PDB-6a9d: Crystal structure of the strigolactone receptor ShHTL7 from Strig...

ID or keywords:

Entry

Database: PDB / ID: 6a9d

Title

Crystal structure of the strigolactone receptor ShHTL7 from Striga hermonthica

Components

Hyposensitive to light 7

Keywords

PLANT PROTEIN / Receptor / Strigolactones / Protein / Inhibitor

Function / homology

Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Hyposensitive to light 7

Function and homology information

Biological species

Striga hermonthica (purple witchweed)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.302 Å

Authors

Zhang, Y.Y. / Xi, Z. / Wang, D.W.

Funding support

China, 3items

Citation

Journal: To Be Published
Title: Crystal structure of the strigolactone receptor ShHTL5 from Striga hermonthica
Authors: Zhang, Y.Y. / Xi, Z. / Wang, D.W.

History

Deposition	Jul 13, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2021	Group: Database references / Category: citation / Item: _citation.unpublished_flag
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6a9d.cif.gz	228.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6a9d.ent.gz	182.7 KB	Display	PDB format
PDBx/mmJSON format	6a9d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6a9d_validation.pdf.gz	455.5 KB	Display	wwPDB validaton report
Full document	6a9d_full_validation.pdf.gz	463.5 KB	Display
Data in XML	6a9d_validation.xml.gz	21.6 KB	Display
Data in CIF	6a9d_validation.cif.gz	29.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a9/6a9d ftp://data.pdbj.org/pub/pdb/validation_reports/a9/6a9d	HTTPS FTP

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Related structure data

Related structure data	5cbkS S: Starting model for refinement
Similar structure data	3dr2-d 2oik-d 1sqn-d 3gk0-4 5t22-d 5xk2-1 6p53-d 1i4n-d 2v8w-d 3buu-d 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	#165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Hyposensitive to light 7

B: Hyposensitive to light 7

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	92.548, 92.500, 75.428
Angle α, β, γ (deg.)	90.000, 116.920, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and resid 3 through 268)
2	1	chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 3 - 268 / Label seq-ID: 17 - 282

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	(chain A and resid 3 through 268)	A	A
2	chain B	B	B

#1: Protein	Hyposensitive to light 7 Mass: 31648.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Striga hermonthica (purple witchweed) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3PNA2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.27 Å³/Da / Density % sol: 45.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 0.2M MgCl2, 20% PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 11, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 25025 / % possible obs: 99.6 % / Redundancy: 3.3 % / R_merge(I) obs: 0.098 / R_pim(I) all: 0.065 / R_rim(I) all: 0.118 / Χ²: 1.069 / Net I/σ(I): 6.6 / Num. measured all: 83014

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.34	3.2	0.386	1259	0.893	0.252	0.462	0.514	99.5
2.34-2.38	3.3	0.344	1229	0.929	0.22	0.409	0.524	99.9
2.38-2.43	3.5	0.317	1285	0.938	0.199	0.375	0.522	99.8
2.43-2.48	3.5	0.288	1222	0.94	0.182	0.342	0.621	100
2.48-2.53	3.4	0.259	1240	0.957	0.165	0.308	0.643	100
2.53-2.59	3.4	0.238	1254	0.949	0.153	0.283	0.766	99.8
2.59-2.66	3.4	0.226	1256	0.946	0.145	0.269	0.845	99.5
2.66-2.73	3.3	0.202	1253	0.947	0.134	0.244	0.933	99.8
2.73-2.81	3.2	0.179	1233	0.968	0.118	0.215	0.986	99.8
2.81-2.9	3.2	0.168	1246	0.962	0.111	0.202	1.085	99.9
2.9-3	3.5	0.158	1252	0.969	0.101	0.188	1.016	99.8
3-3.12	3.4	0.14	1258	0.976	0.09	0.167	1.164	100
3.12-3.26	3.4	0.128	1252	0.978	0.083	0.154	1.303	99.8
3.26-3.44	3.3	0.113	1265	0.982	0.074	0.135	1.396	99.5
3.44-3.65	3.1	0.1	1220	0.982	0.067	0.121	1.583	99.3
3.65-3.93	3.2	0.092	1250	0.984	0.061	0.111	1.603	99.4
3.93-4.33	3.3	0.087	1262	0.988	0.057	0.104	1.694	99.6
4.33-4.95	3.2	0.082	1250	0.985	0.055	0.099	1.594	99
4.95-6.24	3.1	0.081	1257	0.986	0.056	0.099	1.502	98.9
6.24-50	3.3	0.066	1282	0.99	0.043	0.079	1.266	98.8

