PDB-8yzu: STC truncated SydA

ID or keywords:

Entry

Database: PDB / ID: 8yzu

Title

STC truncated SydA

Components

truncated 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: 2.01 Å

Authors

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

Funding support

China, 2items

Citation

Journal: To Be Published
Title: STC truncated 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	8yzu.cif.gz	512.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8yzu.ent.gz	424.3 KB	Display	PDB format
PDBx/mmJSON format	8yzu.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/yz/8yzu ftp://data.pdbj.org/pub/pdb/validation_reports/yz/8yzu	HTTPS FTP

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Related structure data

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: truncated SydA

B: truncated SydA

C: truncated SydA

D: truncated SydA

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)	57.151, 125.000, 93.140
Angle α, β, γ (deg.)	90.00, 100.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	truncated SydA Mass: 35177.867 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.: 857 / 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: 2.32 Å³/Da / Density % sol: 47.07 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium tartrate dibasic, 20% w/v polyethylene glycol 3350, pH 7.0

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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 11, 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: 2.01→31.25 Å / Num. obs: 79134 / % possible obs: 92.64 % / Redundancy: 5 % / R_pim(I) all: 0.068 / R_rim(I) all: 0.174 / Net I/σ(I): 8.06
Reflection shell	Resolution: 2.01→2.08 Å / Num. unique obs: 79088 / R_pim(I) all: 0.068

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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: 2.01→31.25 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2303	2000	2.53 %
R_work	0.1849	-	-
obs	0.186	79088	92.66 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.01→31.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9948	0	48	857	10853

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	0.914
X-RAY DIFFRACTION	f_dihedral_angle_d	5.476	1384
X-RAY DIFFRACTION	f_chiral_restr	0.05	1528
X-RAY DIFFRACTION	f_plane_restr	0.009	1788

