PDB-9lei: Nitrile synthetase ArtA

ID or keywords:

Entry

Database: PDB / ID: 9lei

Title

Nitrile synthetase ArtA

Components

Nitrile synthetase

Keywords

BIOSYNTHETIC PROTEIN / Argininosuccinate synthetase like enzyme / Cyano amino acid / nitrile group

Biological species

Penicillium aurantiogriseum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Ma, H.L. / Zhang, K.K.

Funding support

China, 3items

Citation

Journal: Acs Catalysis / Year: 2025
Title: Structural and Mechanistic Basis for Nitrile Synthetase by an Argininosuccinate Synthetase-Like Enzyme
Authors: Zeng, Y. / Zhang, K. / Lu, T. / Yin, X. / Wang, Q. / Xiong, L. / Guo, H. / Li, J. / Lu, X. / Liu, L. / Ma, H. / Gao, Z.

History

Deposition	Jan 7, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jan 14, 2026	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9lei.cif.gz	619 KB	Display	PDBx/mmCIF format
PDB format	pdb9lei.ent.gz	506.7 KB	Display	PDB format
PDBx/mmJSON format	9lei.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/le/9lei ftp://data.pdbj.org/pub/pdb/validation_reports/le/9lei	HTTPS FTP

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Related structure data

Related structure data	9lehC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nitrile synthetase

B: Nitrile synthetase

C: Nitrile synthetase

D: Nitrile synthetase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	91.178, 106.764, 94.630
Angle α, β, γ (deg.)	90.00, 108.68, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Nitrile synthetase Mass: 47887.043 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium aurantiogriseum (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1472 / Source method: isolated from a natural source / Formula: H₂O
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: 2.28 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NaAc, PEG4000, Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 132566 / % possible obs: 99.8 % / Redundancy: 6.3 % / CC_1/2: 0.01 / CC star: 0.143 / Χ²: 1.007 / Net I/σ(I): 5.7
Reflection shell	Resolution: 1.9→5.16 Å / Num. unique obs: 137495 / CC_1/2: 0.01 / CC star: 0.143

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
autoPX		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→44.82 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1901	6633	5 %
R_work	0.1626	-	-
obs	0.164	132537	98.21 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→44.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11705	0	36	1472	13213

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11976
X-RAY DIFFRACTION	f_angle_d	1.294	16223
X-RAY DIFFRACTION	f_dihedral_angle_d	17.207	1622
X-RAY DIFFRACTION	f_chiral_restr	0.07	1828
X-RAY DIFFRACTION	f_plane_restr	0.009	2092

