PDB-8yzx: Sesquiterpene synthase SydA

ID or keywords:

Entry

Database: PDB / ID: 8yzx

Title

Sesquiterpene synthase SydA

Components

SydA

Keywords

BIOSYNTHETIC PROTEIN / sesquiterpene synthase

Function / homology

PYROPHOSPHATE 2-

Function and homology information

Biological species

Aspergillus versicolor (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.8 Å

Authors

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

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Sesquiterpene synthase SydA
Authors: Fan, A. / Fan, S. / Wu, M.

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	8yzx.cif.gz	524.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8yzx.ent.gz	440.9 KB	Display	PDB format
PDBx/mmJSON format	8yzx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yzx_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	8yzx_full_validation.pdf.gz	3.9 MB	Display
Data in XML	8yzx_validation.xml.gz	49.5 KB	Display
Data in CIF	8yzx_validation.cif.gz	64.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yz/8yzx ftp://data.pdbj.org/pub/pdb/validation_reports/yz/8yzx	HTTPS FTP

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Related structure data

Related structure data	8yzu
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

B: SydA

C: SydA

D: SydA

hetero molecules

147 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)	157.928, 157.928, 224.841
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	95
Space group name H-M	P4₃22

#1: Protein	SydA Mass: 36392.293 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.82 Å³/Da / Density % sol: 74.49 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.223M magnesium formate, 0.1M Bis-tris pH6.5

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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: Nov 26, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 3.394→27.92 Å / Num. obs: 28218 / % possible obs: 98.25 % / Redundancy: 25.5 % / R_pim(I) all: 0.064 / Net I/σ(I): 9
Reflection shell	Resolution: 3.394→3.802 Å / R_pim(I) all: 0.064

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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: 3.8→27.92 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2119	2000	7.5 %
R_work	0.1794	-	-
obs	0.1818	26670	93.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.8→27.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10273	0	48	6	10327

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003
X-RAY DIFFRACTION	f_angle_d	0.681
X-RAY DIFFRACTION	f_dihedral_angle_d	9.051	1425
X-RAY DIFFRACTION	f_chiral_restr	0.044	1589
X-RAY DIFFRACTION	f_plane_restr	0.006	1841

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 (%)
3.8-3.9	0.2766	135	0.2535	1665	X-RAY DIFFRACTION	91
3.9-4	0.2522	138	0.238	1710	X-RAY DIFFRACTION	92
4-4.12	0.2387	138	0.199	1695	X-RAY DIFFRACTION	92
4.12-4.25	0.2355	142	0.1858	1750	X-RAY DIFFRACTION	94
4.25-4.4	0.2271	145	0.1837	1783	X-RAY DIFFRACTION	96
4.4-4.58	0.2089	141	0.1721	1737	X-RAY DIFFRACTION	94
4.58-4.79	0.1856	146	0.1597	1802	X-RAY DIFFRACTION	95
4.79-5.04	0.1917	141	0.1622	1750	X-RAY DIFFRACTION	94
5.04-5.35	0.1819	142	0.1708	1748	X-RAY DIFFRACTION	93
5.35-5.76	0.2453	142	0.1921	1753	X-RAY DIFFRACTION	93
5.76-6.33	0.2219	145	0.1958	1787	X-RAY DIFFRACTION	94
6.33-7.23	0.2373	145	0.1947	1789	X-RAY DIFFRACTION	94
7.24-9.06	0.1912	151	0.1606	1856	X-RAY DIFFRACTION	95

