PDB-6dxb: Crystal structure of chalcone synthase from Arabidopsis thaliana

ID or keywords:

Entry

Database: PDB / ID: 6dxb

Title

Crystal structure of chalcone synthase from Arabidopsis thaliana

Components

Chalcone synthase

Keywords

TRANSFERASE / Thiolase / Flavonoid / Polyketide synthase

Function / homology

Function and homology information

regulation of anthocyanin biosynthetic process / plant-type vacuole membrane / : / chalcone synthase / auxin polar transport / naringenin-chalcone synthase activity / response to jasmonic acid / response to auxin / flavonoid biosynthetic process / response to gravity ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.549 Å

Authors

Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.

Funding support

United States, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.
Authors: Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.

History

Deposition	Jun 28, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6dxb.cif.gz	878.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6dxb_validation.pdf.gz	433.3 KB	Display	wwPDB validaton report
Full document	6dxb_full_validation.pdf.gz	435.1 KB	Display
Data in XML	6dxb_validation.xml.gz	68.9 KB	Display
Data in CIF	6dxb_validation.cif.gz	105.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/6dxb ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dxb	HTTPS FTP

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Related structure data

Related structure data	6dx7C 6dx8C 6dx9C 6dxaC 6dxcC 6dxdC 6dxeC 6dxfC C: citing same article (ref.)
Similar structure data	1chw-1 1i8b-1 6dxe-d 1d6f-1 3wy0-d 1i88-1 6j1m-d 1i89-1 1bi5-1 1cgz-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Chalcone synthase

C: Chalcone synthase

B: Chalcone synthase

D: Chalcone synthase

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

1

A: Chalcone synthase

C: Chalcone synthase

defined by author&software
Evidence: gel filtration
86.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Chalcone synthase

D: Chalcone synthase

defined by author&software
86.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.640, 137.560, 108.560
Angle α, β, γ (deg.)	90.000, 95.590, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chalcone synthase / Naringenin-chalcone synthase / Protein TRANSPARENT TESTA 4 Mass: 43202.660 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CHS, TT4, At5g13930, MAC12.11, MAC12.14 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13114, chalcone synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1680 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.33 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 0.3 M ammonium acetate, 14% (v/v) PEG 8000, and 5 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2010
Radiation	Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.549→38.681 Å / Num. obs: 227280 / % possible obs: 98.48 % / Redundancy: 1.9 % / CC_1/2: 0.996 / R_merge(I) obs: 0.04372 / R_pim(I) all: 0.04372 / R_rim(I) all: 0.06182 / Net I/σ(I): 10.17
Reflection shell	Resolution: 1.549→1.604 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.2437 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 21992 / CC_1/2: 0.837 / R_pim(I) all: 0.2437 / R_rim(I) all: 0.3447 / % possible all: 95.43

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
PHENIX	1.8.4_1496	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.549→38.681 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.18

	R_factor	Num. reflection	% reflection
R_free	0.1633	1963	8.6 %
R_work	0.1407	-	-
obs	0.1409	227260	98.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 106.48 Å² / B_iso mean: 17.52 Å² / B_iso min: 5.25 Å²

Refinement step

Cycle: final / Resolution: 1.549→38.681 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11944	0	0	1680	13624
B_iso mean	-	-	-	28.32	-
Num. residues	-	-	-	-	1554

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	12306
X-RAY DIFFRACTION	f_angle_d	1.264	16676
X-RAY DIFFRACTION	f_chiral_restr	0.05	1892
X-RAY DIFFRACTION	f_plane_restr	0.007	2160
X-RAY DIFFRACTION	f_dihedral_angle_d	12.916	4576

