PDB-4q3g: Structure of the OsSERK2 leucine rich repeat extracellular domain

ID or keywords:

Entry

Database: PDB / ID: 4q3g

Title

Structure of the OsSERK2 leucine rich repeat extracellular domain

Components

OsSERK2

Keywords

TRANSFERASE /

Leucine rich repeat /

toll-like receptors /

brassinosteroid

Function / homology

Function and homology information

protein kinase activity /

phosphorylation /

ATP binding /

membrane
Similarity search - Function

Biological species

Oryza sativa (Asian cultivated rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.787 Å

Authors

McAndrew, R.P. / Pruitt, R.N. / Kamita, S.G. / Pereira, J.H. / Majumder, D. / Hammock, B.D. / Adams, P.D. / Ronald, P.C.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of the OsSERK2 leucine-rich repeat extracellular domain.
Authors: McAndrew, R. / Pruitt, R.N. / Kamita, S.G. / Pereira, J.H. / Majumdar, D. / Hammock, B.D. / Adams, P.D. / Ronald, P.C.

History

Deposition	Apr 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2014	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4q3g.cif.gz	180.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4q3g.ent.gz	149.5 KB	Display	PDB format
PDBx/mmJSON format	4q3g.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3g ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3g	HTTPS FTP

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Related structure data

Related structure data	4q3iC C: citing same article (ref.)
Similar structure data	4q3i-2 5mik-d 4z3f-d 2xp1-d 4omz-4 6jle-d 1u2w-1 4po4-2 3jth-d 3b57-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 (5) #143 - Nov 2011 Toll-like Receptors similarity (4) #68 - Aug 2005 Neurotrophins similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: OsSERK2

B: OsSERK2

hetero molecules

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

1

A: OsSERK2

hetero molecules

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

2

B: OsSERK2

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.900, 81.656, 126.489
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

OsSERK2

Mass: 27257.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Oryza sativa (Asian cultivated rice) / References: UniProt: Q01JP8*PLUS

#2: Sugar

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

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

#3: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.36 Å³/Da / Density % sol: 47.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Bis-Tris pH 6.5, 200 mM MgCl2, and 23% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2013
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.78→50 Å / Num. all: 14452 / Num. obs: 13469 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.78→2.8 Å / % possible all: 94.5

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.phaser: dev_1525)	model building
PHENIX	(phenix.refine: dev_1616)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	dev_1525	phasing

Refinement

Resolution: 2.787→42.579 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 34.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2767	508	4.98 %
R_work	0.2387	-	-
obs	0.2406	10204	75.64 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.787→42.579 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3422	0	28	15	3465

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	3526
X-RAY DIFFRACTION	f_angle_d	0.902	4803
X-RAY DIFFRACTION	f_dihedral_angle_d	11.716	1297
X-RAY DIFFRACTION	f_chiral_restr	0.032	563
X-RAY DIFFRACTION	f_plane_restr	0.004	620

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 (%)
2.7867-3.067	0.3562	63	0.2838	1196	X-RAY DIFFRACTION	38
3.067-3.5107	0.337	126	0.2832	2446	X-RAY DIFFRACTION	78
3.5107-4.4223	0.2676	155	0.2235	2953	X-RAY DIFFRACTION	93
4.4223-42.5839	0.2472	164	0.2248	3101	X-RAY DIFFRACTION	93