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
SHELX		data reduction
SCALEPACK		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CBK

5cbk

Resolution: 2.302→39.286 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2404	1271	5.09 %
R_work	0.1831	23716	-
obs	0.186	24987	99.23 %

Solvent computation

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

Displacement parameters

B_iso max: 147.68 Å² / B_iso mean: 57.3768 Å² / B_iso min: 31.3 Å²

Refinement step

Cycle: final / Resolution: 2.302→39.286 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4216	0	6	61	4283
B_iso mean	-	-	86.03	48.92	-
Num. residues	-	-	-	-	541

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4318
X-RAY DIFFRACTION	f_angle_d	1.169	5871
X-RAY DIFFRACTION	f_chiral_restr	0.064	674
X-RAY DIFFRACTION	f_plane_restr	0.009	750
X-RAY DIFFRACTION	f_dihedral_angle_d	6.522	2590

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2416	X-RAY DIFFRACTION	8.247	TORSIONAL
1	2	B	2416	X-RAY DIFFRACTION	8.247	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 9

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.302-2.3942	0.2889	128	0.2336	2567	2695	97
2.3942-2.5031	0.3214	140	0.2229	2641	2781	100
2.5031-2.6351	0.2932	145	0.2151	2615	2760	100
2.6351-2.8001	0.2954	152	0.2255	2629	2781	100
2.8001-3.0163	0.273	137	0.2141	2641	2778	100
3.0163-3.3197	0.2666	144	0.1983	2666	2810	100
3.3197-3.7997	0.2236	150	0.1779	2619	2769	99
3.7997-4.7859	0.2075	139	0.1518	2649	2788	99
4.7859-39.2913	0.219	136	0.1703	2689	2825	99

