PDB-8yzy: STC SydA mutant - W297Y

ID or keywords:

Entry

Database: PDB / ID: 8yzy

Title

STC SydA mutant - W297Y

Components

SydA mutant W297Y

Keywords

BIOSYNTHETIC PROTEIN / sesquiterpene synthase mutant

Function / homology

PYROPHOSPHATE 2-

Function and homology information

Biological species

Aspergillus versicolor (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Fan, A. / Fan, S. / Wu, M.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: STC SydA mutant - W297Y
Authors: Fan, A. / Fan, S.

History

Deposition	Apr 8, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yzy.cif.gz	518.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8yzy.ent.gz	428.3 KB	Display	PDB format
PDBx/mmJSON format	8yzy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yzy_validation.pdf.gz	5.4 MB	Display	wwPDB validaton report
Full document	8yzy_full_validation.pdf.gz	5.4 MB	Display
Data in XML	8yzy_validation.xml.gz	61.1 KB	Display
Data in CIF	8yzy_validation.cif.gz	82.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/8yzy ftp://data.pdbj.org/pub/pdb/validation_reports/yz/8yzy	HTTPS FTP

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Related structure data

Related structure data	8yzu 8yzx
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1)

Deposited unit

A: SydA mutant W297Y

B: SydA mutant W297Y

C: SydA mutant W297Y

D: SydA mutant W297Y

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	52.892, 127.635, 89.143
Angle α, β, γ (deg.)	90.00, 93.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	SydA mutant W297Y Mass: 35251.941 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus versicolor (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-POP / PYROPHOSPHATE 2- Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₂O₇P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.14 Å³/Da / Density % sol: 42.53 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.1M Ammonium tartrate dibasic pH 7.0, 12% w/v Polyethylene glycol 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 26, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.73→27.3 Å / Num. obs: 114819 / % possible obs: 94.17 % / Redundancy: 6 % / R_pim(I) all: 0.046 / Net I/σ(I): 22.8
Reflection shell	Resolution: 1.73→1.79 Å / Num. unique obs: 114786 / R_pim(I) all: 0.046

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→27.3 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.192	2000	1.74 %
R_work	0.1553	-	-
obs	0.1559	114786	94.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.73→27.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9934	0	8	863	10805

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	8.355	1386
X-RAY DIFFRACTION	f_chiral_restr	0.061	1525
X-RAY DIFFRACTION	f_plane_restr	0.012	1781