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 (%)
2.01-2.06	0.3006	103	0.2633	3976	X-RAY DIFFRACTION	67
2.06-2.12	0.2841	120	0.2397	4612	X-RAY DIFFRACTION	77
2.12-2.18	0.3047	126	0.2283	4860	X-RAY DIFFRACTION	83
2.18-2.25	0.2714	135	0.2203	5219	X-RAY DIFFRACTION	88
2.25-2.33	0.228	143	0.2119	5509	X-RAY DIFFRACTION	93
2.33-2.42	0.2461	147	0.2083	5704	X-RAY DIFFRACTION	96
2.42-2.53	0.2452	152	0.1938	5817	X-RAY DIFFRACTION	98
2.53-2.67	0.2373	151	0.1912	5833	X-RAY DIFFRACTION	98
2.67-2.83	0.2219	153	0.1829	5872	X-RAY DIFFRACTION	99
2.83-3.05	0.2516	152	0.1862	5898	X-RAY DIFFRACTION	99
3.05-3.36	0.2356	154	0.1829	5919	X-RAY DIFFRACTION	99
3.36-3.84	0.2062	154	0.1654	5921	X-RAY DIFFRACTION	100
3.84-4.84	0.2054	154	0.1489	5956	X-RAY DIFFRACTION	100
4.84-10	0.1998	156	0.1757	5992	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	3.6353	-1.4347	-2.5006	2.3193	-0.896	3.9115	-0.1284	0.3053	-0.1012	-0.3612	0.0774	0.1264	-0.0691	-0.0811	0.0056	0.3935	0.0008	-0.2444	0.1861	-0.0348	0.3262	16.0695	11.2973	-14.8947
2	0.6919	0.2395	0.3225	0.7725	0.4125	1.5046	0.0425	-0.3505	0.2055	0.434	-0.2362	0.5713	-0.1342	-0.5318	0.2177	0.3765	-0.0492	0.1766	0.272	-0.1411	0.3503	11.0833	7.1938	14.4831
3	0.9224	0.1128	-0.3514	2.0428	0.1318	0.5896	0.1675	-0.0613	0.1488	0.5205	-0.1452	0.0836	0.0039	-0.0887	-0.0953	0.2675	-0.0584	0.0882	0.1636	-0.0302	0.1539	23.6084	3.4109	13.5972
4	0.9416	0.1611	-0.1086	2.2269	-0.1703	1.4617	0.089	-0.0429	-0.0414	0.5331	-0.1221	-0.0032	0.0375	-0.0146	0.0285	0.2009	-0.025	0.0322	0.1359	-0.0129	0.0966	25.7881	-4.9401	10.7123
5	1.8314	0.0047	0.6632	3.4315	0.7699	4.4328	0.1173	0.421	0.165	-0.5964	0.1193	-0.6257	-0.3029	0.385	-0.0842	0.1789	0.0258	0.0733	0.1732	-0.0343	0.2843	30.9391	-1.6252	-8.6459
6	0.6416	0.2133	0.2782	1.2851	0.3737	0.1989	0.0793	-0.0714	-0.0788	0.1702	-0.1261	0.4654	0.055	0.0054	0.0454	0.1092	-0.0014	0.0519	0.1411	-0.0293	0.2313	13.7065	-6.9684	2.2231
7	2.5007	-0.6537	0.1041	1.9385	-0.3903	1.1997	0.0855	0.2358	0.1666	-0.5083	-0.0365	-0.156	-0.0392	0.2066	-0.0576	0.2488	-0.0062	-0.0022	0.1374	0.0191	0.1124	26.7159	7.4418	-11.4736
8	4.0719	3.6183	-2.4599	6.1026	-3.0332	3.3667	-0.1098	0.2036	-0.2681	-0.4022	-0.0092	0.3663	-0.1281	-0.3918	0.1389	0.2359	0.0333	-0.1395	0.2464	-0.0375	0.2865	12.2669	-3.0454	-12.6396
9	0.9989	0.8902	-0.0883	1.4317	0.2018	0.1602	0.0088	0.0394	-0.0653	-0.0335	-0.0876	0.5245	0.0213	-0.102	-0.0033	0.0615	0.0311	0.0281	0.1906	-0.0707	0.4432	8.4414	4.0014	-0.029
10	5.5341	-0.5665	0.9046	4.5559	1.7018	3.1175	0.1141	0.2445	-0.0899	-0.3507	0.0443	0.0696	-0.004	-0.1807	-0.1662	0.2393	0.0583	-0.0214	0.202	-0.0185	0.1018	24.847	-32.9287	-18.8404
11	0.9742	-0.1134	0.2796	0.93	-0.6371	1.5045	0.0975	0.0451	-0.0489	0.1815	-0.1637	-0.6653	0.1839	0.468	0.0466	0.2357	0.0533	-0.1683	0.2086	-0.004	0.4796	46.3719	-30.0599	2.0709
12	1.6268	0.0399	0.2736	1.7126	0.3543	0.5737	0.0684	-0.0937	-0.0227	0.5014	-0.0315	-0.3683	0.1603	0.0027	-0.031	0.1812	-0.0128	-0.0711	0.1254	0.0096	0.1809	34.4199	-23.4057	8.6127
13	4.1231	0.0597	1.3077	2.7254	-0.2625	4.1019	-0.0485	0.0859	-0.2912	-0.112	0.0968	0.6584	0.2438	-0.5355	-0.0049	0.0967	-0.016	0.0111	0.2785	-0.0401	0.2743	16.834	-20.544	-4.6408
14	1.242	0.2006	-0.1901	1.4998	-0.0667	0.7359	0.1068	-0.0564	0.1908	-0.1934	-0.115	-0.0758	-0.0552	-0.0426	-0.0293	0.0617	0.0443	0.0359	0.182	-0.0075	0.1792	31.7011	-19.5853	-6.78
15	4.3613	3.3716	-0.4612	5.1276	-0.3008	1.2476	0.0616	0.4014	0.2631	-0.7191	0.0249	-0.0903	-0.1098	-0.0427	-0.0301	0.316	0.1091	0.0629	0.243	0.0226	0.1701	29.5107	-18.5787	-18.7174
16	1.3559	0.6004	-0.353	1.8854	-0.5459	0.5632	0.1049	0.097	0.0049	-0.3068	-0.0497	-0.3597	-0.0143	0.1244	0.1266	0.0806	0.0704	0.1143	0.1994	-0.0146	0.2643	40.0178	-26.2727	-11.112
17	2.8269	-0.6611	1.1568	2.1623	-2.1654	2.2626	0.1159	-0.0833	-0.045	-0.4171	-0.16	-0.0424	0.0749	0.3109	0.0396	0.699	0.0251	-0.1485	0.273	-0.0121	0.1502	10.4135	-41.8467	-26.2508
18	1.1376	0.1045	0.2303	0.2485	0.153	0.9955	0.1349	-0.1159	-0.0305	-0.0606	-0.0705	0.1936	0.1015	-0.4048	-0.0371	0.6531	-0.0678	-0.1554	0.2574	-0.0124	0.2863	-14.4071	-36.8969	-42.7779
19	1.9741	-0.5865	-1.0493	1.3983	0.7912	3.0052	0.0327	-0.0814	-0.2225	0.0171	-0.0265	-0.001	0.2632	0.0424	-0.0506	0.5967	-0.0619	-0.1749	0.1995	0.0266	0.2283	-10.2053	-38.0843	-45.3098
