PDB-9wts: Structure of the EpHTT from Echinacea purpurea

ID or keywords:

Entry

Database: PDB / ID: 9wts

Title

Structure of the EpHTT from Echinacea purpurea

Components

Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

Keywords

TRANSFERASE / hydroxycinnamoyl-CoA:tartaric acid hydroxycinnamoyl transferase

Function / homology

rosmarinate synthase activity / : / Transferase family / Chloramphenicol acetyltransferase-like domain superfamily / Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

Function and homology information

Biological species

Echinacea purpurea (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Tang, D. / Bao, H. / Jiang, D. / Huang, X.F.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Structure of the EpHTT Protein from Echinacea purpurea
Authors: Hui, B. / Di, J.

History

Deposition	Sep 16, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9wts.cif.gz	352.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9wts.ent.gz	291.1 KB	Display	PDB format
PDBx/mmJSON format	9wts.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9wts_validation.pdf.gz	456.9 KB	Display	wwPDB validaton report
Full document	9wts_full_validation.pdf.gz	467.1 KB	Display
Data in XML	9wts_validation.xml.gz	38.9 KB	Display
Data in CIF	9wts_validation.cif.gz	51.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wt/9wts ftp://data.pdbj.org/pub/pdb/validation_reports/wt/9wts	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

B: Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

hetero molecules

96.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

hetero molecules

defined by author
48.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase

hetero molecules

defined by author
48.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.049, 181.623, 129.754
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Hydroxycinnamoyl-CoA: tartaric acid hydroxycinnamoyl transferase Mass: 48216.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Echinacea purpurea (plant) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A890VZR5
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.87 Å³/Da / Density % sol: 57.19 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: PEG 6000,sodium cacodylate,calcium acetate,Glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.29→35.11 Å / Num. obs: 49222 / % possible obs: 96.65 % / Redundancy: 7 % / CC_1/2: 0.995 / Net I/σ(I): 20.1
Reflection shell	Resolution: 2.29→2.35 Å / Num. unique obs: 49484 / CC_1/2: 0.99

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.29→35.11 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2348	1960	4.06 %
R_work	0.184	-	-
obs	0.1861	48298	96.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.29→35.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6715	0	12	246	6973

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6908
X-RAY DIFFRACTION	f_angle_d	0.988	9370
X-RAY DIFFRACTION	f_dihedral_angle_d	7.835	928
X-RAY DIFFRACTION	f_chiral_restr	0.053	1010
X-RAY DIFFRACTION	f_plane_restr	0.01	1211

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 (%)
2.29-2.35	0.395	119	0.3333	2735	X-RAY DIFFRACTION	81
2.35-2.42	0.3255	134	0.2941	3204	X-RAY DIFFRACTION	95
2.42-2.49	0.3373	137	0.2767	3280	X-RAY DIFFRACTION	97
2.49-2.57	0.3313	137	0.2538	3270	X-RAY DIFFRACTION	97
2.57-2.66	0.2952	138	0.2378	3296	X-RAY DIFFRACTION	97
2.66-2.77	0.2678	139	0.2295	3335	X-RAY DIFFRACTION	98
2.77-2.89	0.2842	140	0.2345	3269	X-RAY DIFFRACTION	97
2.89-3.04	0.3015	142	0.2301	3368	X-RAY DIFFRACTION	99
3.04-3.23	0.257	144	0.209	3388	X-RAY DIFFRACTION	99
3.23-3.48	0.2449	145	0.1987	3390	X-RAY DIFFRACTION	99
3.48-3.83	0.2186	145	0.1732	3428	X-RAY DIFFRACTION	100
3.83-4.39	0.2348	142	0.149	3346	X-RAY DIFFRACTION	97
4.39-5.52	0.1804	148	0.1419	3484	X-RAY DIFFRACTION	100
5.52-35.11	0.1925	150	0.1533	3545	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	2.0928	-1.2721	-0.0824	6.4334	0.8185	1.9427	-0.0586	-0.0802	0.0613	0.1261	0.1791	0.6453	0.1714	-0.2022	-0.1022	0.5071	-0.0409	0.0582	0.4413	0.112	0.3237	-10.8537	21.7078	-14.3153
2	1.9788	-0.7502	-0.163	3.6183	0.043	1.5623	-0.0417	-0.1127	-0.0527	0.3812	0.1733	0.2544	0.3057	-0.0171	-0.1268	0.5226	0.0138	0.038	0.3871	0.0705	0.2911	-6.5392	20.2211	-12.8922
3	3.0338	1.0821	0.0316	5.0184	0.5075	0.9988	-0.0765	-0.1953	-0.2864	0.2469	0.297	-1.1256	0.3901	0.3782	-0.2034	0.6068	0.1651	-0.0879	0.5452	-0.1089	0.4745	20.8308	17.7485	-19.0571
4	1.3805	-0.4087	-0.2084	3.1997	0.1743	1.7512	-0.1859	-0.187	0.0158	0.4799	0.3505	-0.4333	0.2772	0.3057	-0.1695	0.5203	0.1031	-0.0516	0.4783	-0.0408	0.3451	11.7629	22.3827	-15.7165
5	1.6965	-0.5111	1.0586	6.0991	-0.3138	2.0372	-0.1475	0.1564	0.1725	-0.4564	0.2907	-0.7422	-0.2551	0.2996	-0.1141	0.5912	-0.203	0.1458	0.4458	-0.0645	0.6077	21.2681	66.9983	-34.7742
6	0.8869	-0.6172	-0.0155	2.849	-0.1481	1.5063	-0.129	-0.0148	0.2909	0.0856	0.2081	-0.4516	-0.4632	0.1133	-0.0828	0.5859	-0.136	0.0417	0.4237	-0.0701	0.5963	19.3933	70.6285	-28.4691
7	4.0025	2.3273	3.5466	3.532	1.1835	4.1175	-0.0014	-0.005	-0.237	0.6447	0.01	-0.712	-0.4046	0.3	-0.0448	0.7598	0.0447	-0.0185	0.5786	0.009	0.5776	17.8216	64.6689	-4.2135
8	0.8801	0.6731	-0.1515	5.7493	-0.7255	1.7636	0.0287	-0.317	0.2798	1.0106	0.0215	0.5555	-0.5131	-0.1283	-0.0858	0.8211	0.1064	0.1056	0.509	-0.0862	0.6003	2.7073	71.4376	-8.5438
9	2.2852	0.8661	-3.7384	2.0531	-1.7248	8.1573	0.1158	-0.1796	0.2535	0.3504	0.2759	0.0035	-0.344	0.1707	-0.3716	0.5349	-0.0134	0.042	0.3061	-0.0736	0.4345	9.7184	57.9721	-16.8372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 70 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 192 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 193 through 332 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 333 through 428 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 70 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 71 through 204 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 205 through 230 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 231 through 360 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 361 through 428 )

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