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 (%)
1.9-1.92	0.2412	193	0.2146	3725	X-RAY DIFFRACTION	89
1.92-1.94	0.2435	192	0.2027	3860	X-RAY DIFFRACTION	90
1.94-1.97	0.2252	200	0.1895	3948	X-RAY DIFFRACTION	93
1.97-1.99	0.2187	191	0.1769	4018	X-RAY DIFFRACTION	94
1.99-2.02	0.2025	208	0.1719	4083	X-RAY DIFFRACTION	96
2.02-2.05	0.2146	209	0.1799	4159	X-RAY DIFFRACTION	97
2.05-2.08	0.2098	212	0.1791	4142	X-RAY DIFFRACTION	97
2.08-2.11	0.2004	214	0.1718	4181	X-RAY DIFFRACTION	98
2.11-2.14	0.206	238	0.1726	4207	X-RAY DIFFRACTION	99
2.14-2.17	0.1982	255	0.1672	4226	X-RAY DIFFRACTION	99
2.17-2.21	0.2002	232	0.167	4145	X-RAY DIFFRACTION	98
2.21-2.25	0.2037	238	0.1704	4217	X-RAY DIFFRACTION	99
2.25-2.3	0.2374	217	0.1691	4278	X-RAY DIFFRACTION	100
2.3-2.34	0.2229	215	0.1688	4269	X-RAY DIFFRACTION	100
2.34-2.39	0.2163	219	0.1693	4235	X-RAY DIFFRACTION	100
2.39-2.45	0.206	257	0.1674	4245	X-RAY DIFFRACTION	100
2.45-2.51	0.2062	234	0.1679	4264	X-RAY DIFFRACTION	100
2.51-2.58	0.2006	230	0.1695	4262	X-RAY DIFFRACTION	100
2.58-2.65	0.2125	216	0.1753	4228	X-RAY DIFFRACTION	99
2.65-2.74	0.1896	225	0.1624	4275	X-RAY DIFFRACTION	100
2.74-2.84	0.1872	221	0.1624	4273	X-RAY DIFFRACTION	100
2.84-2.95	0.2031	215	0.1604	4280	X-RAY DIFFRACTION	100
2.95-3.09	0.1879	228	0.1554	4261	X-RAY DIFFRACTION	100
3.09-3.25	0.1722	230	0.1624	4305	X-RAY DIFFRACTION	100
3.25-3.45	0.1729	247	0.1496	4251	X-RAY DIFFRACTION	100
3.45-3.72	0.1781	222	0.1469	4283	X-RAY DIFFRACTION	100
3.72-4.09	0.1485	199	0.1382	4330	X-RAY DIFFRACTION	100
4.09-4.68	0.1482	248	0.1414	4295	X-RAY DIFFRACTION	100
4.68-5.9	0.1697	237	0.1638	4308	X-RAY DIFFRACTION	100
5.9-44.82	0.2126	191	0.1772	4351	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	1.7421	-0.1326	-1.2635	1.72	0.6059	1.2989	0.1966	-0.6334	0.188	0.5712	-0.1705	0.0608	-0.0385	0.1251	0.0279	0.2687	-0.0915	0.0473	0.3338	-0.0493	0.1796	-21.593	-21.451	-6.4029
2	1.2802	0.4633	-0.9961	1.3013	-0.5143	2.0624	-0.1567	-0.313	-0.3969	0.2095	-0.1576	-0.1878	0.1973	-0.0067	0.0003	0.157	-0.0034	-0.0049	0.1789	0.0693	0.1698	-12.1207	-31.2715	-18.6764
3	0.9119	0.2342	-0.6014	0.5696	-0.0337	0.6969	0.2334	-0.3634	0.1694	0.1205	-0.1513	-0.0123	-0.1601	0.0919	-0.0144	0.1569	-0.0461	0.0032	0.1925	-0.0178	0.1301	-13.6251	-18.488	-15.3065
4	0.6798	0.1731	-0.1499	0.7671	-0.0738	0.5566	-0.006	0.0041	-0.0598	0.0458	0.0279	-0	0.0201	-0.0054	-0.0272	0.0905	-0.0016	0.0007	0.0567	-0.0087	0.1052	2.8323	-21.8376	-36.2122
5	2.4633	0.3385	0.3723	1.968	0.3114	2.8622	0.0577	0.3585	0.0769	-0.4141	0.0502	-0.103	-0.1252	-0.1016	-0.1396	0.197	0.0106	0.0473	0.1513	0.0182	0.1673	28.781	-0.9934	-70.9262
6	2.4274	0.3069	-2.2112	0.5609	-0.2138	3.243	0.0958	-0.0954	-0.1012	-0.0603	-0.0828	-0.1701	-0.1536	0.3215	-0.0105	0.1119	-0.0053	0.0062	0.1161	-0.0006	0.2259	31.5314	-1.6712	-52.6405
7	1.0511	0.2708	-0.7729	0.5793	-0.16	1.2002	0.0507	0.0571	0.0541	-0.059	-0.0182	-0.0836	-0.1062	-0.0792	-0.0641	0.0862	0.0141	0.0121	0.0708	0.0028	0.1462	18.9255	-0.4396	-56.1988
8	1.6774	-0.9163	-1.0479	1.345	0.968	1.4687	0.0724	0.242	-0.1665	-0.0931	-0.2677	0.123	0.0729	-0.1516	0.0961	0.1935	0.0075	0.005	0.1834	0.014	0.1983	25.9146	-9.7863	-69.5968
9	0.7392	-0.015	-0.1518	0.6168	-0.1421	0.7237	0.0207	-0.0275	0.0524	0.0964	-0.0133	-0.0589	-0.0327	0.0539	-0.0057	0.0922	-0.0185	-0.0163	0.0577	-0.0079	0.1081	15.0889	-8.628	-35.7964
10	1.1645	0.1228	-0.3812	1.1557	1.2568	1.9918	-0.0883	0.2968	-0.0969	-0.3071	0.1133	-0.0642	-0.1383	0.0409	-0.0235	0.2253	-0.0363	0.0017	0.2563	-0.0299	0.132	-16.1478	-5.4712	-77.4807
11	0.4083	-0.0252	0.2037	0.814	0.1108	0.925	-0.0149	0.039	-0.0157	0.0493	0.0365	0.067	0.0923	-0.2119	-0.0337	0.0806	-0.0219	-0.0062	0.1826	0.0076	0.0968	-25.3886	4.6257	-53.77
12	1.6013	0.2447	-0.538	1.6381	0.4469	2.1377	-0.0828	-0.3958	-0.0953	0.3559	0.0029	0.198	0.4662	-0.4265	0.0238	0.3351	-0.0277	0.0462	0.3186	0.0224	0.1959	-18.7825	25.7054	-7.5298
13	0.4434	0.2565	0.1027	0.8798	1.3627	3.2889	0.0041	-0.1222	0.0152	0.1574	-0.0982	0.1072	0.0676	-0.221	0.0226	0.1928	0.0421	0.0157	0.1555	-0.0163	0.1653	-15.0167	23.6437	-24.2806
14	0.5652	0.0446	-0.6832	0.6962	0.8493	2.7997	-0.187	0.279	-0.3404	0.2421	-0.1396	0.3246	0.3979	-0.6975	0.1143	0.3725	-0.0796	0.0963	0.4174	0.0248	0.3954	-26.8875	23.0152	-11.8277
15	1.5464	0.6507	-0.6558	1.5754	-0.1536	1.2392	0.0424	-0.049	0.163	0.245	0.0019	0.1773	-0.1733	-0.2995	-0.0398	0.1567	0.0479	-0.0003	0.1989	-0.013	0.1429	-23.9978	24.3266	-42.8928
16	0.8494	-0.0219	0.0437	0.9806	-0.0327	1.2653	-0.0441	0.0558	0.0279	0.0541	0.0521	-0.0279	-0.0034	-0.0776	-0.0023	0.0741	-0.0015	-0.0028	0.067	-0.018	0.0948	-12.4627	15.9622	-48.3971

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 102 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 103 through 196 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 197 through 392 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 13 through 62 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 63 through 102 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 103 through 158 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 159 through 196 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 197 through 390 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 13 through 204 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 205 through 383 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 13 through 62 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 63 through 158 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 159 through 196 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 197 through 257 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 258 through 392 )

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