PDB-6dx8: Crystal structure of chalcone synthase from Selaginella moellendorffii

ID or keywords:

Entry

Database: PDB / ID: 6dx8

Title

Crystal structure of chalcone synthase from Selaginella moellendorffii

Components

Chalcone synthase

Keywords

TRANSFERASE / Thiolase / Flavonoid / Polyketide synthase

Function / homology

Function and homology information

polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

Selaginella moellendorffii (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 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	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6dx8.cif.gz	431.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	6dx8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6dx8_validation.pdf.gz	439.4 KB	Display	wwPDB validaton report
Full document	6dx8_full_validation.pdf.gz	441.8 KB	Display
Data in XML	6dx8_validation.xml.gz	32.1 KB	Display
Data in CIF	6dx8_validation.cif.gz	48.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/6dx8 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dx8	HTTPS FTP

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Related structure data

Related structure data	6dx7C 6dx9C 6dxaC 6dxbC 6dxcC 6dxdC 6dxeC 6dxfC C: citing same article (ref.)
Similar structure data	6dxc-d 4kti-d 1d6i-2 3wd8-1 6cqb-d 3eut-2 3a5q-d 6l7j-1 6dxf-d 6dx7-2 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

B: Chalcone synthase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	55.170, 66.670, 102.550
Angle α, β, γ (deg.)	90.000, 91.350, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Chalcone synthase Mass: 41993.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selaginella moellendorffii (plant) / Plasmid: pHis8-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D8S128
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.34 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.1 M MOPSO (pH 6.6), 0.3 M Mg(NO3)2, 19% (v/v) PEG 4000, and 5 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2015
Radiation	Monochromator: single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.7→39.01 Å / Num. obs: 145478 / % possible obs: 90.6 % / Redundancy: 6 % / CC_1/2: 0.995 / R_merge(I) obs: 0.1427 / R_pim(I) all: 0.06384 / R_rim(I) all: 0.1566 / Net I/σ(I): 12.32
Reflection shell	Resolution: 1.7→1.761 Å / Redundancy: 6.2 % / Num. unique obs: 6434 / CC_1/2: 0.822 / R_pim(I) all: 0.51 / % possible all: 79.18

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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: 1.7→39.009 Å / FOM work R set: 0.8327 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 24.07 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2349	3936	2.71 %
R_work	0.1911	141542	-
obs	0.1923	145478	90.52 %

Solvent computation

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

Displacement parameters

B_iso max: 146.28 Å² / B_iso mean: 22.24 Å² / B_iso min: 4.42 Å²

Refinement step

Cycle: final / Resolution: 1.7→39.009 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5770	0	0	549	6319
B_iso mean	-	-	-	29.55	-
Num. residues	-	-	-	-	757

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	5890
X-RAY DIFFRACTION	f_angle_d	1.313	7984
X-RAY DIFFRACTION	f_chiral_restr	0.054	919
X-RAY DIFFRACTION	f_plane_restr	0.007	1029
X-RAY DIFFRACTION	f_dihedral_angle_d	12.705	2188

