	9ql9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ql/9ql9 ftp://data.pdbj.org/pub/pdb/validation_reports/ql/9ql9	HTTPS FTP

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Related structure data

Related structure data	53315C 53316C 9qihC 9qjgC 9qqwC 9qr2C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (13) #183 - Mar 2015 Phototropin similarity (8) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: histidine kinase

B: histidine kinase

39.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	41.543, 57.153, 135.448
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 10 through 121 or resid 138 through 173))
d_2	ens_1	chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	HIS	HIS	ILE	ILE	A	A	10 - 121	6 - 117
d_1	2	GLY	GLY	ASP	ASP	A	A	138 - 173	134 - 169
d_2	1	HIS	HIS	ASP	ASP	B	B	10 - 173	6 - 169

NCS oper: (Code: givenMatrix: (0.726661219712, 0.676178280985, -0.121434772989), (0.676204859597, -0.735191202684, -0.0473379694694), (-0.121286683623, -0.047716116986, -0.99146997562)Vector: 16. ...

#1: Protein	histidine kinase Mass: 19663.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: LA_2223 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8F424, histidine kinase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 50 mM Tris, 100 mM MgCl2, 15% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000039 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000039 Å / Relative weight: 1
Reflection	Resolution: 1.5→43.68 Å / Num. obs: 691258 / % possible obs: 99.7 % / Redundancy: 13.2 % / B_iso Wilson estimate: 26.37 Å² / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.04452 / R_pim(I) all: 0.0129 / R_rim(I) all: 0.0464 / Net I/σ(I): 25.3
Reflection shell	Resolution: 1.5→1.55 Å / Redundancy: 13.7 % / R_merge(I) obs: 1.526 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 5150 / CC_1/2: 0.932 / CC star: 0.982 / R_pim(I) all: 0.4268 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→43.68 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2371	4950	4.98 %
R_work	0.1954	94490	-
obs	0.1975	99440	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→43.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2432	0	0	207	2639

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0135	2481
X-RAY DIFFRACTION	f_angle_d	1.3318	3347
X-RAY DIFFRACTION	f_chiral_restr	0.0838	366
X-RAY DIFFRACTION	f_plane_restr	0.0103	435
X-RAY DIFFRACTION	f_dihedral_angle_d	18.2021	932

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.1748256157 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.5-1.52	0.3447	173	0.3665	3069	X-RAY DIFFRACTION	99.05
1.52-1.53	0.418	176	0.3342	3188	X-RAY DIFFRACTION	99.32
1.53-1.55	0.3784	137	0.3183	3109	X-RAY DIFFRACTION	98.6
1.55-1.57	0.2866	158	0.3011	3165	X-RAY DIFFRACTION	99.52
1.57-1.59	0.3031	193	0.3004	3133	X-RAY DIFFRACTION	99.73
1.59-1.62	0.3032	146	0.2644	3144	X-RAY DIFFRACTION	99.79
1.62-1.64	0.3269	206	0.2582	3113	X-RAY DIFFRACTION	99.37
1.64-1.66	0.2903	142	0.2475	3177	X-RAY DIFFRACTION	99.4
1.66-1.69	0.3142	158	0.2459	3144	X-RAY DIFFRACTION	99.37
1.69-1.72	0.3402	176	0.2772	3139	X-RAY DIFFRACTION	99.43
1.72-1.75	0.2986	184	0.2577	3128	X-RAY DIFFRACTION	99.67
1.75-1.78	0.2638	150	0.2475	3136	X-RAY DIFFRACTION	99.82
1.78-1.81	0.2613	150	0.238	3224	X-RAY DIFFRACTION	99.76
1.81-1.85	0.2234	159	0.2166	3110	X-RAY DIFFRACTION	99.51
1.85-1.89	0.2919	167	0.2191	3150	X-RAY DIFFRACTION	99.61
1.89-1.93	0.2302	170	0.1961	3165	X-RAY DIFFRACTION	99.88
1.93-1.98	0.1894	149	0.1934	3203	X-RAY DIFFRACTION	99.73
1.98-2.04	0.2271	136	0.1994	3136	X-RAY DIFFRACTION	99.79
2.04-2.1	0.2483	158	0.2139	3194	X-RAY DIFFRACTION	99.97
2.1-2.16	0.2361	164	0.19	3132	X-RAY DIFFRACTION	100
2.16-2.24	0.2333	170	0.1823	3144	X-RAY DIFFRACTION	99.94
2.24-2.33	0.2518	165	0.1951	3196	X-RAY DIFFRACTION	99.94
2.33-2.44	0.1964	187	0.1999	3131	X-RAY DIFFRACTION	100
2.44-2.56	0.2286	145	0.1913	3162	X-RAY DIFFRACTION	100
2.57-2.73	0.2292	163	0.2113	3197	X-RAY DIFFRACTION	100
2.73-2.94	0.2248	156	0.2089	3155	X-RAY DIFFRACTION	99.97
2.94-3.23	0.2448	193	0.1973	3122	X-RAY DIFFRACTION	99.94
3.23-3.7	0.2658	163	0.1729	3135	X-RAY DIFFRACTION	99.22
3.7-4.66	0.2088	173	0.157	3166	X-RAY DIFFRACTION	99.94
4.66-43.68	0.2155	183	0.1828	3123	X-RAY DIFFRACTION	99.76

Refinement TLS params.

