PDB-6fg7: Crystal structure of the BIR2 ectodomain from Arabidopsis thaliana.

ID or keywords:

Entry

Database: PDB / ID: 6fg7

Title

Crystal structure of the BIR2 ectodomain from Arabidopsis thaliana.

Components

Inactive LRR receptor-like serine/threonine-protein kinase BIR2

Keywords

PROTEIN BINDING / leucine rich repeat receptor /

membrane receptor /

pseudokinase /

ectodomain

Function / homology

Function and homology information

regulation of defense response to fungus / negative regulation of defense response to bacterium /

chloroplast / defense response /

nucleotide binding /

plasma membrane /

cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Hothorn, M. / Hohmann, U.

Funding support

Switzerland, 1items

Citation

Journal: Nat Plants / Year: 2018
Title: The SERK3 elongated allele defines a role for BIR ectodomains in brassinosteroid signalling.
Authors: Hohmann, U. / Nicolet, J. / Moretti, A. / Hothorn, L.A. / Hothorn, M.

History

Deposition	Jan 10, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 24, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 16, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Sep 5, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6fg7.cif.gz	165.2 KB	Display	PDBx/mmCIF format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fg/6fg7 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/6fg7	HTTPS FTP

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Related structure data

Related structure data	6fg8C 6g3wC C: citing same article (ref.)
Similar structure data	4ggg-1 1tbx-d 5l0f-1 1r1m-d 4x2m-2 1vei-d 5xnv-d 5l0i-d 5nwp-1 1c05-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#248 - Aug 2020 Phytosulfokine Receptor similarity (4) #143 - Nov 2011 Toll-like Receptors similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #245 - May 2020 Spliceosomes similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: Inactive LRR receptor-like serine/threonine-protein kinase BIR2

B: Inactive LRR receptor-like serine/threonine-protein kinase BIR2

hetero molecules

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

1

A: Inactive LRR receptor-like serine/threonine-protein kinase BIR2

hetero molecules

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

2

B: Inactive LRR receptor-like serine/threonine-protein kinase BIR2

hetero molecules

defined by author
28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	153.770, 153.770, 110.055
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	181
Space group name H-M	P6₄22

Components on special symmetry positions

ID	Model	Components
1	1	A-1162- HOH

#1: Protein

Inactive LRR receptor-like serine/threonine-protein kinase BIR2 / Protein BAK1-INTERACTING RECEPTOR-LIKE KINASE 2

Mass: 27731.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Arabidopsis thaliana (thale cress) / Gene: BIR2, At3g28450, MFJ20.14 / Organ: seedling / Cell line (production host): 38 / Production host:

Trichoplusia ni (cabbage looper) / References: UniProt: Q9LSI9

#2: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide

/ Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-MLI / MALONATE ION /

Malonic acid

Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.68 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1.8 M sodium malonate pH 4.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 1.9→45.77 Å / Num. obs: 60341 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / B_iso Wilson estimate: 35 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.221 / R_sym value: 0.213 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.9→2.02 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 9433 / CC_1/2: 0.429 / R_rim(I) all: 2.88 / R_sym value: 2.77 / % possible all: 97.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→45.77 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.949 / SU B: 8.347 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23267	3017	5 %	RANDOM
R_work	0.21444	-	-	-
obs	0.21535	57323	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 37.278 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.57 Å²	0.28 Å²	0 Å²
2-	-	0.57 Å²	-0 Å²
3-	-	-	-1.83 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→45.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2944	0	59	119	3122

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	3117
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2900
X-RAY DIFFRACTION	r_angle_refined_deg	1.336	1.993	4243
X-RAY DIFFRACTION	r_angle_other_deg	0.929	3	6699
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.8	5	397
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.857	24.861	144
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.743	15	514
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.276	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	481
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	3581
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	711
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.491	1.775	1552
X-RAY DIFFRACTION	r_mcbond_other	0.485	1.772	1551
X-RAY DIFFRACTION	r_mcangle_it	0.885	2.655	1940
X-RAY DIFFRACTION	r_mcangle_other	0.886	2.657	1941
X-RAY DIFFRACTION	r_scbond_it	0.784	1.936	1564
X-RAY DIFFRACTION	r_scbond_other	0.783	1.934	1562
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.26	2.883	2296
X-RAY DIFFRACTION	r_long_range_B_refined	4.191	21.752	3355
X-RAY DIFFRACTION	r_long_range_B_other	4.147	21.555	3338
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.901→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.387	211	-
R_work	0.391	4026	-
obs	-	-	96.12 %