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.549-1.5877	0.1997	133	0.1993	15331	15464	94
1.5877-1.6307	0.1982	137	0.1799	16014	16151	98
1.6307-1.6786	0.1977	137	0.1672	16092	16229	99
1.6786-1.7328	0.2011	142	0.1563	16098	16240	99
1.7328-1.7948	0.1745	141	0.149	16128	16269	99
1.7948-1.8666	0.1691	139	0.1475	16060	16199	98
1.8666-1.9516	0.1711	143	0.1418	16110	16253	98
1.9516-2.0545	0.1612	136	0.1361	16007	16143	98
2.0545-2.1832	0.1625	139	0.1316	16071	16210	98
2.1832-2.3517	0.1466	142	0.1274	16085	16227	99
2.3517-2.5883	0.1626	143	0.1324	16220	16363	99
2.5883-2.9627	0.1467	143	0.1385	16271	16414	100
2.9627-3.7323	0.1526	143	0.1384	16349	16492	100
3.7323-38.6926	0.1594	145	0.1323	16461	16606	100

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	0.894	0.6563	0.7986	1.3377	0.8882	1.5072	0.0045	-0.0804	-0.0033	0.0463	-0.0531	0.0149	0.1049	-0.1045	0.059	0.0543	0.0081	0.0162	0.0686	0.0045	0.0593	13.5837	-20.7577	16.3422
2	7.7437	0.4477	5.307	1.8136	-0.0207	3.781	0.1081	0.0365	-0.2478	-0.32	0.0228	0.0437	0.386	-0.0657	-0.3285	0.2387	-0.0416	0.0007	0.1101	-0.0221	0.1081	3.5151	-40.0806	-6.0147
3	0.5867	-0.9224	1.1472	2.222	-1.5058	2.6276	0.0286	-0.0518	-0.0588	-0.1561	0.0104	0.202	0.1981	-0.2631	-0.0345	0.1245	-0.0639	-0.0128	0.1429	-0.0238	0.1386	-1.0732	-27.7599	1.4857
4	1.3247	-0.0285	3.0933	0.3263	-0.2261	8.8298	0.0015	-0.1065	-0.0011	0.0071	0.03	0.1015	0.1085	-0.4037	-0.0773	0.0631	-0.0144	0.0099	0.0992	-0.006	0.0881	3.8056	-16.7786	14.6119
5	0.2225	0.0402	0.1135	0.5139	0.0879	0.6328	0.0002	0.0347	-0.027	-0.0358	0.0083	-0.0067	0.0406	-0.0253	-0.0075	0.0577	-0.0138	0.0012	0.075	-0.0001	0.0622	12.9101	-15.4172	13.0966
6	0.8211	-0.182	-0.7121	0.995	0.8478	1.7696	0.0048	-0.1074	-0.0515	0.154	0.0148	-0.0703	0.1282	0.1184	-0.0044	0.0999	0.0024	-0.0253	0.1078	0.0149	0.1049	24.5539	-18.4797	26.7171
7	5.1447	-3.1179	1.4419	1.899	-0.9144	0.4451	0.2084	0.3963	-0.3619	-0.2584	-0.1133	0.1242	0.2411	0.1091	-0.109	0.1583	0.0129	-0.0212	0.1357	-0.0544	0.1544	18.125	-23.253	-5.2665
8	2.1138	-0.0436	1.1943	1.4699	0.0243	3.6082	0.0091	0.0833	-0.1043	-0.0175	0.0296	-0.2563	0.2624	0.3668	-0.0061	0.1077	0.0359	-0.004	0.0676	-0.0111	0.1477	32.2309	-30.9717	12.6427
9	4.6805	-0.4017	-0.5521	0.838	0.5409	1.8416	-0.015	-0.0977	-0.3511	0.026	0.0654	-0.1651	0.3081	0.0783	-0.0447	0.1683	-0.0029	-0.0022	0.0511	-0.0043	0.1338	20.6933	-37.7156	12.6342
10	0.9205	0.0543	0.005	1.0551	-0.5959	2.6916	-0.0242	-0.0856	-0.087	0.1474	0.0013	-0.0783	0.1995	0.0288	0.0195	0.1207	0.0124	-0.012	0.0505	-0.0054	0.0984	22.5418	-29.0407	21.1537
11	1.3264	-0.2568	0.8858	1.1723	-0.3282	1.3029	-0.0164	0.067	0.0411	-0.0392	-0.0363	-0.0799	-0.12	0.0968	0.114	0.0394	0.0034	0.0276	0.0632	-0.0207	0.0617	24.16	2.2428	2.2261
12	3.6623	0.6545	3.6078	0.9281	1.0801	4.1793	-0.2112	-0.2286	0.2994	-0.5443	-0.1925	0.5791	-0.5062	-0.4559	0.3388	0.2716	0.1037	-0.1311	0.2068	-0.0349	0.2411	0.3961	15.1178	-12.1666
13	1.0589	0.4094	0.7413	0.8426	0.3623	1.0936	0.0017	0.0824	-0.0024	-0.1475	-0.0131	0.0197	-0.0642	0.0246	0.008	0.0909	-0.0017	0.0096	0.0941	0.0066	0.0617	17.2968	-0.1124	-10.5329