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	0.2492	-0.2739	0.0069	0.2292	-0.1044	0.0784	0.1949	0.2136	-0.3121	-0.4586	-0.2329	-0.0221	0.33	-0.5115	-0	0.7077	-0.0331	0.081	0.9511	-0.058	0.7774	74.1615	-51.3493	5.4641
2	0.0229	0.4596	-0.1843	0.4298	-0.3393	0.2487	0.1079	-0.1172	-0.1511	-0.1366	-0.0177	0.412	-0.2276	-0.5104	0	0.7363	0.1853	0.1159	0.8123	0.0097	0.7343	48.47	-40.6526	13.8966
3	0.4997	-0.1998	0.86	0.1993	-0.3049	0.7058	-0.0486	-0.0443	-0.0141	0.3245	0.0238	-0.0136	-0.4421	-0.2855	-0	0.6373	0.0993	0.0262	0.5652	-0.0541	0.6386	59.8095	-39.9995	26.3835
4	0.1274	-0.1075	-0.082	0.0856	-0.0003	0.0656	-0.0501	-0.2418	-0.3181	0.3215	0.3587	0.3124	-0.3266	0.2898	-0.0001	0.992	0.0496	-0.146	0.8639	-0.0111	0.7366	75.1327	-42.796	11.7374
5	0.2277	0.032	0.0319	0.2657	-0.2825	0.2531	0.075	0.3656	-0.4335	0.0101	0.2043	0.0605	-0.2279	-0.1691	-0.0002	0.4466	-0.0003	0.0314	0.6912	-0.0611	0.6361	62.256	-57.2307	18.8481
6	0.3276	-0.2587	0.3181	0.1645	-0.1316	0.5237	-0.5643	-0.3147	0.9099	0.486	-0.3531	-0.5721	-0.5819	0.3028	-0.0724	0.7571	-0.3047	0.3985	1.0238	-0.1938	0.2162	58.5394	-53.7098	2.6837
7	0.6716	0.1854	-0.7587	0.3086	-0.4016	0.8931	-0.0036	0.181	-0.0274	-0.2816	0.2353	0.0705	0.1397	0.1515	0	0.8597	0.0835	-0.0389	0.7274	0.0953	0.7469	25.1394	-23.9574	30.498
8	0.2206	-0.2311	-0.2889	0.0939	0.3472	0.1803	0.3396	0.2702	0.0249	-0.3353	-0.43	-0.0144	0.6054	0.445	-0	0.6984	0.1342	0.1294	0.715	-0.0258	0.8973	27.5143	-35.1074	30.7382
9	0.365	0.3327	-0.0802	0.3405	0.264	0.3399	-0.137	0.3508	-0.5046	0.2492	-0.0597	-0.0338	0.866	0.1242	0.0001	0.8862	0.0457	0.1938	0.7108	-0.0325	0.7868	17.5638	-42.5044	40.2556
10	0.0329	-0.0187	-0.0723	0.0979	-0.006	0.0489	0.0482	0.5665	0.1133	0.5409	-0.3226	0.2553	0.4432	-0.3295	0	0.4545	-0.0774	0.0681	0.8343	-0.0103	0.9565	8.1579	-24.5749	45.9173
11	0.2555	0.395	-0.51	0.4298	-0.7538	1.104	0.4192	0.0432	-0.2125	-0.1267	-0.0992	0.1994	0.1296	-0.2167	0.0001	0.6844	0.0861	0.1889	0.7049	-0.0253	0.7244	23.1907	-25.3956	43.386
12	0.2379	0.0827	0.3433	0.5086	0.4312	0.3725	0.2965	0.1507	0.2456	-0.2377	-0.2955	-0.03	0.3459	-0.028	-0	0.8044	0.0818	0.1683	0.7778	0.0566	0.7828	29.8486	-18.7184	44.0623
13	0.0835	0.1866	-0.0016	0.0922	0.1382	0.1028	-0.2533	-0.2323	-0.0908	-0.1867	0.274	0.8676	0.0435	0.9824	-0.0002	0.8166	-0.0636	-0.0619	1.331	0.2248	0.7678	26.2787	-7.5915	27.4753
14	0.0996	0.0207	0.1452	0.0661	-0.0676	0.0482	0.431	-0.1131	-0.0419	0.8085	0.1131	0.3072	0.2431	0.8182	-0.0001	0.9104	0.1195	-0.2189	0.8997	-0.0796	0.6537	83.1768	-61.1684	48.8538
15	1.2751	-0.2537	0.4115	0.2466	0.0804	1.0947	-0.3193	-0.18	0.144	0.2297	0.1878	-0.0414	-0.472	-0.3595	0.0001	0.7575	0.1348	-0.0314	0.6336	-0.0371	0.7171	68.0069	-37.7461	47.314
16	0.9753	-0.5552	0.4564	0.453	-0.3998	0.6904	-0.293	-0.0925	0.0087	0.0303	0.2431	-0.1	-0.2184	0.1024	0.0001	0.8149	0.0121	-0.0847	0.7936	-0.0768	0.718	80.629	-46.9995	40.5704
17	0.661	-0.3685	-0.0646	0.1425	-0.051	-0.0581	-0.8908	0.2453	-0.6691	0.171	0.711	0.5617	0.083	-0.194	-0.0111	1.0421	0.066	-0.1387	0.9722	0.0362	0.7868	91.202	-53.7369	56.6664