20	0.3752	0.1233	0.3864	0.1985	-0.0824	0.6766	0.037	0.0912	-0.0799	-0.2068	-0.0335	0.0475	0.0256	-0.008	-0.0089	0.6107	0.0013	-0.1593	0.1966	-0.039	0.1961	-1.7267	-28.2544	-52.8834
21	6.4345	0.5893	1.544	2.8636	-1.0249	3.0484	-0.0914	-0.0432	-0.1313	-0.085	-0.0111	-0.3371	0.0931	0.3312	0.1216	0.6683	0.0335	-0.0768	0.2305	-0.0049	0.204	16.3583	-29.0014	-41.7164
22	0.3075	0.1942	-0.0685	0.4832	-0.1613	0.5187	0.1247	-0.0456	-0.0586	-0.132	-0.0656	0.078	0.023	0.0091	-0.0658	0.5417	-0.0246	-0.1134	0.1692	-0.0169	0.1577	2.0956	-27.4296	-36.4688
23	2.8263	-2.4725	0.0864	2.7172	-0.2073	0.0328	0.0215	-0.2473	0.1375	0.2963	0.0397	-0.0759	0.0008	0.0527	-0.0123	0.5753	-0.0153	-0.1019	0.3158	-0.0211	0.1882	5.8532	-26.7624	-25.2981
24	0.6473	-0.2846	-0.0094	0.7645	-0.2087	0.2533	0.0705	-0.1787	-0.0977	0.2096	0.0473	0.0759	0.1573	0.0765	-0.0984	0.579	-0.0641	-0.1149	0.2248	0.0043	0.1696	-5.5751	-34.4452	-31.1647
25	1.1078	0.5626	0.0414	0.9461	0.5255	3.9693	-0.1101	-0.1933	0.1842	0.3441	0.001	-0.0429	-0.0308	0.0465	0.0653	0.7758	-0.1335	-0.1943	0.3094	0.0249	0.2137	20.7506	2.3503	-30.4241
26	1.0536	-0.2706	0.8255	0.4313	-0.9352	2.1626	-0.1182	0.2676	0.1278	0.0676	-0.1371	-0.147	-0.2015	0.5031	0.1187	0.8345	-0.1075	-0.1794	0.2951	0.0414	0.182	19.8886	-0.7794	-60.138
27	0.2006	-0.0061	0.086	0.1229	0.0559	0.4962	-0.0481	0.054	0.0575	-0.1508	-0.0137	0.0774	-0.1524	0.0086	-0.0371	0.8011	-0.0553	-0.231	0.1908	-0.0153	0.0634	6.7233	-7.1203	-56.0691
28	4.6467	0.4512	-1.3663	3.2044	-0.4737	6.5127	0.1201	-0.5409	0.1815	0.3347	-0.0027	0.2343	-0.1366	-0.1073	-0.0562	0.6397	-0.0414	-0.0987	0.2569	-0.0163	0.2339	4.1527	-9.6168	-34.1408
29	0.8334	-0.2077	-0.1525	1.09	0.4178	1.0265	0.0239	-0.0348	-0.1177	-0.0527	-0.076	-0.047	-0.0446	-0.0402	-0.0307	0.6197	-0.0583	-0.1377	0.215	0.0385	0.1582	16.0573	-11.0895	-43.6443
30	1.4088	-1.5886	-1.0804	2.8661	1.981	2.1514	-0.126	-0.355	-0.0609	0.2863	0.1352	-0.0116	0.1496	0.3691	-0.0391	0.7446	-0.0817	-0.1835	0.3661	0.0839	0.251	23.2762	-12.2464	-34.0093
31	0.6488	-0.4634	0.3788	1.3913	-0.5225	0.3258	0.0186	-0.0221	-0.0416	0.0016	-0.0259	-0.0796	0.0062	0.1343	-0.114	0.6774	-0.1384	-0.16	0.2936	0.0506	0.1563	25.1214	-4.7759	-46.8339

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 56 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 124 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 125 through 166 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 167 through 186 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 187 through 233 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 234 through 254 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 255 through 276 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 277 through 312 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 7 through 28 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 29 through 56 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 57 through 166 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 167 through 186 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 187 through 254 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 255 through 276 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 277 through 312 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 7 through 28 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 29 through 56 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 57 through 81 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 82 through 166 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 167 through 186 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 187 through 254 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 255 through 277 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 278 through 312 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 7 through 28 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 29 through 56 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 57 through 166 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 167 through 186 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 187 through 254 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 255 through 276 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 277 through 312 )

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