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 (%)
1.73-1.78	0.2932	124	0.243	7240	X-RAY DIFFRACTION	85
1.78-1.83	0.2964	134	0.2205	7590	X-RAY DIFFRACTION	88
1.83-1.88	0.2707	135	0.2036	7538	X-RAY DIFFRACTION	89
1.88-1.94	0.2194	131	0.2034	7677	X-RAY DIFFRACTION	90
1.94-2.01	0.2355	149	0.1791	7752	X-RAY DIFFRACTION	91
2.01-2.09	0.2314	133	0.1673	7904	X-RAY DIFFRACTION	93
2.09-2.18	0.2279	155	0.1613	8071	X-RAY DIFFRACTION	94
2.18-2.3	0.1852	133	0.1587	8192	X-RAY DIFFRACTION	96
2.3-2.44	0.1977	150	0.1532	8219	X-RAY DIFFRACTION	97
2.44-2.63	0.206	149	0.158	8477	X-RAY DIFFRACTION	99
2.63-2.9	0.1694	150	0.1572	8458	X-RAY DIFFRACTION	99
2.9-3.32	0.2026	154	0.1562	8523	X-RAY DIFFRACTION	99
3.32-4.18	0.1696	149	0.1308	8511	X-RAY DIFFRACTION	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	2.6371	1.2637	-1.2048	4.6651	-1.2329	4.3383	0.0653	0.5554	0.1779	-0.5811	-0.112	-0.2469	-0.3495	-0.1976	0.0184	0.3533	0.0518	-0.0138	0.3193	0.1468	0.2566	10.2629	10.3939	-12.5138
2	0.9432	-0.1875	0.0364	1.6187	-0.649	2.3513	-0.2752	-0.5272	0.4727	0.4453	-0.0362	0.1161	-0.4528	-0.5464	0.2685	0.2938	0.0735	-0.0253	0.2239	-0.1033	0.2583	13.5435	6.9502	16.6937
3	2.5141	-0.9359	0.5693	1.7136	0.1436	0.912	-0.0853	-0.113	0.307	0.0477	0.0163	-0.1543	-0.2305	0.0533	0.0462	0.2075	-0.0157	-0.0185	0.1193	0.0027	0.1111	25.3684	0.944	14.244
4	2.4048	-0.0685	0.0908	2.4525	-0.2195	3.3151	-0.0037	0.3097	0.0849	-0.1975	-0.0826	-0.2321	-0.2679	0.191	0.0502	0.1697	-0.0099	-0.0025	0.1581	0.0045	0.1423	27.1003	-5.1315	-2.3997
5	1.7406	-0.3761	-0.3812	2.0141	-0.3066	1.5582	0.066	0.1319	0.077	-0.0853	-0.0941	-0.0213	-0.0939	0.0209	0.0605	0.1095	0.0046	-0.0143	0.1211	0.0062	0.1058	15.5672	-3.4519	-0.2528
6	4.8433	3.6909	-2.9876	7.6556	-5.0232	4.8723	-0.1761	0.5389	0.1674	-0.4495	0.2514	0.2722	0.0682	-0.607	-0.0435	0.193	0.0154	-0.0328	0.304	-0.0096	0.1661	8.0848	-3.767	-9.3206
7	2.4134	1.2669	-0.3153	5.302	-0.5967	1.5016	0.0865	0.1656	0.117	0.0449	0.0021	0.175	-0.2406	-0.2253	-0.078	0.1261	0.0389	0.0044	0.1553	0.0122	0.1372	7.369	3.8844	3.4352
8	5.2248	0.2767	1.126	4.9892	1.4321	3.2448	0.0271	0.2124	0.093	-0.1466	-0.0553	0.5411	-0.1515	-0.1024	0.0048	0.2468	0.0174	-0.0475	0.1338	0.0092	0.1734	18.6547	-34.8382	-18.8858
9	1.8273	0.5267	1.0221	1.5493	-0.0286	2.1818	-0.2081	0.4561	-0.244	-0.0412	0.0168	-0.784	0.6634	0.356	0.0847	0.1922	0.0395	0.1462	0.2872	-0.0369	0.352	43.1831	-32.5784	-1.417
10	0.5485	0.8688	-0.4802	2.8048	-1.6494	5.0926	-0.0772	0.0354	-0.2225	0.0083	0.0238	-0.1567	0.7275	0.0491	0.0773	0.2406	0.0296	0.0267	0.1437	-0.0566	0.3034	37.3089	-35.1962	3.3931
11	5.2704	0.9224	-2.6697	3.9589	-0.833	5.2756	-0.221	0.0534	-0.7047	-0.2343	0.0145	-0.0997	0.2491	0.1354	0.1545	0.1211	0.0087	-0.0005	0.0956	-0.0309	0.2575	38.8475	-27.0808	1.3459
12	1.5762	1.058	0.4773	6.0469	2.1043	3.1652	0.0592	-0.2419	-0.7315	0.1488	-0.0378	0.735	0.4672	-0.6056	-0.0007	0.2409	-0.0609	-0.0054	0.2651	0.0464	0.4177	25.8912	-24.1233	16.1838
13	0.1879	0.0352	0.173	2.5516	-0.4617	3.6067	-0.0348	-0.0716	-0.2019	0.2652	-0.1076	-0.3121	0.0282	0.2631	0.1201	0.1411	0.004	-0.0267	0.1613	-0.0141	0.1962	37.0967	-20.7733	12.3671