18	0.0063	0.1093	-0.0321	0.1628	-0.1954	0.1356	-0.0991	0.2953	0.3836	0.0529	-0.0946	0.2211	0.1025	0.1276	0	1.0189	0.0726	0.1763	0.9957	0.1167	0.752	16.559	-23.0239	78.6959
19	0.3698	-0.0718	0.288	0.1544	-0.2667	0.5869	-0.3866	0.2918	-0.0294	0.8425	0.0225	0.2474	0.8639	-0.0229	0.0004	1.1172	-0.168	0.2951	0.7203	-0.023	0.9082	8.8585	-48.2881	68.0837
20	0.0105	-0.0924	-0.1326	0.2156	0.3041	0.4004	-0.1415	1.0903	-0.1334	-0.1925	-0.3092	0.0236	0.073	0.3275	0	0.963	-0.0507	0.2145	0.8458	-0.0039	0.9915	18.1659	-47.929	53.647
21	0.0016	-0.0028	0.0081	0.2349	-0.0545	0.2453	0.1862	0.1447	0.164	0.3255	-0.6161	-0.1035	0.4739	-0.3415	0.0015	0.5436	0.2354	0.0699	0.668	0.1508	0.6298	27.3242	-29.4173	61.4557
22	0.1323	0.3461	-0.1021	0.0346	-0.1867	0.0879	0.4205	0.6153	-0.0953	0.0396	-0.7073	0.2296	0.9704	-0.3639	0.003	0.869	-0.1153	0.1647	0.9492	-0.0458	0.9328	4.714	-34.2343	55.3724
23	0.0669	0.1151	0.1377	0.1466	0.2175	0.2529	0.2829	0.608	0.0911	-0.2712	-0.0904	0.3369	0.6582	0.7794	-0.0001	0.9044	0.1011	0.1782	0.6917	0.1187	0.6691	23.0768	-28.2149	72.4461
24	0.4421	-0.3468	-0.0672	0.0439	0.0406	0.4217	0.0826	0.3245	-0.0357	-0.1072	-0.4988	0.1332	0.1242	0.0769	0.0002	0.8854	-0.0693	0.1606	0.939	-0.0193	0.9476	4.3029	-26.9897	64.9193
25	0.0599	-0.1209	0.1896	0.043	0.0053	0.3191	0.5129	-0.0787	-0.6625	-0.6422	-0.4511	-0.0493	-0.2435	0.0243	0.0003	0.7282	-0.0034	0.0722	0.9202	-0.0144	0.5953	3.9248	-32.0889	81.2768

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 28 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 81 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 82 through 228 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 229 through 254 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 255 through 300 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 301 through 322 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 7 through 58 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 59 through 101 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 102 through 166 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 167 through 186 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 187 through 254 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 255 through 300 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 301 through 323 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 7 through 28 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 29 through 202 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 203 through 300 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 301 through 322 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 7 through 28 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 29 through 105 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 106 through 161 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 162 through 186 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 187 through 227 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 228 through 254 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 255 through 300 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 301 through 322 )

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