PDB-4wum: X-ray crystal structure of Chalcone Synthase from Freesia hybrida

ID or keywords:

Entry

Database: PDB / ID: 4wum

Title

X-ray crystal structure of Chalcone Synthase from Freesia hybrida

Components

Chalcone synthase

Keywords

TRANSFERASE / Chalon Synthase 2 /

Polyketide synthase

Function / homology

Function and homology information

chalcone synthase /

naringenin-chalcone synthase activity / biosynthetic process
Similarity search - Function

Biological species

Freesia hybrid cultivar (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.77 Å

Authors

Almqvist, J. / Jiang, W.S. / Wang, L. / Huang, Y.

Citation

Journal: Plos One / Year: 2015
Title: Molecular and Biochemical Analysis of Chalcone Synthase from Freesia hybrid in Flavonoid Biosynthetic Pathway.
Authors: Sun, W. / Meng, X. / Liang, L. / Jiang, W. / Huang, Y. / He, J. / Hu, H. / Almqvist, J. / Gao, X. / Wang, L.

History

Deposition	Nov 2, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Nov 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4wum.cif.gz	628.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4wum.ent.gz	517.6 KB	Display	PDB format
PDBx/mmJSON format	4wum.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/wu/4wum ftp://data.pdbj.org/pub/pdb/validation_reports/wu/4wum	HTTPS FTP

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Related structure data

Related structure data	1bi5S S: Starting model for refinement
Similar structure data	1u0u-2 1cgz-1 1u0v-d 6dxd-1 1jwx-1 1u0u-1 1bq6-1 1z1e-1 1d6f-1 6l78-1 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

B: Chalcone synthase

C: Chalcone synthase

D: Chalcone synthase

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

1

A: Chalcone synthase

B: Chalcone synthase

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

2

C: Chalcone synthase

D: Chalcone synthase

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

Unit cell

Length a, b, c (Å)	79.430, 79.510, 232.340
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid A
2	1	chain B and segid A
3	1	chain C and segid A
4	1	chain D and segid A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain A and segid A	A
2	1	1	chain B and segid A	B
3	1	1	chain C and segid A	C
4	1	1	chain D and segid A	D

#1: Protein	Chalcone synthase / Mass: 42641.012 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Freesia hybrid cultivar (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: G3FJ87, chalcone synthase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1796 / 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: 2.15 Å³/Da / Density % sol: 42.81 %
Crystal grow	Temperature: 302 K / Method: vapor diffusion Details: 20% w/v PEG 3350, 0.2M di-ammonium hydrogen citrate

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Data collection

Diffraction

Mean temperature: 105 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-2 / Wavelength: 0.9334 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2012

Radiation

Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9334 Å / Relative weight: 1

Reflection

Resolution: 1.77→50 Å / Num. obs: 143780 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16 % / R_merge F obs: 0.997 / R_merge(I) obs: 0.148 / R_rim(I) all: 0.16 / Χ²: 0.993 / Net I/σ(I): 11.63 / Num. measured all: 1012203

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.77-1.82		0.624	0.918	1.66	46142	10534	10449	1.042	99.2
1.82-1.87		0.727	0.779	2.29	54542	10191	10185	0.864	99.9
1.87-1.92		0.854	0.694	3.1	69611	10023	10023	0.75	100
1.92-1.98		0.919	0.539	4.25	73149	9727	9727	0.579	100
1.98-2.04		0.938	0.45	5.12	70938	9436	9436	0.483	100
2.04-2.12		0.953	0.37	6.15	68504	9106	9104	0.398	100
2.12-2.2		0.971	0.298	7.47	66291	8808	8808	0.321	100
2.2-2.29		0.979	0.246	8.89	63736	8474	8473	0.264	100
2.29-2.39		0.983	0.228	9.44	61235	8134	8133	0.245	100
2.39-2.5		0.986	0.192	11.02	58842	7825	7824	0.207	100
2.5-2.64		0.991	0.166	12.4	55665	7398	7398	0.179	100
2.64-2.8		0.993	0.141	14.39	52730	7043	7042	0.152	100
2.8-2.99		0.995	0.117	16.81	49457	6627	6627	0.126	100
2.99-3.23		0.997	0.092	20.06	46113	6222	6221	0.099	100
3.23-3.54		0.998	0.068	25.06	42018	5696	5695	0.073	100
3.54-3.96		0.998	0.056	28.92	38045	5208	5207	0.06	100
3.96-4.57		0.999	0.047	32.45	33253	4600	4599	0.051	100
4.57-5.6		0.999	0.047	32.13	28369	3942	3942	0.051	100
5.6-7.92		0.999	0.051	29.12	21919	3101	3099	0.055	99.9
	7.92	0.999	0.036	34.92	11644	1800	1788	0.039	99.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	8.37 Å	46.9 Å
Translation	8.37 Å	46.9 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BI5