14	0.2672	0.0276	0.2339	0.4528	0.0002	0.8681	-0.0184	0.0237	-0.0152	-0.0411	-0.0024	-0.0169	-0.0359	0.002	-0.0068	0.0494	-0.0057	0.0007	0.0833	0.003	0.0855	22.3983	-4.1504	2.693
15	0.1034	-0.076	-0.1796	0.425	0.0438	0.6421	0.0194	-0.0352	0.0332	-0.0315	-0.0255	-0.0219	-0.0705	-0.0662	0.0549	0.0731	0.005	-0.0066	0.0705	0.0066	0.0784	16.3129	1.9661	9.4503
16	3.6325	0.7016	1.4172	1.658	0.5768	2.5676	-0.0137	-0.3034	0.2178	0.071	-0.0102	0.0464	-0.1241	-0.0701	-0.0054	0.0947	0.0118	-0.012	0.0476	-0.0078	0.1053	16.8851	14.0351	18.6336
17	2.3906	-0.2876	-0.6602	1.1711	1.1955	3.4196	0.0078	-0.0526	0.2588	-0.0769	0.0104	-0.0077	-0.3989	0.0049	-0.0035	0.1564	0.0023	-0.0245	0.0632	0.0209	0.1403	17.103	18.6207	6.1315
18	5.4085	1.9236	1.9282	2.7946	2.0875	2.6019	-0.1003	0.0826	0.1326	-0.2234	0.0663	-0.0957	-0.2837	0.1581	-0.0522	0.1066	-0.0245	0.0004	0.0883	0.0169	0.0916	28.5474	12.8101	3.7727
19	2.5006	1.145	-0.161	1.8451	-0.0385	1.1516	-0.0506	-0.0108	0.1266	0.0084	0.0349	-0.1027	-0.1994	0.1018	0.0006	0.0862	-0.0173	-0.0165	0.0668	-0.0006	0.0849	25.6455	11.7658	14.4394
20	0.6622	-0.2592	-0.1907	0.5938	0.0202	0.4323	-0.0196	0.0009	-0.0295	-0.0307	-0.01	0.0119	0.0477	-0.0124	0.0288	0.0719	-0.0171	0.0016	0.058	-0.002	0.076	-8.198	-30.8244	53.7727
21	1.5099	-0.7899	-1.1993	0.7494	0.5467	1.5086	-0.0432	-0.0961	-0.0054	0.0324	0.0289	-0.012	0.092	0.0127	-0.0189	0.0775	-0.0088	0.0069	0.058	0.002	0.0926	-9.5993	-31.22	59.2226
22	0.521	-0.0226	-0.1974	0.8202	-0.1585	0.7672	-0.0508	-0.1132	-0.0751	0.1177	0.0042	-0.0009	0.0891	0.0182	0.0498	0.1032	0.0231	0.0115	0.0922	0.0116	0.0817	-3.7153	-34.3884	71.1157
23	0.5581	0.2748	-0.6943	1.1026	-0.8473	2.0045	0.0535	-0.0524	0.0697	0.0837	-0.0122	0.043	-0.1288	0.0205	-0.0578	0.0373	0.0282	-0.018	0.0559	-0.0234	0.061	-9.6658	-3.0849	60.1893
24	4.5436	-0.7132	-3.932	1.7274	0.8116	3.4374	0.1949	0.3614	0.1523	-0.2261	-0.1686	-0.027	-0.0372	-0.1981	-0.0606	0.1558	0.0749	0.0048	0.1718	0.0198	0.0928	-5.4213	5.6094	31.6556
25	0.2894	-0.0769	-0.2081	0.3446	-0.1091	0.8272	-0.0091	-0.0614	0.0448	0.0506	-0.0031	-0.0588	-0.0488	0.0489	0.005	0.0786	-0.0013	-0.0169	0.0768	-0.0235	0.075	0.4598	-5.8874	58.0758
26	0.4467	0.0319	-0.3257	0.4026	-0.208	0.4384	0.0121	0.0242	0.0139	-0.0081	0.0039	0.0336	-0.0292	-0.0777	-0.0034	0.0983	0.0113	-0.0053	0.0854	-0.0179	0.0788	-10.0077	-8.0062	56.1003
27	0.8446	-0.0172	0.041	0.4872	-0.0916	0.1121	-0.0019	0.0621	0.0585	0.0108	-0.0265	0.0424	-0.0246	-0.1177	-0.014	0.0804	0.0142	-0.0013	0.0666	0.0119	0.0936	-16.4893	-8.8046	54.9837
28	1.9928	-0.0818	-1.0385	1.1381	0.3352	3.0211	0.0316	0.0582	-0.0016	-0.0894	-0.0602	0.2206	-0.0408	-0.3585	0.0251	0.0901	0.0364	-0.0305	0.1135	-0.0041	0.1486	-30.2872	-2.5376	54.1345
29	3.2395	0.8984	0.5283	1.0953	0.2916	2.1304	0.0229	-0.0049	0.2737	-0.0958	0.0269	0.247	-0.1745	-0.1958	-0.0213	0.1369	0.0349	-0.0163	0.0782	0.0072	0.144	-21.4794	6.6839	50.1948
30	3.5356	-1.8966	-1.7642	2.6454	2.0269	3.6067	0.0574	-0.0506	0.1059	-0.0454	-0.0204	0.0141	-0.2656	-0.0007	-0.0558	0.1213	0.0092	0.0042	0.0772	-0.0046	0.0717	-15.7465	6.6754	61.9753
31	0.8448	-0.3086	-0.2739	3.1394	1.5917	1.7322	0.0297	-0.042	0.1108	0.1011	-0.0212	0.1531	-0.135	-0.1532	0.0057	0.0909	0.037	0.0126	0.0869	-0.0052	0.0961	-24.8357	0.2873	62.0112