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

ID	L11 (°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)
1	1.46135905484	0.620787092166	1.36114178923	0.887435480877	0.228863997253	0.804313864827	-0.120412100915	-0.102777068867	0.0692096679639	0.16947601017	0.150935706799	0.00832946515169	-0.067764465079	0.427460140869	0.000746147087381	0.252390410543	-0.0107124403749	-0.0133427674639	0.258757009076	-0.00266684689331	0.272085790016	9.44453967305	-14.7438545572	-15.1395709386
2	0.415586987822	-0.33635598139	0.635441423838	0.550409214528	0.197542479805	0.69178061001	-0.0519147440418	0.206869373664	-0.0179785472966	0.0146733976649	0.0350771632484	-0.124559237998	-0.156783342177	0.183786390438	-7.34619790819E-5	0.258261270401	-0.0421716343446	0.0113074241226	0.286454956463	-0.019714323199	0.273960686666	9.34881876616	-12.3062352119	-23.336040433
3	-0.370403436231	0.420503484159	0.101715015879	0.817461485635	-0.117912080055	0.638719309545	0.0311420320686	0.0238153662462	-0.076354334624	-0.00898567551787	0.13776045093	-0.11010027602	0.161332974711	-0.0336979692053	9.07547455408E-5	0.247157065221	0.0056431723755	-0.00168686123614	0.302107992017	-0.0339342086948	0.266910737175	5.05014144544	-24.3061277472	-29.854111835
4	0.133309474513	0.115647525017	0.16758091755	0.326924791762	-0.204845126577	0.288660603921	-0.131845254288	0.193279789457	0.124617540513	0.0418948907529	0.24302684379	-0.0674740056279	-0.167854316176	-0.114325269696	3.08712581826E-5	0.30382023755	-0.01322319067	0.0167794080447	0.294998095325	0.00564801524942	0.249785534759	3.06048060895	-8.90317184767	-27.4085262448
5	0.545729032833	0.345004691845	0.882002959017	0.487242556135	-0.445794826417	1.68947612877	0.0520750644509	0.0640333672768	-0.061438783087	-0.0243086632076	-0.0714486864046	0.142033553621	-0.0308991790077	-0.546989496446	-0.000365402297625	0.262711732495	-0.0104506130202	-0.00437149390397	0.403429650047	-0.0411434194722	0.287991587038	-5.9056288096	-15.8340374845	-26.9520249008
6	2.34056303189	-0.137030010826	0.290316189605	2.01599975392	-0.703415296442	0.842005377717	0.0492876392316	0.316438172106	-0.0828505622158	-0.0386053284591	-0.0813699279789	0.184796119353	-0.0114475767345	-0.344537319461	0.000389878991489	0.220407114284	-0.00578941061131	-0.00461642469431	0.291920428107	-0.0127146631301	0.230299963355	-4.05732992734	-14.6569001948	-22.6411927328
7	1.50246764829	-0.518221110439	-0.368062796872	0.40891313825	-0.456939522263	0.996317531892	0.214914369451	0.182945304787	-0.0976171314864	-0.0538439343054	0.178855906541	-0.456766981136	-0.191487299842	0.441437287047	0.0201837050124	0.211368767953	0.0171974674782	-0.035421438376	0.321362275958	-0.0254811522729	0.327805867531	15.4852580943	-27.5765717291	-17.11927067
8	0.175204282548	0.0698125747307	-0.155406971308	0.291723096248	-0.40493436408	0.715137013111	-0.110076174821	-0.131294178455	-0.175093235012	0.518434938175	0.203535485036	-0.0760102588908	-0.0867535963484	0.237915980083	0.0435659052245	0.240799184774	0.0284742736853	-0.0917023246806	0.249506746386	-0.0656145440104	0.268027759494	16.0740990079	-24.127400417	-1.71263705081
9	0.271293500681	-0.0726599914451	0.191439437938	0.0368191016725	-0.0788768090631	0.406120517007	0.355405143914	0.401507599118	-0.105033477551	-0.266483909158	-0.0521099582665	-0.235317992124	0.542969011498	0.495305733465	0.0402958065577	0.408544392397	0.190940262453	-0.102260756227	0.444426997604	-0.142375229035	0.451458074588	19.4382965089	-37.2012019552	-19.6889592351
10	1.38085301424	-0.375440387538	0.500924447601	0.476482376	-0.0663214930297	0.251710952563	0.184619833517	0.102487430613	-0.159998789902	0.049350341853	0.0113452657722	0.0805779351969	-0.0918209144626	-0.387323778603	0.000682684954488	0.265740314507	-0.0105143595215	-0.0497126149693	0.228497953544	0.00628007225363	0.296993836362	6.04559885813	-27.0064054047	-9.14329186167
11	0.108379109045	-0.0246672120446	0.0602351227895	0.0140380457975	0.091931076272	0.114747699572	0.0361898229877	-0.591840933741	0.0693160040635	0.579831415782	-0.08654167832	0.0333255426762	0.159993064854	-0.101611240445	0.000530829751314	0.372013558641	-0.0197912383467	-0.018511571421	0.278654984651	0.00931287217197	0.294430756589	10.2506705272	-21.3424522304	7.57341307614
12	0.805122502965	-0.306644338091	-0.0831424840255	0.186063825793	-0.00151449676591	0.0886862989943	0.0738596508411	-0.0476005616426	-0.306682107689	0.406627637407	0.312085558849	-0.117767487679	0.974999599794	0.192209928041	0.150545863291	0.555199794392	0.0900415139241	-0.175879495838	0.244698302453	-0.0830175870682	0.420273865727	16.0925724773	-37.7835762259	-7.32020514842
13	0.210810851478	0.0814435532386	-0.137793454074	0.716267508753	-0.584090189224	0.622211196655	0.111022853864	0.14641476089	-0.3704558661	0.140586873868	0.169358164109	0.259027209785	0.66107606197	0.0063415912528	0.320922911715	0.499722173056	0.0750621940656	-0.189855210457	0.244186545204	-0.109924284677	0.46020545315	13.1702628543	-42.2939239864	-11.1269716203
14	0.05262582794	0.0658233912263	0.00495242871401	0.230226688341	0.212249529731	0.183260988333	0.144586897608	0.403246959205	-0.135759652966	0.185283713158	0.102558398589	0.530713272992	0.815672307975	-0.461991804319	0.00341893485725	0.540605353013	-0.213032736198	-0.0942299799914	0.545513367105	0.089206771573	0.577346743082	-2.44524435602	-35.2076046444	-0.305845478572
15	1.69755815921	0.219048591312	-0.673497971874	1.0362465188	-0.120851257449	0.98150897145	0.267358319979	0.141607421925	-0.349459300753	0.338451489144	-0.0590640225935	0.249560464524	1.3610579836	-0.895059512631	0.106129663116	0.46564744818	-0.158123397057	-0.123003130649	0.405606926878	-0.00122371599542	0.489051308193	3.07571846079	-38.5234494152	-12.7101309311
16	1.45740934467	0.407308595553	0.773575383794	1.09055206951	0.0509926687714	0.268860875061	0.40693615402	0.0166002770711	-0.125846221751	0.51520215373	0.058349674918	-0.0173018675613	1.01811333409	0.0823024247998	0.0415885723877	0.509667555589	0.0121509501945	-0.128140798156	0.303071668827	-0.0543455556776	0.441850754925	10.2942878057	-39.3042603496	-8.45411884313