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	10.0033	0.551	1.226	4.7015	0.5011	1.7334	-0.0061	-0.2405	0.624	-0.0811	0.0495	0.0461	-0.3557	-0.0256	-0.0434	0.2039	0.0007	0.0697	0.2915	-0.0591	0.1463	93.531	76.8758	26.2658
2	4.4378	-0.1311	0.6198	1.9333	1.6124	6.4919	0.0177	-0.1737	0.2065	0.0941	-0.0422	0.0034	-0.2636	-0.4293	0.0244	0.067	-0.0532	0.0379	0.4343	-0.0174	0.0573	86.2416	66.7375	26.4194
3	15.1238	1.5124	1.0377	5.1061	-0.9149	3.2552	0.1693	-0.5047	-0.089	0.253	0.1827	-0.6464	0.2737	0.1515	-0.3519	0.171	0.0117	-0.0242	0.2644	-0.0486	0.2471	101.4015	64.01	27.6764
4	9.6379	-1.955	-6.1713	10.8346	0.4538	9.3664	-0.2462	-1.3151	-0.1035	1.5801	0.2025	-0.9416	-0.7145	1.0001	0.0437	0.4112	-0.1279	-0.0511	0.5535	-0.0707	0.2547	101.302	68.359	31.2007
5	9.2964	2.7245	1.8336	1.849	1.2333	2.8348	0.3445	-0.1917	-0.4961	-0.0013	-0.1873	-0.1392	0.0805	-0.5355	-0.1572	0.1145	-0.0359	0.0315	0.3435	-0.0088	0.0613	90.4274	65.0822	15.8731
6	6.0428	1.7516	0.0835	6.6624	3.2697	5.4878	0.1677	-0.229	0.4264	0.0584	0.0519	-0.1385	-0.4372	-0.2844	-0.2196	0.1478	-0.0291	0.0686	0.2721	-0.0166	0.0721	96.5645	72.3959	18.1023
7	6.4585	-0.4228	2.5375	4.1755	0.8348	3.2507	0.3942	-0.0971	0.6817	-0.2188	-0.2944	0.0989	-0.3522	-0.8433	-0.0998	0.1655	0.1031	0.1455	0.4881	0.075	0.1698	91.5324	71.4277	8.9538
8	3.3604	0.071	0.6575	2.0914	0.6565	4.2831	0.107	-0.057	0.2696	-0.1506	0.0648	-0.1507	-0.5455	-0.4455	-0.1717	0.1131	-0.0112	0.0589	0.2418	-0.0184	0.0497	100.135	71.2539	8.7296
9	9.8731	-2.7205	0.8203	4.2635	-0.9537	4.131	0.22	0.3	0.7794	-0.5279	0.0342	-0.095	-0.45	-0.6881	-0.2542	0.1769	0.0492	0.0574	0.2994	0.0327	0.101	98.2841	70.86	-1.3611
10	1.5197	-2.6174	-1.1871	5.4586	-0.3985	7.2124	0.107	-0.0663	0.2823	0.1001	0.1209	-0.4907	-0.7929	0.0643	-0.2279	0.1416	-0.0637	0.0816	0.1527	-0.0291	0.1542	107.9059	65.9147	5.1447
11	5.635	-0.927	2.2442	3.7725	0.1446	4.3001	0.0625	0.23	0.3085	-0.1133	-0.0558	-0.223	-0.3979	-0.4308	-0.0067	0.1432	-0.0114	0.0402	0.1834	0.0133	0.0324	104.2929	66.7466	-5.7785
12	4.2392	0.3776	4.2263	2.0552	-0.4577	9.9076	0.146	0.3428	-0.3548	-0.1456	0.0876	0.0121	0.3455	-0.3918	-0.2336	0.1295	-0.0258	0.0197	0.2267	-0.0229	0.051	103.217	62.0101	-7.9513
13	4.3205	5.9213	-1.8909	12.7791	1.7244	4.8242	-0.0419	-0.0248	-0.2894	0.2922	0.2954	-0.8217	0.3612	0.3313	-0.2535	0.395	-0.0312	0.0691	0.2875	-0.0312	0.2599	114.8066	42.4445	-10.8292
14	2.7507	3.6796	-1.4502	7.926	-2.0247	3.4842	-0.0695	-0.0025	-0.2421	-0.1404	0.1218	0.1782	0.0806	-0.1229	-0.0523	0.2928	-0.0212	0.0214	0.1672	-0.0269	0.1897	106.3203	35.4806	-9.0721
15	2.8895	1.8266	-0.22	6.3362	-1.206	6.3281	-0.1855	0.3955	0.0467	-0.5737	0.1205	-0.1494	0.2606	-0.0071	0.0649	0.3934	-0.1757	-0.0231	0.1812	-0.0172	0.0557	98.2363	37.9385	-9.3586
16	1.1337	0.9303	1.8902	9.1575	0.4155	4.8269	0.121	0.2681	-0.0578	-0.3583	0.0221	-0.3029	0.0782	-0.1276	-0.1431	0.2802	0.0203	0.0183	0.3557	0.0106	0.1647	104.8262	50.3463	-14.2297
17	9.2699	5.7718	-6.297	3.6151	-3.9907	6.3724	0.102	-0.0877	0.4629	0.0262	0.0077	0.2868	0.0545	-0.067	-0.1098	0.2128	-0.0433	-0.0263	0.216	-0.0119	0.1573	100.9461	45.9746	-1.0304
18	2.2196	2.9398	-0.8913	6.1694	-0.6143	3.091	-0.0929	0.1168	-0.2732	-0.3846	0.1694	-0.3976	0.6571	0.2332	-0.0765	0.3304	-0.0513	-0.0307	0.1694	-0.0411	0.0498	107.1267	39.869	-0.4495
19	5.2393	-1.126	-0.1314	10.3685	-3.5053	2.3701	0.0888	-0.1557	-0.135	-0.2682	0.2106	0.9618	0.4264	-0.0935	-0.2994	0.2717	-0.1375	-0.0114	0.1582	-0.0047	0.0961	100.6298	39.996	5.9822
20	9.696	4.6345	-4.7524	4.7838	-4.9939	6.4063	-0.0331	0.108	-0.5947	-0.1129	-0.2975	-0.6628	0.4935	0.371	0.3306	0.352	0.0014	-0.046	0.135	0.0046	0.2149	112.5706	38.1782	7.2118
21	2.1558	0.6049	0.8547	5.1549	-2.6918	4.4224	0.0795	0.0035	-0.1661	-0.0698	-0.2286	-0.3013	0.6358	0.2436	0.1491	0.2428	-0.0609	0.0126	0.1211	-0.001	0.0361	110.7699	44.8894	8.7361
22	2.8261	2.5024	-1.7947	4.5447	-3.1913	5.0023	0.0898	-0.2762	-0.0051	0.1955	-0.307	-0.1807	0.3282	0.0696	0.2172	0.2472	-0.1019	-0.0278	0.1173	-0.0069	0.0321	112.461	49.1063	16.5581
23	8.5585	-6.1921	3.6818	11.3813	-3.4251	9.7624	-0.2089	-0.4371	0.5107	0.3761	-0.1146	-0.6336	-0.1985	0.2072	0.3235	0.1889	-0.1493	-0.0142	0.189	0.0145	0.1426	114.2081	55.6054	22.0513
24	3.6489	3.4051	0.0136	7.5799	-1.2276	9.5652	0.1151	-0.504	0.3596	0.5339	-0.282	-0.4073	0.0783	-0.387	0.1669	0.2606	-0.1181	-0.0216	0.2416	-0.0798	0.1735	107.9001	50.4096	25.2173