1bi5

Resolution: 1.77→46.903 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2271	7191	5 %
R_work	0.1857	136546	-
obs	0.1878	143737	99.89 %

Solvent computation

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

Displacement parameters

B_iso max: 135.94 Å² / B_iso mean: 20.0176 Å² / B_iso min: 4.96 Å²

Refinement step

Cycle: final / Resolution: 1.77→46.903 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11956	0	0	1796	13752
B_iso mean	-	-	-	29.1	-
Num. residues	-	-	-	-	1556

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	12168
X-RAY DIFFRACTION	f_angle_d	1.275	16444
X-RAY DIFFRACTION	f_chiral_restr	0.062	1876
X-RAY DIFFRACTION	f_plane_restr	0.006	2124
X-RAY DIFFRACTION	f_dihedral_angle_d	13.942	4580

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	7488	X-RAY DIFFRACTION	4.211	TORSIONAL
1	2	B	7488	X-RAY DIFFRACTION	4.211	TORSIONAL
1	3	C	7488	X-RAY DIFFRACTION	4.211	TORSIONAL
1	4	D	7488	X-RAY DIFFRACTION	4.211	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7699-1.79	0.2959	229	0.2645	4397	4626	98
1.79-1.8111	0.3184	237	0.2547	4504	4741	99
1.8111-1.8332	0.2709	229	0.2342	4474	4703	100
1.8332-1.8564	0.2872	235	0.229	4503	4738	100
1.8564-1.8808	0.2748	232	0.2301	4511	4743	100
1.8808-1.9066	0.2886	245	0.2213	4516	4761	100
1.9066-1.9338	0.2462	242	0.1957	4546	4788	100
1.9338-1.9627	0.2502	235	0.1845	4459	4694	100
1.9627-1.9934	0.2523	242	0.1895	4550	4792	100
1.9934-2.026	0.2386	235	0.1863	4499	4734	100
2.026-2.061	0.2461	238	0.1903	4515	4753	100
2.061-2.0984	0.2564	232	0.1889	4558	4790	100
2.0984-2.1388	0.2213	237	0.1777	4490	4727	100
2.1388-2.1825	0.2499	239	0.1826	4522	4761	100
2.1825-2.2299	0.1956	238	0.1724	4513	4751	100
2.2299-2.2818	0.1895	239	0.1762	4572	4811	100
2.2818-2.3388	0.2252	242	0.1817	4562	4804	100
2.3388-2.4021	0.2415	237	0.1861	4515	4752	100
2.4021-2.4728	0.2017	239	0.1796	4525	4764	100
2.4728-2.5526	0.233	242	0.182	4575	4817	100
2.5526-2.6438	0.2283	243	0.1846	4539	4782	100
2.6438-2.7496	0.2184	242	0.1803	4553	4795	100
2.7496-2.8748	0.2318	243	0.1879	4558	4801	100
2.8748-3.0263	0.2004	239	0.1857	4599	4838	100
3.0263-3.2159	0.2471	240	0.1803	4567	4807	100
3.2159-3.4641	0.2109	246	0.1769	4602	4848	100
3.4641-3.8126	0.2041	244	0.1667	4608	4852	100
3.8126-4.3639	0.2119	253	0.1667	4641	4894	100
4.3639-5.4967	0.2208	244	0.1647	4695	4939	100
5.4967-46.919	0.19	253	0.2018	4878	5131	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	0.9858	-0.06	-0.1969	0.5718	0.312	1.5371	0.0028	0.2501	-0.0818	-0.0768	0.0259	-0.1549	0.0357	0.1767	0.0281	0.0725	-0.0077	-0.0012	0.0885	0.002	0.1136	35.6384	-10.0146	-62.0257
