PDB-9gb9: Crystal structure of Lotus japonicus CERK6 kinase domain D460N

ID or keywords:

Entry

Database: PDB / ID: 9gb9

Title

Crystal structure of Lotus japonicus CERK6 kinase domain D460N

Components

LysM type receptor kinase

Keywords

PLANT PROTEIN / Immunity / Kinase / Phosphorylation

Function / homology

Function and homology information

transmembrane receptor protein kinase activity / innate immune response / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function

Biological species

Lotus japonicus (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Simonsen, B.W. / Gysel, K. / Andersen, K.R.

Funding support

Denmark, 1items

Citation

Journal: Biorxiv / Year: 2024
Title: Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis
Authors: Tsitsikli, M. / Simonsen, B.W. / Larsen, M.M. / Andersen, C.G. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Luu, T.B. / Hansen, S.B. / Kaya, G. / Stougaard, J. / Andersen, K.R. / Radutoiu, S.

History

Deposition	Jul 30, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 27, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2025	Group: Structure summary / Category: audit_author

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gb9.cif.gz	570.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9gb9.ent.gz	392.3 KB	Display	PDB format
PDBx/mmJSON format	9gb9.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/gb/9gb9 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/9gb9	HTTPS FTP

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Related structure data

Related structure data	9gfzC 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	#134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: LysM type receptor kinase

B: LysM type receptor kinase

C: LysM type receptor kinase

D: LysM type receptor kinase

hetero molecules

133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: LysM type receptor kinase

hetero molecules

defined by author
Evidence: gel filtration
33 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: LysM type receptor kinase

hetero molecules

defined by author
Evidence: gel filtration
33.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: LysM type receptor kinase

hetero molecules

defined by author
Evidence: gel filtration
33.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: LysM type receptor kinase

hetero molecules

defined by author
Evidence: gel filtration
33.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.920, 59.990, 103.740
Angle α, β, γ (deg.)	106.457, 97.306, 106.638
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	LysM type receptor kinase Mass: 32879.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: D3KTZ6
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M imidazole pH 8.0, 5% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.85→48.45 Å / Num. obs: 110336 / % possible obs: 99.87 % / Redundancy: 7 % / B_iso Wilson estimate: 33.2 Å² / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.1269 / R_pim(I) all: 0.05138 / R_rim(I) all: 0.137 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.76 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 5055 / CC_1/2: 0.545 / R_pim(I) all: 0.7178 / R_rim(I) all: 1.904 / % possible all: 99.33

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
XDS	Jun 30, 2023	data reduction
XSCALE	Jun 30, 2023	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→48.45 Å / SU ML: 0.2979 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 29.1569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2425	3029	2.75 %
R_work	0.2089	107246	-
obs	0.2098	110275	99.87 %

Solvent computation

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

Displacement parameters

B_iso mean: 50.04 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8751	0	90	943	9784

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9068
X-RAY DIFFRACTION	f_angle_d	0.6855	12230
X-RAY DIFFRACTION	f_chiral_restr	0.0495	1389
X-RAY DIFFRACTION	f_plane_restr	0.0064	1563
X-RAY DIFFRACTION	f_dihedral_angle_d	12.5094	3388

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 (%)
1.85-1.88	0.4648	139	0.4017	4916	X-RAY DIFFRACTION	99.33
1.88-1.91	0.3724	136	0.3669	4748	X-RAY DIFFRACTION	99.94
1.91-1.94	0.3782	139	0.3254	4975	X-RAY DIFFRACTION	99.92
1.94-1.98	0.3297	133	0.2833	4824	X-RAY DIFFRACTION	99.96
1.98-2.02	0.3036	141	0.2738	4882	X-RAY DIFFRACTION	99.9
2.02-2.06	0.314	136	0.2604	4912	X-RAY DIFFRACTION	99.9
2.06-2.1	0.2845	144	0.2445	4849	X-RAY DIFFRACTION	99.94
2.1-2.15	0.2422	134	0.2289	4897	X-RAY DIFFRACTION	99.86
2.15-2.2	0.2814	135	0.2376	4860	X-RAY DIFFRACTION	99.92
2.2-2.26	0.2647	138	0.2326	4862	X-RAY DIFFRACTION	99.86
2.26-2.33	0.3057	141	0.228	4863	X-RAY DIFFRACTION	99.8
2.33-2.41	0.2792	139	0.2087	4930	X-RAY DIFFRACTION	99.96
2.41-2.49	0.2254	133	0.2115	4874	X-RAY DIFFRACTION	99.94
2.49-2.59	0.2691	133	0.2084	4864	X-RAY DIFFRACTION	99.94
2.59-2.71	0.209	139	0.2014	4848	X-RAY DIFFRACTION	100
2.71-2.85	0.2867	143	0.2133	4953	X-RAY DIFFRACTION	99.94
2.85-3.03	0.2532	138	0.2125	4823	X-RAY DIFFRACTION	99.94
3.03-3.27	0.2521	141	0.2044	4868	X-RAY DIFFRACTION	99.96
3.27-3.59	0.2433	139	0.1946	4879	X-RAY DIFFRACTION	99.98
3.59-4.11	0.1932	137	0.1804	4876	X-RAY DIFFRACTION	99.88
4.11-5.18	0.1881	141	0.1723	4868	X-RAY DIFFRACTION	99.74
5.18-48.45	0.2247	130	0.2031	4875	X-RAY DIFFRACTION	99.64