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	29 - 39
2	X-RAY DIFFRACTION	2	A	40 - 69
3	X-RAY DIFFRACTION	3	A	70 - 74
4	X-RAY DIFFRACTION	4	A	75 - 80
5	X-RAY DIFFRACTION	5	A	81 - 93
6	X-RAY DIFFRACTION	6	A	94 - 108
7	X-RAY DIFFRACTION	7	A	109 - 123
8	X-RAY DIFFRACTION	8	A	124 - 157
9	X-RAY DIFFRACTION	9	A	158 - 171
10	X-RAY DIFFRACTION	10	A	172 - 181
11	X-RAY DIFFRACTION	11	A	182 - 198
12	X-RAY DIFFRACTION	12	A	199 - 217
13	X-RAY DIFFRACTION	13	B	29 - 33
14	X-RAY DIFFRACTION	14	B	34 - 42
15	X-RAY DIFFRACTION	15	B	43 - 71
16	X-RAY DIFFRACTION	16	B	72 - 80
17	X-RAY DIFFRACTION	17	B	81 - 86
18	X-RAY DIFFRACTION	18	B	87 - 106
19	X-RAY DIFFRACTION	19	B	107 - 113
20	X-RAY DIFFRACTION	20	B	114 - 123
21	X-RAY DIFFRACTION	21	B	124 - 163
22	X-RAY DIFFRACTION	22	B	164 - 189
23	X-RAY DIFFRACTION	23	B	190 - 199
24	X-RAY DIFFRACTION	24	B	200 - 216

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