2	0.5837	-0.0286	-0.0906	0.4483	-0.2243	1.6466	0.0278	0.0843	-0.1109	-0.08	-0.0275	-0.0109	0.15	0.0615	0.0177	0.0998	0.0184	-0.01	0.0597	-0.0154	0.0932	22.7734	-14.6289	-63.1362
3	1.1143	0.9397	0.8394	3.4212	0.1523	1.8278	0.0537	-0.0281	-0.0416	-0.0147	-0.0276	0.2123	0.2799	-0.1668	-0.1227	0.0694	-0.0284	0.0086	0.064	-0.0459	0.1301	11.6095	-11.8042	-49.1712
4	0.3348	-0.0043	0.3609	0.3676	0.1363	0.4517	0.0019	0.092	0.0057	0.0097	0.0021	-0.0515	-0.1205	0.1159	-0.0152	0.089	0.004	-0.0142	0.0692	0.0076	0.081	24.5045	-3.6354	-49.7913
5	0.5231	0.1424	-0.1938	2.6171	-0.0422	1.422	-0.004	-0.0606	-0.0187	0.2079	-0.0005	0.2208	-0.0214	-0.0523	0.1176	0.1625	-0.0259	0.0345	0.0512	0.0083	0.0731	19.2385	-12.9563	-40.2154
6	0.5591	-0.0654	0.2388	0.49	0.4895	0.6563	-0.0032	0.1087	-0.0049	-0.0357	0.0131	-0.1173	-0.0911	0.1661	0.0138	0.0848	-0.0154	0.0127	0.1015	-0.0033	0.0964	32.6915	-3.8573	-59.6522
7	0.9346	-0.0569	-0.071	0.6145	-0.1197	1.2808	-0.0016	-0.0362	-0.0485	0.0883	0.0367	-0.2364	0.0124	0.2054	0.0135	0.0817	0.0092	-0.0307	0.0984	-0.0095	0.1476	43.066	-5.2288	-48.0479
8	0.56	-0.144	-0.0222	0.6207	0.054	0.5838	0.0078	0.0642	0.0714	-0.0813	-0.0475	0.0358	-0.1208	-0.0432	0.0328	0.1113	0.0153	-0.0091	0.0521	-0.0062	0.0847	10.7183	10.0642	-62.1026
9	4.9503	3.0117	-0.8504	6.4173	0.8055	1.9812	-0.0419	0.0064	0.1803	-0.081	0.0267	-0.2628	-0.1789	0.2527	-0.1654	0.0676	-0.037	-0.0249	0.1035	0.0351	0.1105	28.1871	9.0809	-48.8907
10	0.1183	-0.0725	-0.077	0.2333	-0.0036	0.0653	0.0022	0.0503	0.0091	-0.0327	-0.0203	0.0628	0.0841	0.0412	0.0152	0.1075	0.0036	-0.0092	0.0771	0.0036	0.0788	15.2586	0.9218	-49.629
11	1.4272	-0.3271	0.1666	2.9822	-0.4252	1.1064	-0.0113	-0.2517	0.1401	0.0729	0.0168	-0.1313	-0.0875	0.0999	0.0038	0.1253	-0.0201	-0.0442	0.1148	-0.0277	0.0813	20.6562	9.9302	-39.8783
12	0.4346	-0.0514	0.0642	0.579	-0.2271	0.5465	0	0.0113	-0.0054	-0.0032	-0.0357	0.0743	0.0108	-0.0862	0.0471	0.0813	0.0161	-0.0169	0.059	-0.0186	0.0775	6.8969	4.233	-56.0568
13	3.1039	0.811	-1.5835	1.5073	-1.5258	1.7631	-0.0301	0.0488	-0.3052	-0.081	-0.1003	0.2725	0.364	-0.2692	-0.067	0.1264	-0.0708	0.0175	0.1563	-0.0242	0.1538	7.1703	-6.8621	-69.1181
14	0.7415	0.0277	0.2895	0.6985	0.1164	1.2281	-0.0055	-0.0932	0.0928	0.1139	-0.0243	0.2158	-0.0527	-0.1585	0.019	0.086	0.0127	0.0279	0.0842	-0.0198	0.1307	-3.336	2.4039	-47.6671