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 48 )	A	7 - 48
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 67 )	A	49 - 67
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 95 )	A	68 - 95
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 96 through 122 )	A	96 - 122
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 123 through 230 )	A	123 - 230
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 231 through 252 )	A	231 - 252
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 253 through 276 )	A	253 - 276
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 277 through 312 )	A	277 - 312
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 313 through 343 )	A	313 - 343
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 344 through 395 )	A	344 - 395
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 8 through 48 )	C	8 - 48
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 49 through 67 )	C	49 - 67
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 68 through 122 )	C	68 - 122
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 123 through 230 )	C	123 - 230
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 231 through 276 )	C	231 - 276
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 277 through 312 )	C	277 - 312
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 313 through 343 )	C	313 - 343
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 344 through 362 )	C	344 - 362
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 363 through 395 )	C	363 - 395
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 7 through 184 )	B	7 - 184
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 185 through 242 )	B	185 - 242
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 243 through 395 )	B	243 - 395
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 8 through 48 )	D	8 - 48
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 49 through 68 )	D	49 - 68
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 69 through 159 )	D	69 - 159
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 160 through 230 )	D	160 - 230
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 231 through 276 )	D	231 - 276
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 277 through 312 )	D	277 - 312
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 313 through 343 )	D	313 - 343
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 344 through 362 )	D	344 - 362
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 363 through 395 )	D	363 - 395

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