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7207	0.3707	107	0.3179	4408	4515	79
1.7207-1.7425	0.2965	134	0.3104	4383	4517	79
1.7425-1.7655	0.4079	121	0.302	4449	4570	80
1.7655-1.7896	0.335	137	0.302	4503	4640	81
1.7896-1.8152	0.3232	131	0.2888	4588	4719	83
1.8152-1.8423	0.3221	135	0.2763	4757	4892	84
1.8423-1.8711	0.3529	129	0.2646	4814	4943	87
1.8711-1.9018	0.307	127	0.2778	4747	4874	85
1.9018-1.9346	0.408	135	0.3117	4864	4999	87
1.9346-1.9697	0.219	141	0.2351	4817	4958	86
1.9697-2.0076	0.2617	139	0.219	4864	5003	88
2.0076-2.0486	0.284	127	0.2156	4905	5032	87
2.0486-2.0931	0.3527	140	0.2507	4900	5040	88
2.0931-2.1418	0.2404	133	0.2009	4971	5104	89
2.1418-2.1954	0.2578	135	0.1994	5040	5175	90
2.1954-2.2547	0.3078	137	0.24	5149	5286	92
2.2547-2.3211	0.2527	151	0.1962	5111	5262	92
2.3211-2.396	0.2614	140	0.1763	5268	5408	93
2.396-2.4816	0.2137	148	0.1735	5284	5432	95
2.4816-2.5809	0.2163	150	0.1729	5322	5472	96
2.5809-2.6984	0.2101	158	0.1735	5463	5621	97
2.6984-2.8406	0.203	160	0.1689	5462	5622	98
2.8406-3.0185	0.2318	152	0.1696	5554	5706	99
3.0185-3.2515	0.1727	146	0.1601	5590	5736	100
3.2515-3.5785	0.1834	153	0.1504	5571	5724	100
3.5785-4.0958	0.1644	149	0.1387	5602	5751	100
4.0958-5.1584	0.1736	156	0.1238	5589	5745	100
5.1584-39.0188	0.1938	165	0.1692	5567	5732	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	0.5824	-0.019	0.0111	0.3143	0.1977	1.321	-0.1096	0.3111	-0.1074	-0.1524	-0.0431	0.079	-0.1516	-0.0673	0.0099	0.1579	-0.0508	-0.0478	0.2863	-0.0203	0.1153	46.1944	-15.1443	113.2513
2	0.2421	0.1333	0.0485	1.0785	0.4054	1.7084	-0.1643	0.3916	-0.1053	-0.1681	0.0562	0.0199	-0.0238	0.0593	0.1255	0.1437	-0.0363	-0.0159	0.3137	-0.1168	0.1614	46.6026	-19.7357	105.8838
3	1.6475	-0.5682	-0.5952	1.5439	0.4879	1.6701	-0.0556	0.2707	0.0543	-0.2615	-0.0079	0.2629	-0.1413	-0.261	0.0107	0.235	-0.0581	-0.0964	0.4458	0.0923	0.1873	52.5859	-3.673	103.7542
4	1.2298	0.4647	-1.4062	0.5933	-1.0184	2.7464	-0.0004	0.1293	0.0664	0.0061	-0.068	0.0689	-0.1953	0.0032	-0.0546	0.1059	0.0054	-0.0352	0.1226	0.0089	0.0946	49.71	-5.2768	124.9539
5	0.7134	0.0918	-0.1453	0.7152	0.066	0.5277	-0.0133	-0.0179	0.0695	-0.047	-0.0115	0.0724	-0.1082	0.0764	-0.004	0.0671	0.0098	-0.0116	0.0757	-0.0051	0.0776	55.1427	-3.8362	134.3541
6	0.8216	0.0712	0.0214	0.3819	-0.0199	0.5723	-0.1039	0.1724	-0.1557	-0.0913	0.027	0.0483	-0.0042	0.0213	0.0349	0.0753	-0.0058	-0.0123	0.1028	-0.0234	0.0778	57.2412	-14.6666	124.4638
7	0.6465	0.0247	-0.0412	0.4916	0.0339	0.4061	-0.0846	0.0505	-0.2078	-0.0482	0.0391	0.0923	0.0669	-0.0735	0.06	0.0911	0.0144	-0.0003	0.0954	0.0295	0.1442	59.8524	-22.5798	130.6409
8	0.3212	-0.0428	0.2027	1.7203	-0.2129	0.3464	-0.0549	0.1664	-0.2342	-0.1124	0.0149	-0.0598	0.0968	0.1122	0.0314	0.1536	0.002	0.0227	0.1147	-0.0677	0.234	63.7554	-26.5063	115.0813
9	0.6206	0.0453	-0.1455	0.5321	0.0212	0.2604	-0.0579	-0.0643	-0.4704	-0.028	0.0119	0.0591	0.0894	0.0032	-0.0243	0.0751	-0.0061	0.0133	0.047	0.0172	0.2768	51.2577	-31.1156	128.7077