15	0.3817	-0.0112	0.1212	0.5475	-0.1873	0.8351	-0.0101	0.0579	-0.0704	-0.1345	0.0213	0.1016	0.1457	-0.0244	0.0191	0.0873	-0.0162	-0.0125	0.0963	-0.0032	0.0978	7.4248	-8.9567	-4.5424
16	3.1559	-1.572	-0.2993	1.86	-1.5108	2.5869	-0.0201	0.0122	0.1786	0.0058	0.0466	0.2216	-0.2887	-0.2051	-0.0506	0.093	0.022	-0.0419	0.0637	-0.0313	0.1488	8.0775	8.2657	8.8835
17	0.0876	0.0154	-0.1171	0.3777	-0.2448	0.29	0.0127	0.0125	-0.0727	-0.0711	0.0361	-0.0952	0.0931	0.064	-0.0688	0.0611	-0.0052	-0.0066	0.0986	0.0196	0.0866	16.4693	-5.408	6.3854
18	4.3833	-0.0361	-0.2434	2.8155	-1.0354	1.7924	-0.0442	-0.3091	0.1667	0.4307	0.0726	0.2609	-0.2061	-0.0976	-0.065	0.0853	0.0143	0.0409	0.1445	-0.0371	0.0794	12.3427	1.6762	22.0944
19	0.6451	0.1411	0.5423	0.7634	-0.006	0.4736	-0.028	-0.0072	-0.1215	-0.0642	0.0057	0.0428	0.0949	0.0797	0.057	0.0731	0.0123	0.0015	0.0777	0.0011	0.0768	12.6166	-12.2113	2.4671
20	0.6064	-1.5327	1.4562	3.8801	-3.6854	3.4985	0.0997	0.1453	-0.0926	-0.331	-0.2489	-0.1131	0.3338	0.3756	0.1009	0.1459	0.0485	0.0031	0.1336	-0.0088	0.1647	25.4941	-16.0368	-6.9434
21	0.6008	0.1302	-0.024	1.0248	0.1588	1.4004	0.0499	-0.0821	-0.2241	0.0598	-0.0006	0.0532	0.218	0.0024	0.0048	0.0976	-0.0062	-0.0065	0.0766	0.0341	0.1435	13.6524	-23.141	10.5769
22	0.5921	0.1402	0.0675	0.6766	-0.0228	0.6739	-0.0461	0.0803	0.034	-0.0702	0.0029	-0.0578	-0.0352	0.1164	0.043	0.05	-0.0131	-0.0046	0.1017	0.0064	0.0794	29.926	9.1576	-4.0054
23	5.8108	-2.6876	0.0617	3.7366	1.1734	0.7366	0.0428	0.127	-0.2541	-0.0719	-0.0808	-0.2096	0.3242	0.1578	-0.0837	0.1078	0.0449	0.0231	0.0849	0.0329	0.1094	28.926	-8.3633	9.2018
24	0.0981	0.0013	-0.0288	0.0756	0.0715	0.1211	-0.0356	0.0465	0.0572	-0.0329	0.0232	0.0296	0.0041	-0.1164	0.0146	0.0804	-0.0086	0.0001	0.117	0.0092	0.0944	20.7758	4.6056	8.4594
25	2.0506	-0.2013	-0.3611	0.9015	-0.0018	2.8698	0.0243	-0.1019	-0.1367	0.1936	0.0409	-0.1192	0.1294	0.0189	-0.0256	0.099	0.0248	-0.0252	0.1213	0.0466	0.0758	29.7498	-0.7986	18.2203
26	0.4926	0.1156	-0.2468	0.5034	0.083	0.5294	-0.0341	-0.0194	0.0496	-0.0076	0.0051	0.007	-0.1099	-0.0044	0.0428	0.0612	-0.012	-0.0159	0.0801	0.013	0.0748	24.0783	12.9694	2.0326
27	2.011	-1.248	-1.5549	3.4642	1.7315	1.4213	-0.1001	0.0174	0.2463	-0.0691	-0.0036	0.2518	-0.317	-0.4099	-0.0416	0.1636	0.081	-0.0317	0.1516	0.006	0.1406	13.0598	12.7759	-11.1026
28	0.6376	0.0865	0.0085	0.7018	-0.226	1.1212	-0.0445	-0.1102	0.2203	0.1083	0.0088	-0.0834	-0.1646	0.052	0.0089	0.0963	-0.0079	-0.0295	0.0841	-0.0299	0.1383	22.2603	23.2308	10.4164

