PDB-8x6q: Crystal structure of OsHSL1 L204F/F298L/I335F complexed with 2-ac...

ID or keywords:

Entry

Database: PDB / ID: 8x6q

Title

Crystal structure of OsHSL1 L204F/F298L/I335F complexed with 2-acetyl-cyclohexane-2,4-dione

Components

HPPD Inhibitor Sensitive 1-like 1 protein

Keywords

OXIDOREDUCTASE / Complex / substrate

Function / homology

Function and homology information

oxidoreductase activity / metal ion binding
Similarity search - Function

Biological species

Oryza sativa (Asian cultivated rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.39 Å

Authors

Lin, H.-Y. / Dong, J. / Yang, G.-F.

Funding support

China, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An artificially evolved gene for herbicide-resistant rice breeding.
Authors: Dong, J. / Yu, X.H. / Dong, J. / Wang, G.H. / Wang, X.L. / Wang, D.W. / Yan, Y.C. / Xiao, H. / Ye, B.Q. / Lin, H.Y. / Yang, G.F.

History

Deposition	Nov 21, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x6q.cif.gz	567 KB	Display	PDBx/mmCIF format
PDB format	pdb8x6q.ent.gz	469.2 KB	Display	PDB format
PDBx/mmJSON format	8x6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x6q_validation.pdf.gz	491.9 KB	Display	wwPDB validaton report
Full document	8x6q_full_validation.pdf.gz	508.5 KB	Display
Data in XML	8x6q_validation.xml.gz	59.3 KB	Display
Data in CIF	8x6q_validation.cif.gz	76.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/8x6q ftp://data.pdbj.org/pub/pdb/validation_reports/x6/8x6q	HTTPS FTP

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Related structure data

Related structure data	8x74C 8x7cC 8x7dC 8xc3C 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	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (3) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: HPPD Inhibitor Sensitive 1-like 1 protein

B: HPPD Inhibitor Sensitive 1-like 1 protein

C: HPPD Inhibitor Sensitive 1-like 1 protein

D: HPPD Inhibitor Sensitive 1-like 1 protein

hetero molecules

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

1

A: HPPD Inhibitor Sensitive 1-like 1 protein

hetero molecules

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

2

B: HPPD Inhibitor Sensitive 1-like 1 protein

hetero molecules

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

3

C: HPPD Inhibitor Sensitive 1-like 1 protein

hetero molecules

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

4

D: HPPD Inhibitor Sensitive 1-like 1 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.927, 58.894, 140.240
Angle α, β, γ (deg.)	89.97, 90.00, 111.98
Int Tables number	1
Space group name H-M	P1

#1: Protein	HPPD Inhibitor Sensitive 1-like 1 protein / HSL1 / Os06g0178500 protein / Putative Fe(II)/2-oxoglutarate-dependent oxygenase Mass: 39814.902 Da / Num. of mol.: 4 / Mutation: L204F, F298L, I335F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8H620
#2: Chemical	ChemComp-Y8R / 2-ethanoyl-3-oxidanyl-cyclohex-2-en-1-one Mass: 154.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₀O₃
#3: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₅H₆O₅
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.21 Å³/Da / Density % sol: 44.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-Tris, PEG3350, ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.06 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.06 Å / Relative weight: 1
Reflection	Resolution: 2.39→40 Å / Num. obs: 52378 / % possible obs: 94.4 % / Redundancy: 1.84 % / CC_1/2: 0.955 / R_merge(I) obs: 0.131 / Net I/σ(I): 4.38
Reflection shell	Resolution: 2.39→2.44 Å / R_merge(I) obs: 0.326 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2509 / CC_1/2: 0.812

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Processing

Software

Name	Version	Classification
PHENIX	(1.18.2_3874: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.39→36.4 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 32.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2954	2619	5 %
R_work	0.2493	-	-
obs	0.2516	52378	97.55 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.39→36.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11189	0	88	313	11590

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11521
X-RAY DIFFRACTION	f_angle_d	0.524	15620
X-RAY DIFFRACTION	f_dihedral_angle_d	27.418	4344
X-RAY DIFFRACTION	f_chiral_restr	0.041	1689
X-RAY DIFFRACTION	f_plane_restr	0.004	2086