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	3.2849	0.5233	0.7122	0.7877	-0.3862	1.311	-0.0239	0.2054	0.5723	-0.2912	-0.4451	0.0269	-0.3434	-0.0465	0.3098	0.3975	-0.0887	-0.1376	0.7687	0.1689	0.2669	5.5102	50.2643	62.2595
2	4.3263	-0.9384	0.7888	3.2884	-1.8654	2.4107	0.0593	-0.0667	-0.5307	-0.8777	0.0909	0.0738	-0.041	-0.7212	-0.2075	0.5665	-0.1993	-0.1063	0.7722	-0.1515	0.2714	-0.2324	44.5731	65.5512
3	1.4844	-1.1848	1.1507	1.2001	0.3828	7.5751	-0.2591	-0.6397	-0.0854	0.2846	-0.4116	0.0166	-0.8171	0.2261	0.493	0.3009	-0.1256	-0.1127	0.3424	0.0984	0.5596	3.0666	50.766	74.9149
4	1.8396	-1.642	0.5524	5.4023	3.5863	6.2407	0.3011	-0.2017	-0.2283	0.0894	-0.7057	0.0588	0.2709	-0.3714	0.3611	0.2148	-0.0702	-0.0892	0.3999	0.0539	0.1615	11.2295	43.4923	70.8308
5	4.049	1.8466	0.2854	1.7929	0.5828	1.3853	0.0553	0.0172	-0.3212	-0.0284	0.0945	-0.0755	0.1965	-0.2155	0.0341	0.2563	-0.2808	-0.0873	0.5268	0.1754	0.4227	19.2194	43.0808	66.5417
6	2.7384	-0.212	0.4635	3.883	1.643	3.9299	0.3113	0.313	0.0068	-0.2192	-0.277	-0.5087	-0.3295	-0.1816	0.0364	0.1395	-0.0232	-0.0328	0.2137	0.009	0.2554	23.0352	43.6623	76.0885
7	4.6142	0.0609	-0.968	3.9276	-0.5889	2.4012	-0.047	0.053	0.2488	-0.6429	0.1565	-0.0448	0.1195	-0.0585	-0.0907	0.2178	-0.1621	-0.0158	0.2813	-0.025	0.24	30.8373	37.5851	79.0689
8	0.9129	0.2135	-0.1966	0.7146	0.4119	1.0694	-0.0461	-0.1094	0.2359	-0.0582	0.2553	-0.1071	0.2026	0.0161	0.34	0.4292	-0.2473	-0.1292	0.2313	-0.1683	0.1983	32.7462	36.1854	82.6208
9	4.1578	0.9591	0.444	3.8864	2.021	1.6431	-0.2862	-0.4915	-0.3696	0.2729	0.0428	0.2963	0.5583	-0.3791	0.1698	0.2656	-0.1634	-0.0704	0.2211	0.0428	0.3089	34.4797	35.1713	88.5378
10	0.4702	0.1173	0.6044	0.5803	0.3676	2.1116	0.165	-0.3072	-0.2392	-0.1661	-0.0482	-0.0246	0.2364	0.118	0.1623	0.6141	0.02	-0.0574	0.4217	0.0981	0.0701	42.1578	27.8943	84.7753
11	0.1595	0.1879	0.2464	2.7469	-0.1627	0.4632	0.1053	-0.3226	-0.2603	0.5045	-0.3041	-0.3388	-0.1048	0.0412	0.3571	0.4169	-0.1988	0.1261	0.7838	0.0523	0.322	-19.1746	32.1693	117.6129
12	1.8089	-0.4446	-0.5966	0.521	-0.7357	2.0928	0.0034	-0.1077	0.2101	0.0651	0.1584	-0.0592	-0.0193	-0.7173	0.2	0.1782	-0.1307	0.1095	0.5286	-0.1622	0.1119	-25.3642	37.0913	114.4471
13	4.4072	1.6386	0.7436	1.4581	1.0582	3.4506	0.2501	-0.1211	0.3333	0.1428	-0.2028	0.001	0.4279	-0.267	-0.0565	0.3165	-0.0307	0.0664	0.252	-0.0372	0.2204	-13.6973	36.2412	107.8713
14	2.1368	-0.0981	0.9547	2.1385	1.669	3.6012	0.1075	-0.5027	0.0731	-0.0696	0.0014	0.1964	0.0421	0.2342	-0.2094	0.2054	-0.1217	0.0486	0.3606	-0.1967	0.1029	-1.0125	39.4242	105.6707
15	4.0855	-0.0137	-0.4313	0.9971	0.6369	1.1195	0.0237	0.1853	-0.018	0.7629	-0.089	-0.1848	0.0575	-0.0667	0.0818	0.3783	0.0069	0.0238	0.1105	0.0209	0.2007	4.9603	39.8504	100.2534
16	3.1217	-0.1597	-0.0308	3.8235	1.0405	2.062	-0.0396	0.0649	0.2341	-0.5607	0.1099	-0.0103	-0.0791	0.346	0.015	0.2193	-0.1065	-0.0318	0.3175	0.0386	0.2485	8.6215	45.7248	94.8267
17	8.3258	-1.9114	-2.9629	4.8903	1.2538	3.4471	0.2131	-0.7417	0.6769	-0.1512	0.0521	-0.0845	-0.2134	0.0025	-0.155	0.1598	-0.0717	-0.0162	0.3849	-0.156	0.396	17.2827	53.5032	95.3452

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 44 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 80 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 81 through 108 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 109 through 120 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 121 through 173 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 174 through 191 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 192 through 213 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 214 through 232 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 233 through 248 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 31 through 44 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 45 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 132 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 133 through 163 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 164 through 191 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 192 through 232 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 233 through 248 )

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