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	3.42845469143	-0.701038162939	-0.868258716317	3.34206859588	-2.05863660369	7.39782644158	-0.0479491413571	0.938568388151	0.0285478794329	-0.521077094123	-0.489627681983	-0.788101951432	0.728543209891	1.69746061598	0.333555545565	0.440210317022	0.061754458152	0.045485193099	0.888407450868	-0.0059000798645	0.560518408879	35.0050533792	24.827470609	13.3564652883
2	7.32243675536	0.525605404554	-0.0476291807222	5.00850123934	-1.30738394226	2.95840099978	0.00879830243425	0.615597285455	0.147338121732	-0.427259154206	-0.105160065818	-0.491111385198	0.206079876466	0.893761189602	0.0854462445692	0.318300504249	0.0425086545616	-0.0155774676679	0.505879724207	-0.0046372550747	0.283482979286	24.8946039921	26.0341293106	8.49714960557
3	4.31583520682	-0.360452767007	-1.49887925762	2.77895331243	-0.0315933541505	7.63771865229	0.00961175682384	-0.353666879993	-0.0576048751412	0.260595024155	0.0248263831317	0.0348181779471	-0.00179388797127	0.129389674843	-0.00166747875779	0.264200587734	0.00536022030021	-0.0237390321003	0.194953677967	-0.0317390894786	0.321786137183	10.9353605777	23.7799209873	12.1662033892
4	1.73900887429	-3.07920040211	-0.634969912071	6.91773911978	3.0676082745	5.04239626481	0.140219423792	0.150548984838	-0.0607081894117	-0.633866837841	0.180469211171	-0.822974004175	0.361605169707	0.59855748293	-0.277013672478	0.478966479424	-0.00227230961526	0.0585876832677	0.304944135333	-0.0151771964359	0.456918656228	16.0876175639	12.1249583886	0.865056639106
5	2.19595309719	0.20735049492	-0.601925679841	3.75912425711	0.461491749834	4.15274384611	-0.129101428958	-0.292395911357	-0.518309786589	0.576932435984	-0.126619187027	0.965758143736	0.575205185296	-0.704046490201	0.0841191045816	0.434329182958	-0.0609591354004	0.140517882642	0.332274120429	0.0558971550189	0.559262204836	-1.80790147448	12.8371017637	14.4707265194
6	7.5342781087	-0.00128709507254	0.346301156774	2.45081374642	3.66264433171	6.85393105068	0.174983464944	-0.139719783077	-0.095679846996	0.235939666671	-0.100912083287	0.46667018694	0.397877756645	-0.627956667072	0.113207054712	0.323076557729	-0.039271771651	-0.0273459350843	0.238150026711	0.039554181549	0.353479091907	-0.625183913431	21.9472272571	3.45682650204
7	7.18512547594	-0.0416702749857	-1.7682906642	7.0432556817	0.81280782485	7.33612836341	0.0143059633764	0.458248477777	-0.265682690423	-0.609514511397	-0.0713888384024	-0.214072633481	0.290785307587	-0.255997163561	0.131852213545	0.295224547268	-0.00972945564438	0.0187575511327	0.232947857279	-0.0173749466448	0.315099954879	7.63095587076	11.5917724804	64.5758632544
8	4.52875784148	1.1440192173	-1.96800841606	2.29871198154	-1.7032655328	6.67547601819	-0.539356506442	1.26052104618	-0.314774333634	-0.730990708828	0.268879649163	0.415491641823	0.520272123033	-1.37670322988	-0.119856969753	0.437376436853	-0.12848482077	-0.0261516503196	0.579043817189	-0.13150342374	0.511505630201	7.76327918295	17.8319410765	53.0126421164
9	6.44598858822	1.60654594968	-2.90221489111	5.8953018016	-1.76466800965	4.42263267332	-0.307445390995	0.539185619939	-0.373176129781	-0.495863455231	0.331329503718	-0.172456769219	0.606085166533	-0.20700109378	-0.0716666454752	0.278998345328	-0.00232694671729	-0.0216333730678	0.305248961488	0.0256277643248	0.200952921275	12.834998306	20.2874451578	55.9950321577
10	3.71947472758	1.83198153925	1.48306899848	6.75206332671	1.73567644961	1.28867963352	-0.0369457407056	-0.310980901909	0.152033060013	0.531606935998	0.0282096218685	0.317185036155	0.0288431213317	-0.0927416217911	0.0187232082281	0.297329915132	-0.0153753747656	0.046806536528	0.264334752101	0.0620443055162	0.253473418722	8.88214662305	31.1900324278	70.2544759632
11	1.11534731272	-1.00520545445	-0.717324339568	2.58948802882	-0.380399175607	3.408875341	0.0555978481547	0.26541616722	-0.143768632742	-0.244894501263	-0.0714265199045	0.112738475559	0.210667792489	-0.284347720055	-0.00736496652819	0.224302471622	-0.0315995293455	-0.0360175568582	0.28496777705	-0.0119704047878	0.351504293102	11.7606716496	33.4731460379	56.7639407196
12	5.01740338196	-0.248909347255	0.406269809125	1.64444484801	1.81017095815	8.84635473823	0.13564007142	0.0648533906334	-0.306268037032	-0.1018452124	0.0362802901341	0.334843522171	-0.0154439816979	-1.23992057622	-0.0903238825591	0.26766072517	-0.0136945240193	-0.0651055429903	0.472381198758	0.0214302934794	0.355997802282	-2.55258543961	38.9375504573	49.244163589