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 6 through 36 )	A	A	6 - 36	1 - 31
2	2	chain 'A' and (resid 37 through 55 )	A	A	37 - 55	32 - 50
3	3	chain 'A' and (resid 56 through 85 )	A	A	56 - 85	51 - 80
4	4	chain 'A' and (resid 86 through 96 )	A	A	86 - 96	81 - 91
5	5	chain 'A' and (resid 97 through 138 )	A	A	97 - 138	92 - 119
6	6	chain 'A' and (resid 139 through 173 )	A	A	139 - 173	120 - 154
7	7	chain 'B' and (resid 10 through 36 )	B	B	10 - 36	1 - 27
8	8	chain 'B' and (resid 37 through 44 )	B	B	37 - 44	28 - 35
9	9	chain 'B' and (resid 45 through 55 )	B	B	45 - 55	36 - 46
10	10	chain 'B' and (resid 56 through 77 )	B	B	56 - 77	47 - 68
11	11	chain 'B' and (resid 78 through 85 )	B	B	78 - 85	69 - 76
12	12	chain 'B' and (resid 86 through 96 )	B	B	86 - 96	77 - 87
13	13	chain 'B' and (resid 97 through 108 )	B	B	97 - 108	88 - 99
14	14	chain 'B' and (resid 109 through 138 )	B	B	109 - 138	100 - 113
15	15	chain 'B' and (resid 139 through 158 )	B	B	139 - 158	114 - 133
16	16	chain 'B' and (resid 159 through 173 )	B	B	159 - 173	134 - 148

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