PDB-7x7z: The crystal structure of 2+2/4+2 cyclase PloI4

ID or keywords:

Entry

Database: PDB / ID: 7x7z

Title

The crystal structure of 2+2/4+2 cyclase PloI4

Components

PloI4

Keywords

LYASE / PloI4 / 2+2/4+2 Cyclase

Function / homology

AOC barrel-like / Allene oxide cyclase-like / Beta Barrel / Mainly Beta

Function and homology information

Biological species

Micromonospora sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.903 Å

Authors

Li, M. / Pan, L.F.

Funding support

China, 1items

Citation

Journal: Nat.Chem. / Year: 2023
Title: A cyclase that catalyses competing 2 + 2 and 4 + 2 cycloadditions.
Authors: Wang, H. / Zou, Y. / Li, M. / Tang, Z. / Wang, J. / Tian, Z. / Strassner, N. / Yang, Q. / Zheng, Q. / Guo, Y. / Liu, W. / Pan, L. / Houk, K.N.

History

Deposition	Mar 10, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 8, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x7z.cif.gz	227.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7x7z.ent.gz	183.8 KB	Display	PDB format
PDBx/mmJSON format	7x7z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/7x7z ftp://data.pdbj.org/pub/pdb/validation_reports/x7/7x7z	HTTPS FTP

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Related structure data

Related structure data	7x80C 7x81C 7x86C 5btuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: PloI4

B: PloI4

C: PloI4

D: PloI4

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

1

A: PloI4

C: PloI4

defined by author&software
Evidence: equilibrium centrifugation
31 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PloI4

D: PloI4

defined by author&software
31 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.659, 101.659, 234.421
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22

#1: Protein	PloI4 Mass: 15498.161 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora sp. (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.88 Å³/Da / Density % sol: 74.82 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.2 M lithium sulfate, 2.5 M sodium chloride, and 0.1 M sodium acetate/ acetic acid (pH 4.5)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.8 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. obs: 28033 / % possible obs: 99.9 % / Redundancy: 13.8 % / R_merge(I) obs: 0.239 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2.9→2.95 Å / R_merge(I) obs: 1.373 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1348

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Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5BTU

5btu

Resolution: 2.903→29.73 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2334	1348	4.83 %
R_work	0.199	26558	-
obs	0.2006	27906	99.71 %

Solvent computation

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

Displacement parameters

B_iso max: 157.99 Å² / B_iso mean: 53.7103 Å² / B_iso min: 9.12 Å²

Refinement step

Cycle: final / Resolution: 2.903→29.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4278	0	0	4	4282
B_iso mean	-	-	-	17.92	-
Num. residues	-	-	-	-	575

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.9034-3.0071	0.3037	149	0.267	2524	98
3.0071-3.1274	0.3102	139	0.2471	2590	100
3.1274-3.2696	0.3469	127	0.2479	2628	100
3.2696-3.4417	0.3214	135	0.239	2604	100
3.4417-3.657	0.2321	144	0.1957	2627	100
3.657-3.9387	0.1947	119	0.1917	2651	100
3.9387-4.334	0.1802	130	0.1826	2646	100
4.334-4.9587	0.1636	136	0.1442	2684	100
4.9587-6.2379	0.2374	130	0.2018	2728	100
6.2379-29.73	0.2292	139	0.194	2876	100

