PDB-4hvm: Crystal structure of tallysomycin biosynthesis protein TlmII

ID or keywords:

Entry

Database: PDB / ID: 4hvm

Title

Crystal structure of tallysomycin biosynthesis protein TlmII

Components

TlmII

Keywords

BIOSYNTHETIC PROTEIN / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / Natural Product Biosynthesis / NATPRO / Enzyme Discovery for Natural Product Biosynthesis / Nonribosomal peptide synthetases / GO.119753

Function / homology

Nonribosomal peptide synthetase, condensation domain / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Condensation domain / Condensation domain / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta / TlmII

Function and homology information

Biological species

Streptoalloteichus hindustanus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.704 Å

Authors

Chang, C. / Bigelow, L. / Bearden, J. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. ...

Citation

Journal: To be Published
Title: Crystal structure of tallysomycin biosynthesis protein TlmII
Authors: Chang, C. / Bigelow, L. / Bearden, J. / Babnigg, G. / Bingman, C.A. / Yennamalli, R. / Lohman, J. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Joachimiak, A.

History

Deposition	Nov 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 21, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 18, 2013	Group: Structure summary
Revision 1.2	Apr 16, 2014	Group: Experimental preparation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4hvm.cif.gz	638.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4hvm_validation.pdf.gz	468.7 KB	Display	wwPDB validaton report
Full document	4hvm_full_validation.pdf.gz	476.5 KB	Display
Data in XML	4hvm_validation.xml.gz	53 KB	Display
Data in CIF	4hvm_validation.cif.gz	71.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hv/4hvm ftp://data.pdbj.org/pub/pdb/validation_reports/hv/4hvm	HTTPS FTP

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Related structure data

Similar structure data	2jjh-d 5iil-d 4uho-d 2jje-d 2cjh-d 5iin-d 4el4-d 6fyq-d 2xar-1 2jjg-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC109184

Similar structure data

Other databases

TargetTrack: MCSG-APC109184

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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: TlmII

B: TlmII

C: TlmII

D: TlmII

hetero molecules

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

1

A: TlmII

hetero molecules

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

2

B: TlmII

hetero molecules

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

3

C: TlmII

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

4

D: TlmII

hetero molecules

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

Unit cell

Length a, b, c (Å)	123.799, 128.015, 129.307
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	TlmII Mass: 54115.988 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria) Gene: tlmII / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: A4KUC0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.37 Å³/Da / Density % sol: 48.03 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.32M Ammonium Sulfate,0.1M HEPES, 22% PEG3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2012
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97921 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. all: 56751 / Num. obs: 56697 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / R_merge(I) obs: 0.09 / Net I/σ(I): 21.4
Reflection shell	Resolution: 2.7→2.72 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.957 / Num. unique all: 1383 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
MLPHARE		phasing
DM		model building
SHELXDE		phasing
RESOLVE		model building
ARP/wARP		model building
COO		model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing
COO		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.704→44.711 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 21.97 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2322	4323	5.13 %	RANDOM
R_work	0.1817	-	-	-
all	0.1843	84237	-	-
obs	0.1843	51539	77.64 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.704→44.711 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12705	0	20	65	12790

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	13010
X-RAY DIFFRACTION	f_angle_d	0.628	17749
X-RAY DIFFRACTION	f_dihedral_angle_d	12.104	4698
X-RAY DIFFRACTION	f_chiral_restr	0.043	1984
X-RAY DIFFRACTION	f_plane_restr	0.003	2328