13	2.11254164265	0.456691541392	0.980260351379	0.887886657471	0.021504545302	0.513145590078	-0.0188429539791	-0.00243351417493	0.0777992973368	0.22602609035	-0.123363351606	0.458083457404	-0.0209020846341	-0.960184672995	0.0683015447449	0.227570974794	0.0205135688423	0.00869748564283	0.39661802318	-0.00640522947303	0.357905867614	2.34358301721	45.0833674392	61.2364904176
14	3.186713844	-1.3892634871	0.650806853157	6.37402029108	0.216801038124	5.85878431457	0.109710517649	-0.0380896055624	0.453427452478	0.357367658821	-0.0932005438921	0.0802391771255	-0.244309260847	-0.213966123999	-0.0031918624536	0.218398029745	-0.00676597531097	0.0299345650497	0.173083854588	-0.0191642815738	0.306200306678	8.06653628573	55.1864678	67.1985460728
15	9.11910998637	-1.0278686671	-1.61150563483	2.45613822991	0.447419770873	5.63281651033	0.0997327488034	0.144042344219	0.415188133227	0.0191399783725	0.00752573848572	-0.0286286609845	-0.355222270425	0.107649485776	-0.25252765167	0.24412192971	-0.0276804458834	-0.00995123439687	0.193460362811	0.0656504857771	0.317976243892	14.5999216195	48.3067680095	53.6343892348
16	2.7565380873	-3.25025957161	3.69301292809	3.9567224431	-5.00136001941	8.68915524692	0.158056553378	-0.774758388677	-0.0225677493257	0.883663317615	-0.271977831146	-0.461978151024	-0.178844019762	0.639147707591	0.0174929877019	0.381908310581	-0.101798191005	-0.103210253908	0.445273200982	0.0678700716707	0.452927370247	31.5948242171	53.9667782015	-7.67423992371
17	2.62508833437	2.10924677749	-3.00909262256	2.14836427116	-2.57204620081	3.52731876258	0.386854904826	-0.257586957562	0.468136796307	0.322343434912	0.193425585994	0.408984640053	-0.661318211395	-0.553126980726	-0.364930285971	0.363351174207	0.016225603447	0.0139421074912	0.358657342021	0.0464537381912	0.364224354273	21.2075506482	59.8137819412	-18.4148246192
18	3.5880342782	0.906455783765	0.0139983608873	2.76056690292	-1.24986532085	1.91539102332	0.0164533954472	-0.144521206608	0.204521611032	0.422590608644	-0.11082014306	-0.237607775447	-0.319406048665	0.229825202262	0.0548926518032	0.284961236409	0.000207195390587	-0.000199205535256	0.188332432509	-0.0207621039454	0.24282016812	17.8387247839	50.233169763	-8.98153310807
19	2.04853971452	0.10886649012	-0.226452858969	1.48296961015	0.033474810064	1.58811931445	-0.0456943495683	0.0438249320005	0.050990078127	0.0488633473681	0.0565496790754	0.11753304644	-0.237905345153	-0.117300422236	0.0191936391712	0.252298066808	0.0141711544597	0.0190810348768	0.18406477635	-0.000429511145322	0.283252083147	-2.36482050138	46.7737058206	-7.75081630811
20	5.09291294257	-0.525269541951	-0.239650254712	4.3097584472	-0.105243789658	2.9822920949	-0.0455097433419	-0.19664281006	-0.171135302893	0.0300711677686	0.216279615017	0.139535823374	0.0903996096215	-0.0613136231472	0.0778220111809	0.235088345507	0.00627775901342	0.0506766941202	0.196686503767	0.0549591990431	0.261659290001	-5.32691544812	37.7740469817	-1.7149529444
21	2.12935793777	-1.03710452074	-0.171618938924	1.91462614055	-1.10717384727	6.12866498268	-0.706686600504	-0.338508758131	-1.0829849447	0.496436830774	0.0258956430061	-0.520965080657	1.67804359133	0.884263275063	0.771299262464	0.804296320606	0.18190744781	0.164721366453	0.437115036298	0.0959246231684	0.77983078645	38.0719879618	11.9318480928	36.2018078565
22	5.41725103175	0.346426017399	-0.876417790323	7.94965907917	-0.0426230354448	4.01224406684	-0.185281805145	-0.589167989996	-0.69711267059	0.46062622959	0.00302683137004	-0.458157549909	0.704853793395	0.618782220419	0.0468826942827	0.410747625442	0.108497870469	-0.0204589648642	0.412521615641	0.00849006430229	0.342536002431	36.8114225902	23.591627533	41.0891257294
23	4.85718079555	0.620570806677	-0.0977199245782	3.08102074365	0.997032450608	3.83235015169	0.0874754027022	-0.345313649741	-0.145231692354	0.0327822105751	-0.0342058497975	-0.127291945944	-0.000342273387005	0.378860512636	-0.0517633219825	0.172344448096	-0.0204549054005	0.0044124181529	0.249772062166	0.000623380016564	0.281376245061	38.322451598	37.1097849875	45.9641181723
24	4.33226698227	0.458694363569	-0.235849926896	3.24307829636	-0.834509191841	5.44737261373	0.0720538193757	0.28799626959	1.35910446383	-0.434090183582	0.0127326182098	-0.141696786473	-1.07157907386	0.44531252482	0.0442485379834	0.53897597098	-0.0908682921251	0.0526912541077	0.296754789151	0.0947750235317	0.622317675555	37.3789218587	52.6971861363	39.3633923223