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	3.2092	-2.2373	-0.2156	1.5752	0.0823	2.1326	0.0132	0.4428	-0.7222	-0.633	-0.4907	0.9834	0.5879	-0.4913	-0.6933	0.3056	-0.1556	-0.139	0.1906	0.0738	0.6486	15.5378	-19.5446	-12.9315
2	0.1048	-0.0572	-0.1558	0.1393	0.0458	0.08	-0.0161	-0.0277	-0.2672	0.0159	-0.1401	0.3202	-0.0023	-0.2702	-0.0005	0.3441	0.0532	0.013	0.6047	0.0479	0.3854	10.5888	2.949	-19.2976
3	0.6733	-0.1995	-0.7823	0.0697	0.1649	0.9756	0.8604	0.1605	-0.2234	-0.0224	-0.0897	-0.1284	-0.7242	-0.2742	0.141	0.346	-0.1296	-0	0.3367	0.0743	0.3963	30.7752	18.4864	-24.5934
4	0.5058	0.7057	-0.0894	3.4303	1.1841	0.6731	0.0679	-0.3958	0.2922	-0.2096	-0.7955	1.1821	-0.1459	-0.3602	-0.5633	0.2302	0.0269	-0.0561	0.5255	0.095	0.4446	8.6528	-1.8105	-15.129
5	0.8248	0.2056	0.7182	0.4647	-0.3874	0.7198	0.0829	0.135	0.0048	-0.0026	0.1467	-0.1957	-0.1269	0.0993	0.0032	0.3204	-0.005	0.0214	0.3818	0.0383	0.267	20.9126	-0.3	-20.0698
6	0.9673	0.1815	0.9903	1.2158	0.1714	1.0508	0.194	0.1544	-0.2742	0.0398	0.0728	0.1838	0.2363	0.1279	-0.001	0.2603	0.0344	-0.004	0.4065	0.0054	0.2963	19.5421	-5.7514	-19.9859
7	0.5886	-0.7341	-0.8956	1.3384	1.4657	1.6724	-0.0397	-0.9312	-0.8046	0.3838	0.6976	0.4909	0.4077	0.2566	0.2812	0.43	-0.053	-0.0175	0.5339	0.2651	0.2642	19.7216	-12.9043	-4.2315
8	1.281	0.4435	-0.8995	0.7599	-0.2284	0.8153	0.1693	1.0549	0.1958	-0.5836	-0.3368	-0.328	0.2487	0.209	-0.0076	0.3639	-0.0221	-0.1182	0.4175	0.0459	0.3047	12.7613	-5.9173	-21.1332
9	0.4523	0.1851	-0.1291	0.7423	0.2263	0.2911	0.3499	-0.1735	-0.0666	0.0789	0.222	-0.0279	-0.2789	-0.2855	0.0168	0.2252	-0.0175	0.0189	0.487	-0.0496	0.3468	37.208	5.2023	9.5111
10	0.8195	0.2857	-0.1701	0.6435	-0.299	0.0155	-0.0941	-0.5203	-0.0466	0.0486	0.0283	-0.1843	-0.0426	0.1953	-0	0.2854	-0.0197	0.0174	0.51	0.0269	0.2928	31.8384	-0.7696	24.2523
11	0.6314	-0.099	-0.4281	0.4491	-0.2193	0.3594	0.4952	-0.1457	0.0813	0.1285	-0.5318	0.4192	-0.1078	0.1016	0.0231	0.2639	-0.0094	0.0122	0.3275	-0.0409	0.2823	29.1828	-3.3472	15.7098
12	0.2896	0.1979	-0.3346	0.1623	-0.2676	0.5171	-0.0883	-0.0268	0.0261	0.315	0.1777	-0.3877	0.0368	-0.0525	-0.0007	0.1689	0.0065	0.0491	0.4127	-0.0278	0.3878	33.6271	-0.9435	12.9786
13	1.0119	0.3792	-0.2809	1.4261	0.5922	1.2721	-0.0384	-0.0477	-0.0355	0.1379	0.0541	0.2824	-0.2992	0.2434	-0.0273	0.1321	0.006	0.0422	0.2248	0.0585	0.1056	36.3789	3.1444	10.3928
14	0.788	0.4485	-0.3223	0.1869	-0.1763	0.0908	0.2032	0.0459	0.2302	-0.1108	-0.1824	0.3548	-0.2741	0.0632	-0.0087	0.2647	0.0882	0.0348	0.4484	0.0075	0.2812	39.1672	-1.7934	-7.2941
15	0.5119	-0.1359	-0.4942	0.7348	0.3489	0.6788	-0.3089	0.5549	-0.0447	-0.2354	-0.1875	-0.0705	0.3956	0.3309	-0.0297	0.3627	0.0285	-0.004	0.5339	0.1233	0.2818	24.5874	9.623	-34.6366
16	0.5776	0.4826	0.0631	1.9134	-0.3037	0.8322	-0.0013	0.1228	-0.0121	0.1763	0.0171	-0.1657	-0.0288	0.0895	0.0002	0.2163	0.0407	-0.0262	0.334	-0.0041	0.2634	36.9285	1.0424	-15.3218
17	1.1148	0.1393	0.4243	1.091	-0.1084	1.3481	0.1214	-0.0015	0.0797	-0.1838	-0.1589	0.0905	0.0564	0.108	-0.0001	0.2063	0.0221	0.0082	0.2952	0.0236	0.2385	37.0361	0.8285	-9.4641
18	0.3103	-0.4969	0.4305	2.0631	-0.3076	1.3555	0.3353	0.0962	0.3501	0.1731	-0.3905	0.7469	0.3361	-0.4335	0.0883	0.0699	0.1542	0.0956	0.4338	0.1371	0.7307	8.9981	3.7938	14.9378