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 (%)
2.39-2.44	0.3948	132	0.2931	2509	X-RAY DIFFRACTION	93
2.44-2.48	0.3632	136	0.2935	2612	X-RAY DIFFRACTION	97
2.48-2.53	0.3464	138	0.2847	2621	X-RAY DIFFRACTION	97
2.54-2.59	0.3461	138	0.2891	2624	X-RAY DIFFRACTION	97
2.59-2.65	0.3415	136	0.2949	2565	X-RAY DIFFRACTION	97
2.65-2.72	0.3482	140	0.2754	2674	X-RAY DIFFRACTION	97
2.72-2.79	0.3788	135	0.2761	2553	X-RAY DIFFRACTION	97
2.79-2.87	0.3343	139	0.2884	2655	X-RAY DIFFRACTION	98
2.87-2.96	0.3934	138	0.2869	2610	X-RAY DIFFRACTION	97
2.96-3.07	0.3135	139	0.2724	2643	X-RAY DIFFRACTION	98
3.07-3.19	0.3113	136	0.2659	2577	X-RAY DIFFRACTION	98
3.19-3.34	0.3257	139	0.2557	2652	X-RAY DIFFRACTION	98
3.34-3.51	0.2819	141	0.2488	2674	X-RAY DIFFRACTION	98
3.51-3.73	0.2473	136	0.231	2591	X-RAY DIFFRACTION	98
3.73-4.02	0.3093	139	0.2202	2633	X-RAY DIFFRACTION	98
4.02-4.43	0.252	139	0.2157	2633	X-RAY DIFFRACTION	98
4.43-5.07	0.2216	140	0.2134	2671	X-RAY DIFFRACTION	98
5.07-6.38	0.2687	139	0.2383	2638	X-RAY DIFFRACTION	98
6.38-36.4	0.2286	139	0.2229	2624	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	2.6334	1.0149	-1.5745	3.6475	-1.011	1.4646	-0.0845	0.057	-0.1518	-0.1374	-0.0378	-0.637	0.2248	0.0634	0.1204	0.3568	-0.0087	-0.0405	0.2599	-0.012	0.1756	3.2997	0.9694	-3.9905
2	1.6462	0.3706	0.303	3.086	-1.005	1.891	0.0262	-0.1643	-0.0063	0.1057	0.1725	0.2956	0.014	-0.4001	-0.1745	0.2185	-0.0107	-0	0.3389	0.0169	0.2233	-13.3532	2.5485	9.9885
3	1.4229	0.5935	-0.293	0.6296	-1.0816	3.9879	-0.0313	-0.0155	-0.1121	-0.1699	0.0517	-0.0191	0.3601	-0.1779	-0.0244	0.2738	-0.0249	-0.0081	0.1913	0.0145	0.2522	-6.2524	-6.3057	3.7195
4	1.8212	-0.1206	0.2796	3.0306	-1.8853	1.9675	-0.0792	-0.0173	-0.0374	0.4273	-0.0346	-0.4553	-0.2019	0.0657	0.1277	0.3574	-0.0298	-0.1097	0.3475	0.0482	0.3426	0.6079	-7.7693	23.197
5	4.6805	0.1856	1.2658	2.7373	0.4369	5.5432	0.0057	0.1858	0.3997	0.1092	-0.14	0.0815	-0.5811	0.2542	0.0135	0.2635	0.0264	0.0205	0.2027	-0.0625	0.2573	-29.6139	38.7946	54.7998
6	1.8757	0.8611	1.8794	2.0155	1.137	2.194	0.2345	-0.2243	-0.3925	0.2559	-0.0689	0.0176	0.3739	-0.1682	-0.1711	0.2785	0.017	-0.007	0.2617	0.0087	0.2446	-31.2224	10.11	46.5421
7	3.2436	-0.4129	-0.1132	1.8836	-0.0479	3.3681	-0.0662	0.1559	0.055	-0.0185	0.0416	-0.2124	-0.1793	0.223	-0.0009	0.2321	-0.0223	-0.0003	0.1671	0.0002	0.2355	-19.7228	32.4246	43.3779
8	2.4323	0.3502	1.6004	1.6489	0.6753	2.2514	0.0717	0.6015	-0.208	-0.1729	0.0839	-0.1278	0.211	0.55	-0.1682	0.2635	0.0496	-0.0271	0.2934	-0.0378	0.3186	-22.6867	13.4724	34.1181
9	1.0046	-0.0231	0.2915	0.9789	0.4077	2.9564	0.0628	-0.0617	-0.1454	0.0052	0.0631	0.016	0.065	-0.1271	-0.1329	0.1873	0.0307	-0.0363	0.1817	-0.0234	0.2147	-33.7866	18.249	43.7735
10	2.2435	1.0386	1.6752	3.846	1.2346	3.8067	-0.0829	0.1559	0.3075	0.0891	-0.1438	0.6698	-0.338	-0.4452	0.2492	0.2473	0.0671	0.0098	0.3559	0.0413	0.4026	-41.8185	23.5775	29.0329
11	1.1377	1.309	0.9502	3.9739	1.9702	2.9036	-0.0175	0.3187	0.1809	-0.1038	0.258	0.0785	-0.37	0.1901	-0.2031	0.2966	0.0234	0.1328	0.2977	-0.0378	0.2797	-42.0546	4.4197	71.1393
12	1.832	0.1182	-0.4543	2.0798	1.0388	1.6173	-0.0461	-0.1115	0.0101	0.1188	0.1095	-0.196	0.1401	0.3259	-0.0768	0.2229	0.0075	-0.032	0.3147	-0.0027	0.2123	-33.4236	-6.8529	79.7806