14	3.7316	-0.111	-1.0914	2.9925	0.0439	2.8586	0.0421	0.0277	-0.1305	0.3159	-0.0889	0.288	0.1189	-0.1463	0.0318	0.149	-0.0079	-0.0062	0.1374	-0.0161	0.1496	25.4689	-19.214	5.1385
15	5.9993	-1.0244	1.3502	4.1965	1.5267	4.0566	0.3412	-0.1652	-0.5169	0.0033	-0.4106	0.6475	0.2626	-0.5357	0.1201	0.1573	-0.0298	-0.0049	0.2289	-0.0343	0.2196	13.5025	-21.6131	-2.5189
16	0.6768	0.0786	0.3616	2.2477	0.1305	1.2174	0.0091	-0.0261	0.1138	-0.0649	-0.0358	-0.1291	-0.097	0.136	0.0154	0.1593	-0.0028	0.0403	0.1529	-0.0084	0.1297	32.8492	-18.1781	-7.8842
17	1.7239	-2.4944	-0.7029	6.4598	1.6528	1.7096	-0.1158	-0.2544	-0.6107	0.3342	-0.0855	1.0459	0.1489	-0.3295	0.1661	0.2232	-0.0146	0.0497	0.2567	-0.0194	0.3306	13.0548	-30.9172	-8.1523
18	6.6225	5.3949	-0.406	6.3416	0.2328	1.1352	-0.2057	0.3913	0.2891	-0.7779	0.2162	0.2508	-0.092	0.1031	-0.0332	0.2927	0.0371	-0.0149	0.2064	0.0056	0.1636	23.5192	-20.7868	-18.9834
19	1.3256	1.1316	0.2679	3.6779	-0.0763	1.5757	0.1338	0.1395	-0.2576	-0.0083	0.1691	-0.5285	-0.0078	0.1686	-0.2425	0.1965	0.0183	0.0665	0.1878	-0.0522	0.1698	34.4314	-29.2758	-13.3345
20	3.2329	-1.586	0.7605	3.8066	1.8198	2.2151	0.1795	0.695	-0.5986	-0.5268	-0.2977	0.7999	0.3388	-0.2367	0.0739	0.3414	0.0806	-0.1634	0.3176	-0.0998	0.3618	-7.3563	-51.9405	25.4786
21	2.6666	-0.1557	0.2095	1.3165	0.4582	1.7954	-0.0283	0.2044	-0.1579	-0.0023	-0.0201	-0.3074	0.2016	0.5773	-0.0519	0.2711	0.1475	-0.0254	0.3014	0.0282	0.3109	18.8764	-47.6066	40.0549
22	1.8668	-0.5139	0.7804	2.2997	-0.9172	5.5464	0.1047	-0.2172	-0.4122	0.1436	0.1537	0.1871	0.91	-0.0479	-0.2187	0.2929	0.0725	0.0011	0.2183	0.0492	0.2794	13.844	-50.3365	45.4309
23	4.2875	0.1903	-2.7599	1.831	-0.483	4.2051	-0.0596	0.1198	-0.3115	-0.107	0.0261	-0.0299	0.1442	0.0349	0.0685	0.1502	0.0528	-0.0081	0.194	0.0272	0.2085	14.7703	-42.1148	42.8803
24	2.2514	0.3041	0.4687	4.2714	1.5729	3.2629	0.0655	-0.1483	-0.2182	0.2564	-0.1926	0.2562	0.252	-0.4707	0.0472	0.228	-0.0282	-0.0167	0.2648	0.0381	0.2185	4.0348	-38.3811	59.7875
25	2.2638	0.4483	-0.5566	3.2077	-1.2467	3.8506	-0.126	-0.1332	-0.1624	0.1036	-0.0979	-0.5271	0.2368	0.5443	0.1396	0.1461	0.0408	-0.0146	0.2632	0.0264	0.2409	14.8167	-34.984	51.2304
26	2.4136	0.1091	0.0569	2.5968	-0.7476	2.7324	-0.0234	-0.0435	-0.0672	0.1858	0.0806	0.234	0.0467	-0.224	0.0045	0.1422	0.0363	-0.0015	0.2241	0.0173	0.2081	1.3067	-34.9389	47.4242
27	7.0316	-1.2988	0.7689	2.571	1.1878	2.9541	0.232	0.0305	-0.6165	-0.0245	-0.1208	0.4111	0.1965	-0.3336	-0.0586	0.1721	0.011	-0.0306	0.2016	0.025	0.2741	-11.5133	-38.1418	40.9907
28	1.5462	-1.2924	-0.015	2.7229	-0.4715	0.9875	0.1614	0.2799	0.1843	-0.2485	-0.1978	-0.2386	0.0127	0.2309	0.019	0.1435	0.0597	0.0371	0.224	0.0443	0.1506	7.4157	-34.2018	33.8875
29	2.2103	-1.5376	-1.325	3.3297	2.0978	1.351	-0.1042	-0.0145	-0.9027	0.1669	-0.2642	1.741	0.1786	-0.2133	0.252	0.2254	0.011	-0.0342	0.2408	-0.0428	0.5441	-11.6412	-47.6781	36.7168
30	2.7925	0.7374	-1.5473	6.5518	-2.1674	2.1663	0.7704	1.3187	-0.1098	-1.4224	-0.6071	0.8897	0.3233	-0.0012	0.0121	0.4998	0.2927	-0.0523	0.5221	-0.0133	0.0636	-2.9805	-37.8401	24.1189
