PDB-9jqg: Crystal structure of rice DWARF14 in complex with Cyclo(L-Leu-L-Pro)

ID or keywords:

Entry

Database: PDB / ID: 9jqg

Title

Crystal structure of rice DWARF14 in complex with Cyclo(L-Leu-L-Pro)

Components

Strigolactone esterase D14

Keywords

HYDROLASE / OsD14 / Cyclo / Strigolactone

Function / homology

Function and homology information

strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm
Similarity search - Function

Biological species

Oryza sativa Japonica Group (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Wang, Q.X. / Feng, Q.X. / Wang, B. / Bai, Y.

Funding support

China, 2items

Citation

Journal: Cell / Year: 2025
Title: Root microbiota regulates tiller number in rice.
Authors: Zhang, J. / Wang, B. / Xu, H. / Liu, W. / Yu, J. / Wang, Q. / Yu, H. / Wei, J.W. / Dai, R. / Zhou, J. / He, Y. / Zou, D. / Yang, J. / Ban, X. / Hu, Q. / Meng, X. / Liu, Y.X. / Wang, B. / Hu, ...

History

Deposition	Sep 27, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release
Revision 1.1	Jun 25, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jqg.cif.gz	237.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9jqg.ent.gz		Display	PDB format
PDBx/mmJSON format	9jqg.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9jqg_validation.pdf.gz	833.1 KB	Display	wwPDB validaton report
Full document	9jqg_full_validation.pdf.gz	838.6 KB	Display
Data in XML	9jqg_validation.xml.gz	31.7 KB	Display
Data in CIF	9jqg_validation.cif.gz	44.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jq/9jqg ftp://data.pdbj.org/pub/pdb/validation_reports/jq/9jqg	HTTPS FTP

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Related structure data

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	#100 - Apr 2008 Adrenergic Receptors similarity (1) #193 - Jan 2016 Siderocalin similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: Strigolactone esterase D14

B: Strigolactone esterase D14

hetero molecules

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

1

A: Strigolactone esterase D14

hetero molecules

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

2

B: Strigolactone esterase D14

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.093, 88.560, 119.202
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2 Mass: 29420.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host: Escherichia coli (E. coli) References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds

#1: Protein

Strigolactone esterase D14 / Protein DWARF 14 / Protein DWARF 88 / Protein HIGH-TILLERING DWARF 2

Mass: 29420.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Oryza sativa Japonica Group (Japanese rice)
Gene: D14, D88, HTD2, Os03g0203200, LOC_Os03g10620 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q10QA5, Hydrolases; Acting on ester bonds

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Non-polymers , 7 types, 530 molecules

#2: Chemical	ChemComp-A1EBP / (3~{S},8~{a}~{S})-3-(2-methylpropyl)-2,3,6,7,8,8~{a}-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Cyclo(L-Leu-L-Pro) Type: peptide-like / Mass: 210.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-BEZ / BENZOIC ACID Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₆O₂
#5: Chemical	ChemComp-PDO / 1,3-PROPANDIOL Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₂
#6: Chemical	ChemComp-BU1 / 1,4-BUTANEDIOL Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#7: Chemical	ChemComp-PGO / S-1,2-PROPANEDIOL Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 518 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
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: 2.16 Å³/Da / Density % sol: 43.18 %
Crystal grow	Temperature: 291.16 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1,6-Hexanediol;1-Butanol; 1,2-Propanediol (racemic); 2-Propanol;1,4 Butanediol;1,3-Propanediol ;Imidazole;MES;Glycerol;PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2024
Radiation	Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.5→48.09 Å / Num. obs: 81350 / % possible obs: 99.7 % / Redundancy: 5.5 % / R_merge(I) obs: 0.065 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3893 / CC_1/2: 0.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX	(1.20.1_4487: ???)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→44.6 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1885	2000	2.46 %
R_work	0.1694	-	-
obs	0.1698	81150	99.51 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→44.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4146	0	81	518	4745

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007
X-RAY DIFFRACTION	f_angle_d	0.886
X-RAY DIFFRACTION	f_dihedral_angle_d	12.728	677
X-RAY DIFFRACTION	f_chiral_restr	0.06	697
X-RAY DIFFRACTION	f_plane_restr	0.008	793

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 (%)
1.5-1.54	0.3055	138	0.2997	5466	X-RAY DIFFRACTION	98
1.54-1.58	0.2853	142	0.25	5592	X-RAY DIFFRACTION	100
1.58-1.63	0.2743	142	0.2212	5642	X-RAY DIFFRACTION	100
1.63-1.68	0.2222	142	0.1973	5611	X-RAY DIFFRACTION	100
1.68-1.74	0.2466	141	0.1909	5607	X-RAY DIFFRACTION	100
1.74-1.81	0.2226	143	0.1934	5637	X-RAY DIFFRACTION	100
1.81-1.9	0.2183	142	0.1963	5628	X-RAY DIFFRACTION	100
1.9-2	0.2286	142	0.1834	5623	X-RAY DIFFRACTION	100
2-2.12	0.2192	142	0.1711	5628	X-RAY DIFFRACTION	100
2.12-2.28	0.1718	144	0.1611	5699	X-RAY DIFFRACTION	100
2.28-2.51	0.1733	144	0.1556	5706	X-RAY DIFFRACTION	100
2.51-2.88	0.1804	144	0.155	5705	X-RAY DIFFRACTION	100
2.88-3.63	0.1586	145	0.1497	5720	X-RAY DIFFRACTION	99
3.63-44.6	0.1508	149	0.1525	5886	X-RAY DIFFRACTION	98