10	0.5056	0.0598	0.0133	0.9839	-0.5446	0.6411	-0.0363	0.1351	0.1887	-0.0939	0.0705	-0.0001	-0.0642	-0.0074	-0.0055	0.1086	-0.0407	0.0458	0.1036	0.158	0.0839	84.6169	4.287	123.2658
11	0.6375	0.0554	0.6691	0.8896	-0.0277	0.7196	-0.0409	0.2844	0.1914	-0.1653	0.0542	-0.0264	-0.127	0.0385	0.0299	0.1969	-0.0403	0.0217	0.1781	0.12	0.1865	82.0296	10.0553	116.1638
12	0.9513	-0.7125	1.3037	0.893	-1.3469	2.5112	0.0111	0.2349	-0.0455	-0.1084	0.0134	0.0146	0.0641	0.1288	0.0518	0.1168	-0.0028	0.0038	0.1029	0.0225	0.0648	81.5196	-10.7279	122.1962
13	0.7814	0.0748	-0.0479	0.3438	-0.0984	0.3275	-0.032	0.0927	-0.0141	-0.0741	0.0034	0.0065	-0.0353	0.0255	0.0128	0.0882	-0.0067	0.0025	0.0703	0.0239	0.0538	74.6768	-9.5537	128.4617
14	0.1915	-0.3098	0.2743	1.3614	-0.4835	0.4538	-0.0152	-0.2026	-0.1379	-0.0133	-0.0483	-0.0057	0.0206	0.0411	0.0235	0.0933	0.0244	0.0208	0.1461	0.0453	0.0609	76.6441	-11.1652	146.1761
15	0.5669	0.2958	0.0768	0.257	0.2779	1.3923	-0.0685	0.0997	0.2381	-0.0848	-0.0341	0.0751	-0.2283	0.023	-0.0957	0.1991	-0.0042	-0.0688	0.1422	0.0915	0.2086	64.5797	8.317	124.8989
16	0.8306	-0.3204	0.2685	3.4126	-3.2039	4.0126	-0.0572	-0.2818	0.1491	0.037	0.0618	0.1666	0.0015	-0.0372	-0.0818	0.1253	0.0233	0.0136	0.1972	-0.0588	0.1568	68.8025	4.9323	149.5975
17	0.7313	-0.136	-0.02	0.9117	0.1958	1.6787	0.0151	-0.1062	0.1848	0.0005	0.0347	-0.0465	-0.1402	0.0184	-0.0217	0.0773	-0.0093	-0.0071	0.0703	-0.0334	0.0929	80.8708	7.7739	143.1664
18	0.7288	-0.0359	0.0155	0.4303	-0.0669	0.7305	0.0173	-0.1703	0.0526	-0.0298	0.012	-0.0318	0.0064	0.0544	-0.0102	0.0738	-0.0087	-0.0029	0.0865	-0.0154	0.0629	81.7279	-1.5219	143.4253

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 9 through 44 )	A	9 - 44
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 68 )	A	45 - 68
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 85 )	A	69 - 85
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 112 )	A	86 - 112
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 113 through 149 )	A	113 - 149
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 150 through 220 )	A	150 - 220
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 221 through 253 )	A	221 - 253
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 254 through 276 )	A	254 - 276
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 277 through 386 )	A	277 - 386
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 8 through 44 )	B	8 - 44
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 45 through 85 )	B	45 - 85
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 86 through 112 )	B	86 - 112
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 113 through 220 )	B	113 - 220
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 221 through 240 )	B	221 - 240
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 241 through 264 )	B	241 - 264
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 265 through 288 )	B	265 - 288
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 289 through 336 )	B	289 - 336
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 337 through 386 )	B	337 - 386

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