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	8.0743	4.8885	4.1769	3.3374	3.9097	6.9276	-0.3493	0.5181	0.0353	-0.5506	0.2528	0.045	-0.8945	-0.0767	0.1912	0.6741	0.013	0.0677	0.411	0.0611	0.31	-39.0355	-10.5496	-9.3366
2	2.4	0.1066	-0.3573	0.5353	0.8482	3.5497	0.058	0.0304	0.1403	-0.0778	0.0762	-0.0416	-0.4228	0.4685	-0.1701	0.5823	-0.0206	0.1077	0.2989	-0.0053	0.3322	-25.9276	-9.8867	-0.8939
3	4.3917	3.5465	-0.2614	2.8581	-0.2586	7.6329	-0.1848	-0.4019	-1.0998	0.2486	0.4556	-0.3212	1.141	1.0563	-0.086	0.5619	0.2293	0.0448	0.6363	-0.0199	0.576	-15.8363	-29.9264	9.2844
4	5.7636	-1.4984	-0.6876	1.6874	-0.3107	5.3221	-0.0363	0.0887	-1.2901	-0.0668	-0.1552	-0.1807	1.4073	-0.4599	0.1169	0.8144	-0.0273	0.1025	0.4625	0.0373	0.6072	-32.3761	-32.0204	11.123
5	5.5382	-0.7871	3.8026	2.1642	-0.6374	2.6295	-0.0075	-0.7191	0.2634	0.2928	-0.0722	0.0089	0.4668	-0.3556	0.1104	0.6127	0.0289	0.0694	0.442	0.0035	0.3374	-37.4945	-17.7037	16.5108
6	2.0048	-0.7381	0.5109	1.6143	1.2597	6.1486	0.1756	0.1347	-1.0214	0.2152	-0.1761	0.1927	0.5074	0.1137	-0.0917	0.68	-0.0004	0.1363	0.3009	0.0035	0.475	-33.6601	-26.2036	1.3644
7	2.7136	1.6912	-0.5146	7.0637	-0.1593	4.6306	-0.0002	0.1457	0.0956	-0.1658	0.2038	0.0296	0.2	1.1208	-0.3163	0.5265	0.1251	0.1174	0.7779	0.0308	0.4893	-12.3895	-21.9686	-1.5665
8	3.658	-1.0371	-0.9373	2.4839	1.4245	4.7656	-0.0727	-0.4696	0.1104	0.1741	0.3196	-0.2968	0.0028	1.162	-0.2944	0.4587	-0.0378	-0.0037	0.543	-0.0923	0.3564	-16.3894	-12.9424	13.3841
9	4.12	0.8426	0.7238	5.4196	-0.7128	3.6147	-0.0387	-0.0307	-0.4822	-0.2074	0.0385	-0.313	0.7941	0.853	-0.0648	0.483	0.1899	0.0652	0.4843	0.0657	0.3675	-4.0962	-40.5675	-25.3544
10	5.4541	4.3038	1.7037	6.9664	0.2784	3.9651	0.1225	0.2121	-0.3626	0.2083	-0.1771	-0.5155	0.5967	0.4529	-0.0259	0.5923	0.2195	0.0126	0.5466	-0.0094	0.3086	-2.4365	-39.7706	-26.051
11	3.4073	1.2684	0.7362	7.591	2.243	5.8935	-0.0487	0.3798	-0.0815	-0.2784	0.2032	-0.8639	0.2649	1.3207	-0.159	0.465	0.0872	0.1123	0.8851	0.0356	0.4463	2.9233	-30.3155	-33.5647
12	4.7855	0.6733	-1.0369	7.1392	-0.2089	8.5883	-0.0409	0.6645	0.3356	0.5744	-0.046	0.0234	-0.127	0.3647	0.0386	0.429	0.0697	0.0464	0.406	0.0811	0.3615	-8.0821	-32.9683	-35.9632
13	4.2753	-0.3851	-1.356	6.0788	0.578	6.2458	-0.0382	0.4701	0.4099	-0.1163	-0.0515	0.3625	-0.2211	0.1963	0.0927	0.4145	0.0007	0.0089	0.407	0.0946	0.3091	-15.0937	-26.0485	-36.8331
14	4.0598	-1.629	5.3386	3.9062	-1.8302	7.0442	-1.187	-1.3001	2.1905	1.2839	0.5489	0.1348	-2.5688	0.2205	0.5224	1.1161	0.1847	-0.0043	0.8592	-0.1291	0.8146	-10.7182	-9.1789	-24.1242
15	7.2194	0.2459	-0.5253	5.4768	0.7044	5.685	0.1337	-0.8847	0.1053	0.6977	0.0156	0.2944	0.1255	0.5431	-0.0453	0.7017	0.0569	0.1388	0.5014	-0.0241	0.3916	-12.749	-24.9602	-13.5046
16	7.0373	-3.5119	3.9803	2.2851	-2.4797	2.7121	-0.4	0.5173	0.5953	0.2315	0.0589	-0.8601	-0.6595	0.2094	0.2462	0.5873	-0.0693	0.0555	0.4791	0.0064	0.463	-2.9894	-18.8959	-24.1297
17	3.7984	-0.7879	-1.2465	3.8878	0.4892	4.5206	-0.0664	0.5243	0.1441	-0.1377	0.0206	0.1936	0.0276	-0.3335	0.0548	0.4113	-0.0086	0.0287	0.4191	0.0655	0.3022	-18.394	-27.6021	-37.612
18	1.9292	0.3031	-0.2359	1.895	-0.1937	6.2008	-0.048	0.1717	-0.0016	-0.0093	0.0817	0.2636	0.5485	-0.4256	-0.0842	0.5525	-0.0052	0.0565	0.305	0.0534	0.4007	-20.3345	-38.5337	-29.1676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -6 through 14 )	A	-6 - 14
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 118 )	A	15 - 118
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 135 )	A	119 - 135
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 136 through 162 )	A	136 - 162
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 180 )	A	163 - 180
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 181 through 194 )	A	181 - 194
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 195 through 207 )	A	195 - 207
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 208 through 268 )	A	208 - 268
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 39 )	B	3 - 39
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 58 )	B	40 - 58
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 59 through 88 )	B	59 - 88
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 89 through 107 )	B	89 - 107
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 135 )	B	108 - 135
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 136 through 149 )	B	136 - 149
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 150 through 180 )	B	150 - 180
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 181 through 194 )	B	181 - 194
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 195 through 231 )	B	195 - 231
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 232 through 268 )	B	232 - 268

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