31	3.5309	-0.8205	-0.4086	3.3847	-0.6372	1.9791	0.6168	0.637	-0.3037	-0.3775	-0.5335	-0.2162	0.1024	0.1919	-0.0308	0.2554	0.1558	0.0457	0.3066	0.0047	0.1256	9.0594	-45.1764	28.777
32	2.415	0.2122	1.9426	1.4745	0.9511	4.2387	-0.1348	-0.1154	0.2368	-0.0721	-0.0445	0.0549	-0.6747	-0.4885	0.146	0.3327	0.0929	0.0036	0.1796	-0.0229	0.2701	-13.7473	-8.7147	44.1958
33	2.549	-1.389	1.1462	3.0609	0.5977	3.0949	0.0618	-0.0792	0.3703	0.0598	-0.0911	-0.2939	-0.3659	-0.0508	0.0105	0.2158	0.0021	0.0286	0.145	-0.0084	0.1335	0.764	-14.2951	55.4114
34	2.4906	-0.4463	0.2753	1.6595	0.1889	2.8966	-0.0015	0.174	0.1149	-0.0305	0.0296	-0.0808	-0.0441	0.0841	-0.0207	0.125	0.0214	-0.0023	0.1487	-0.0012	0.137	-2.6028	-22.7982	43.6033
35	1.651	-0.0663	0.1131	2.3016	-1.6598	4.9656	-0.0678	-0.0523	0.0087	0.1978	-0.0811	0.0726	-0.6583	-0.0221	0.1036	0.1611	0.0317	-0.0303	0.1457	-0.0151	0.1435	-14.8415	-17.9425	39.5132

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 16 through 35 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 261 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 284 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 285 through 319 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 15 through 35 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 36 through 63 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 84 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 85 through 107 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 108 through 125 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 126 through 149 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 150 through 173 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 174 through 193 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 194 through 241 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 242 through 261 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 262 through 284 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 285 through 319 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 15 through 35 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 36 through 63 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 64 through 84 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 85 through 107 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 108 through 131 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 132 through 149 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 150 through 173 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 174 through 193 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 194 through 241 )
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 242 through 261 )
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 262 through 284 )
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 285 through 319 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 13 through 63 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 64 through 149 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 150 through 209 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 210 through 319 )

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