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	9.8004	2.1308	-4.444	6.8997	1.3384	2.8402	-0.119	0.6856	-0.0153	-0.6376	0.1127	0.1414	0.1328	-0.2503	0.0059	0.1112	-0.0106	-0.0216	0.0995	-0.0055	0.101	-10.0012	-5.4453	-19.0119
2	1.5514	-0.1783	-0.7002	2.4859	-0.5549	4.4835	-0.089	-0.0541	-0.0516	0.02	0.0531	0.0471	0.1948	-0.1894	0.0385	0.0723	0.0023	-0.001	0.0553	-0.0092	0.0815	-10.6698	-1.821	-6.814
3	1.2824	0.4523	0.031	0.8613	0.0968	0.6301	0.0014	-0.0264	0.0563	-0.0136	0.0088	-0.0219	-0.0434	0.0639	-0.0095	0.0993	0.0071	0.005	0.0964	-0.0027	0.0849	-5.3683	11.5071	-12.1014
4	1.5718	-0.866	0.6058	2.3691	-1.2719	1.9642	-0.0485	-0.2164	0.0575	0.1841	0.0563	0.0761	-0.0885	-0.1473	-0.0023	0.0971	0.0044	0.0215	0.1043	-0.032	0.0787	-15.6612	13.0455	-1.0084
5	2.0017	0.1047	6.3477	3.975	-3.7363	8.5205	-0.2671	1.0509	-0.125	-0.7603	0.1927	-0.1431	-0.0923	0.5703	0.0774	0.1635	-0.0258	0.0347	0.2665	0.0029	0.1666	14.7057	-8.0693	4.6172
6	5.7494	0.4889	3.0099	3.0021	0.4939	3.4609	-0.017	-0.039	0.1524	0.153	-0.0552	0.0657	-0.1918	0.0207	0.0686	0.105	-0.0217	0.0225	0.0751	0.0293	0.0526	13.3514	-7.0001	19.4942
7	4.2206	-0.1573	1.0245	2.806	0.0968	1.7777	0.0685	0.2854	-0.1837	-0.2367	-0.0373	0.0203	0.0569	0.124	-0.0387	0.1176	-0.0069	0.0282	0.1141	0.0072	0.0559	11.3701	-13.9884	8.8937
8	6.389	0.9213	-1.0263	2.988	0.1465	2.3863	-0.0541	0.0303	-0.1584	-0.0015	-0.0159	0.1283	0.0994	-0.1417	0.07	0.0892	0.006	-0.0062	0.0624	0.0015	0.0604	5.9186	-22.6319	20.1691
9	6.3281	-2.0478	0.5787	9.6682	-7.6162	2.0012	-0.1837	-0.0174	-0.4339	-0.0627	0.104	0.176	0.4792	-0.2615	0.0798	0.2076	-0.0271	0.0288	0.2213	-0.0586	0.2088	-15.354	-17.3511	16.0629
10	6.2223	0.788	7.4938	1.0167	0.5099	9.2356	0.0267	-0.1172	-0.1599	0.0577	0.1569	0.0258	-0.0287	-0.2255	-0.1835	0.0816	0.0147	0.0037	0.1267	-0.0037	0.1245	-10.1588	-5.9214	18.9854
11	2.5165	-0.1338	1.5769	4.6296	0.6436	8.2999	-0.0078	0.0051	0.2472	0.0355	-0.0842	0.031	-0.8358	-0.2902	0.0916	0.1433	0.0219	0.0095	0.1195	0.0004	0.1359	-2.7976	-0.7572	20.5315
12	4.4689	-6.1231	3.8381	8.4253	-5.2113	3.359	-0.0116	0.014	-0.2239	-0.0354	0.131	0.2196	0.0156	-0.1195	-0.1201	0.1067	-0.0141	0.0036	0.1049	-0.0094	0.0993	-1.9187	-20.7087	13.2824
13	4.2814	-3.2937	-2.3769	5.4952	3.0684	2.4294	-0.1015	-0.2601	-0.087	0.3368	0.1162	0.0294	0.193	0.0493	-0.011	0.1285	-0.0027	0.0001	0.0925	0.0182	0.0675	6.3814	-21.7112	29.646
14	9.3842	-2.1654	-0.1291	2.32	0.2945	0.9869	-0.1495	-0.3133	0.0655	0.177	0.0792	-0.0788	-0.0241	0.0392	0.0694	0.1451	-0.0243	-0.021	0.1341	-0.0024	0.084	11.7032	-9.6652	29.8574

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 50 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 110 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 245 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 246 through 318 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 51 through 66 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 67 through 91 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 92 through 140 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 141 through 187 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 188 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 214 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 215 through 231 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 232 through 255 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 256 through 291 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 292 through 318 )

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