19	0.007	0.0798	0.0493	0.6549	0.8975	1.2271	-0.1071	-0.8605	-0.0919	0.5301	0.5528	0.3616	0.547	-0.0079	0.108	0.2734	0.108	0.0206	0.4678	0.1658	0.6317	30.4585	-16.5912	25.5048
20	0.5093	0.6176	-0.4425	0.914	-0.0081	1.339	0.0631	0.0698	0.2612	0.3313	0.1628	0.6655	0.082	-0.1868	0.1907	0.1583	-0.0303	0.0227	0.5481	0.1693	0.5154	10.8186	-1.8707	14.5499
21	0.713	-0.3001	-0.4638	1.0023	-0.373	0.5099	0.1006	-0.0878	0.2615	0.1258	-0.1701	0.3535	0.2426	0.273	0.0017	0.2543	-0.0499	0.0531	0.4033	0.0281	0.3644	20.033	1.1561	21.5972
22	0.2114	0.0548	-0.2655	0.9474	0.1631	0.3539	-0.2865	0.018	0.9483	-0.4374	-0.1931	0.3384	0.5555	-0.2312	-0.0619	0.302	-0.0528	0.0273	0.4354	-0.039	0.3602	16.3553	4.8823	12.9104
23	0.6352	-0.4575	0.4952	0.6553	0.4589	2.2967	-0.1446	-0.1363	0.0861	0.2143	-0.373	0.5697	-0.543	-0.0658	-1.3477	0.1317	0.059	0.2672	0.2874	-0.0672	0.3261	14.9684	4.6335	24.7515
24	0.2021	0.1704	0.1995	1.2584	1.1109	0.96	0.4709	1.0531	0.7538	-0.6964	0.6358	-0.1384	-0.2843	0.2213	0.1274	0.3451	0.0807	0.0546	0.5353	0.2322	0.4019	16.6752	12.0287	3.3761
25	0.4798	0.4829	1.0372	0.3223	0.7026	1.763	-0.0073	-0.7677	0.264	0.1114	0.0125	0.1542	0.1082	-0.0652	-0.0088	0.3995	0.113	0.1615	0.4843	0.0912	0.4917	8.7907	3.5592	19.2223

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 3 through 11 )	A	3 - 11
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 21 )	A	12 - 21
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 22 through 40 )	A	22 - 40
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 through 54 )	A	41 - 54
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 55 through 83 )	A	55 - 83
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 84 through 110 )	A	84 - 110
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 111 through 118 )	A	111 - 118
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 119 through 145 )	A	119 - 145
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 21 )	B	1 - 21
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 22 through 67 )	B	22 - 67
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 68 through 83 )	B	68 - 83
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 84 through 102 )	B	84 - 102
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 103 through 145 )	B	103 - 145
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 21 )	C	1 - 21
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 22 through 40 )	C	22 - 40
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 41 through 83 )	C	41 - 83
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 84 through 145 )	C	84 - 145
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 4 through 21 )	D	4 - 21
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 22 through 40 )	D	22 - 40
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 41 through 67 )	D	41 - 67
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 68 through 83 )	D	68 - 83
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 84 through 96 )	D	84 - 96
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 97 through 110 )	D	97 - 110
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 111 through 118 )	D	111 - 118
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 119 through 145 )	D	119 - 145

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