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 1:69)	A	1 - 69
2	X-RAY DIFFRACTION	2	(chain A and resid 70:151)	A	70 - 151
3	X-RAY DIFFRACTION	3	(chain A and resid 152:156)	A	152 - 156
4	X-RAY DIFFRACTION	4	(chain A and resid 157:181)	A	157 - 181
5	X-RAY DIFFRACTION	5	(chain A and resid 182:187)	A	182 - 187
6	X-RAY DIFFRACTION	6	(chain A and resid 188:270)	A	188 - 270
7	X-RAY DIFFRACTION	7	(chain A and resid 271:389)	A	271 - 389
8	X-RAY DIFFRACTION	8	(chain B and resid 1:151)	B	1 - 151
9	X-RAY DIFFRACTION	9	(chain B and resid 152:156)	B	152 - 156
10	X-RAY DIFFRACTION	10	(chain B and resid 157:181)	B	157 - 181
11	X-RAY DIFFRACTION	11	(chain B and resid 182:187)	B	182 - 187
12	X-RAY DIFFRACTION	12	(chain B and resid 188:250)	B	188 - 250
13	X-RAY DIFFRACTION	13	(chain B and resid 251:270)	B	251 - 270
14	X-RAY DIFFRACTION	14	(chain B and resid 271:389)	B	271 - 389
15	X-RAY DIFFRACTION	15	(chain C and resid 1:151)	C	1 - 151
16	X-RAY DIFFRACTION	16	(chain C and resid 152:156)	C	152 - 156
17	X-RAY DIFFRACTION	17	(chain C and resid 157:178)	C	157 - 178
18	X-RAY DIFFRACTION	18	(chain C and resid 179:183)	C	179 - 183
19	X-RAY DIFFRACTION	19	(chain C and resid 184:250)	C	184 - 250
20	X-RAY DIFFRACTION	20	(chain C and resid 251:279)	C	251 - 279
21	X-RAY DIFFRACTION	21	(chain C and resid 280:389)	C	280 - 389
22	X-RAY DIFFRACTION	22	(chain D and resid 1:151)	D	1 - 151
23	X-RAY DIFFRACTION	23	(chain D and resid 152:156)	D	152 - 156
24	X-RAY DIFFRACTION	24	(chain D and resid 157:181)	D	157 - 181
25	X-RAY DIFFRACTION	25	(chain D and resid 182:187)	D	182 - 187
26	X-RAY DIFFRACTION	26	(chain D and resid 188:250)	D	188 - 250
27	X-RAY DIFFRACTION	27	(chain D and resid 251:270)	D	251 - 270
28	X-RAY DIFFRACTION	28	(chain D and resid 271:389)	D	271 - 389

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