13	1.7418	-0.0338	0.6705	0.2821	0.485	3.9967	0.0931	0.0383	0.0834	-0.0397	-0.0044	-0.082	-0.218	0.0526	-0.0717	0.2456	-0.0471	0.0247	0.1746	-0.0032	0.1994	-39.6913	4.7614	73.8289
14	1.9302	1.6635	0.6986	4.251	2.3808	2.9396	-0.0518	-0.011	0.28	0.2627	-0.1723	0.6161	0.1601	-0.0327	0.2342	0.3129	0.01	0.0729	0.308	-0.0009	0.2915	-46.6188	6.2404	93.1338
15	4.0713	0.4852	-1.0476	1.5706	0.4917	9.221	-0.087	0.3301	-0.0313	0.1102	0.0278	0.05	0.6534	-0.1979	0.0602	0.224	0.0113	0.0304	0.2466	0.0385	0.2507	-40.5299	13.5693	124.9691
16	1.1809	1.4312	0.268	6.0589	-0.1666	1.2484	-0.044	-0.0062	0.079	0.5126	-0.1003	-0.5105	0.0982	0.4017	0.2304	0.263	0.0227	0.0006	0.3666	0.0781	0.3617	-26.0821	29.4405	123.7422
17	2.8463	1.7971	-1.4793	2.1583	-0.9569	2.2654	0.1885	-0.1128	0.5322	0.2128	-0.0676	0.1946	-0.4312	-0.0245	-0.1405	0.2687	0.0344	-0.002	0.2371	0.0069	0.2745	-41.1489	45.7992	113.9676
18	3.3556	-0.7121	-0.2398	2.9839	-0.4679	2.7708	-0.1755	0.381	-0.1501	-0.0668	-0.015	0.3163	0.1201	-0.3247	0.1665	0.1928	-0.0277	-0.0319	0.2273	-0.0022	0.2466	-48.1789	20.5642	113.4235
19	2.6367	0.5342	-1.7418	1.1498	0.2107	2.4787	0.3091	0.5458	0.2191	-0.1817	-0.0605	0.1513	-0.3273	-0.4052	-0.2469	0.2775	0.0884	0.002	0.2456	0.0541	0.3191	-45.2531	39.5067	104.1761
20	1.6379	-1.091	1.0793	2.8206	-0.3377	3.2859	0.031	0.0341	0.1899	0.1899	-0.0693	-0.0671	-0.0663	0.1029	0.0279	0.1905	0.0193	0.0246	0.2341	0.0381	0.1833	-33.6063	34.0633	120.1376
21	2.41	0.6159	-1.0152	1.372	-1.4831	2.2249	-0.0458	0.1378	0.1263	-0.1035	0.0488	-0.1134	-0.1367	-0.0368	0.0264	0.2048	-0.0133	-0.0002	0.1546	-0.0166	0.1759	-34.6403	35.4078	107.8993
22	3.7656	2.0406	-2.7618	4.8044	-2.3631	3.6551	-0.066	0.1334	-0.3723	-0.1008	-0.1318	-0.5753	0.0208	0.2449	0.2634	0.2572	0.0391	0.059	0.327	-0.0804	0.3499	-26.16	29.4615	99.0247

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 210 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 211 through 299 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 300 through 350 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 30 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 31 through 97 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 98 through 158 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 159 through 210 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 211 through 313 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 314 through 350 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 5 through 70 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 71 through 210 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 211 through 299 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 300 through 350 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 3 through 24 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 25 through 48 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 49 through 97 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 98 through 158 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 159 through 210 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 211 through 260 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 261 through 313 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 314 through 350 )

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