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 306 through 358 )	A	A	306 - 358	1 - 49
2	2	chain 'A' and (resid 359 through 403 )	A	A	359 - 403	50 - 94
3	3	chain 'A' and (resid 404 through 455 )	A	A	404 - 455	95 - 146
4	4	chain 'A' and (resid 456 through 497 )	A	A	456 - 497	147 - 181
5	5	chain 'A' and (resid 498 through 577 )	A	A	498 - 577	182 - 253
6	6	chain 'A' and (resid 578 through 599 )	A	A	578 - 599	254 - 275
7	7	chain 'B' and (resid 306 through 344 )	B	D	306 - 344	1 - 35
8	8	chain 'B' and (resid 345 through 369 )	B	D	345 - 369	36 - 60
9	9	chain 'B' and (resid 370 through 387 )	B	D	370 - 387	61 - 78
10	10	chain 'B' and (resid 388 through 412 )	B	D	388 - 412	79 - 103
11	11	chain 'B' and (resid 413 through 475 )	B	D	413 - 475	104 - 164
12	12	chain 'B' and (resid 476 through 497 )	B	D	476 - 497	165 - 186
13	13	chain 'B' and (resid 498 through 531 )	B	D	498 - 531	187 - 215
14	14	chain 'B' and (resid 532 through 576 )	B	D	532 - 576	216 - 260
15	15	chain 'B' and (resid 577 through 599 )	B	D	577 - 599	261 - 283
16	16	chain 'C' and (resid 306 through 320 )	C	K	306 - 320	1 - 15
17	17	chain 'C' and (resid 321 through 336 )	C	K	321 - 336	16 - 29
18	18	chain 'C' and (resid 337 through 412 )	C	K	337 - 412	30 - 105
19	19	chain 'C' and (resid 413 through 577 )	C	K	413 - 577	106 - 260
20	20	chain 'C' and (resid 578 through 599 )	C	K	578 - 599	261 - 282
21	21	chain 'D' and (resid 306 through 344 )	D	T	306 - 344	1 - 35
22	22	chain 'D' and (resid 345 through 412 )	D	T	345 - 412	36 - 103
23	23	chain 'D' and (resid 413 through 514 )	D	T	413 - 514	104 - 201
24	24	chain 'D' and (resid 515 through 599 )	D	T	515 - 599	202 - 277

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