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 (%)
2.7043-2.735	0.2771	39	0.2483	707	X-RAY DIFFRACTION	21
2.735-2.7672	0.3008	41	0.2443	834	X-RAY DIFFRACTION	24
2.7672-2.8009	0.2868	67	0.2448	1016	X-RAY DIFFRACTION	30
2.8009-2.8364	0.2505	75	0.2437	1154	X-RAY DIFFRACTION	34
2.8364-2.8737	0.2976	77	0.2491	1381	X-RAY DIFFRACTION	40
2.8737-2.9131	0.314	104	0.2442	1655	X-RAY DIFFRACTION	49
2.9131-2.9547	0.2901	99	0.2583	1935	X-RAY DIFFRACTION	56
2.9547-2.9988	0.2911	106	0.2548	2054	X-RAY DIFFRACTION	60
2.9988-3.0456	0.2991	121	0.2298	2229	X-RAY DIFFRACTION	64
3.0456-3.0955	0.286	120	0.2275	2334	X-RAY DIFFRACTION	68
3.0955-3.1489	0.2612	133	0.2259	2475	X-RAY DIFFRACTION	72
3.1489-3.2061	0.2489	135	0.2103	2621	X-RAY DIFFRACTION	76
3.2061-3.2678	0.266	139	0.2037	2810	X-RAY DIFFRACTION	82
3.2678-3.3345	0.2437	144	0.1954	3034	X-RAY DIFFRACTION	87
3.3345-3.4069	0.2605	141	0.2033	3052	X-RAY DIFFRACTION	90
3.4069-3.4862	0.2267	172	0.191	3216	X-RAY DIFFRACTION	93
3.4862-3.5733	0.2517	209	0.197	3188	X-RAY DIFFRACTION	94
3.5733-3.6699	0.2586	174	0.1894	3281	X-RAY DIFFRACTION	96
3.6699-3.7778	0.252	203	0.1823	3302	X-RAY DIFFRACTION	97
3.7778-3.8997	0.2354	173	0.167	3404	X-RAY DIFFRACTION	99
3.8997-4.039	0.2319	168	0.1577	3431	X-RAY DIFFRACTION	99
4.039-4.2006	0.1909	172	0.1487	3379	X-RAY DIFFRACTION	100
4.2006-4.3916	0.1919	157	0.1414	3524	X-RAY DIFFRACTION	100
4.3916-4.6229	0.2014	221	0.1428	3384	X-RAY DIFFRACTION	100
4.6229-4.9122	0.196	185	0.1393	3442	X-RAY DIFFRACTION	100
4.9122-5.2909	0.1972	210	0.1483	3388	X-RAY DIFFRACTION	100
5.2909-5.8224	0.2009	166	0.1707	3465	X-RAY DIFFRACTION	100
5.8224-6.6625	0.2141	190	0.1776	3442	X-RAY DIFFRACTION	100
6.6625-8.385	0.2004	183	0.1766	3412	X-RAY DIFFRACTION	100
8.385-44.7176	0.217	199	0.1867	3365	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	1.3633	0.1939	-0.1385	0.6587	-0.6944	2.9398	0.0129	-0.115	-0.2236	0.0683	0.2412	0.4253	0.4464	-0.569	0.0424	0.0669	-0.0369	0.0413	0.2282	0.1068	0.1981	64.6017	39.1643	11.5222
2	2.0203	0.251	0.3224	1.1916	-0.0693	2.5401	0.1012	0.0829	0.0451	0.2058	0.1925	0.0544	0.1374	-0.5664	0.0588	0.1196	-0.0343	0.047	0.154	0.1099	0.1724	63.9381	39.9094	17.0628
3	0.3998	0.1246	-0.509	0.913	-0.4399	2.6123	-0.0287	0.0713	-0.1443	-0.0228	0.0043	0.0721	0.2804	-0.1898	-0.1479	0.2209	0.0107	0.001	0.0918	0.0191	0.0991	77.1092	41.4605	-2.2635
4	0.4391	-0.447	-0.9178	2.0199	0.9397	2.6443	-0.3443	-0.0511	-0.2535	-0.0427	0.1546	0.2546	-0.0736	0.2856	0.0881	0.1392	-0.0436	0.0349	0.3612	0.062	0.1892	91.9079	53.0485	7.8582
5	1.4985	0.3781	-0.2878	1.1434	-0.8252	2.5294	-0.0167	-0.0103	0.023	-0.1138	0.0905	-0.0751	0.1829	0.0956	0.0607	0.0928	0.0029	0.0216	0.0844	0.0095	0.112	86.1931	44.6919	-2.7596
6	1.2843	0.2479	-0.5103	1.0667	-0.4178	1.3842	0.1431	-0.1529	0.013	-0.1339	-0.1286	-0.0313	0.2208	0.0712	-0.2712	0.2319	-0.0037	-0.0077	0.1947	0.0756	0.1759	83.3357	35.7534	11.1649
7	1.5044	1.3579	-0.7107	2.8809	-0.7984	2.1131	-0.1244	-0.1908	0.2008	-0.2503	0.1009	0.0689	0.1079	0.3686	0.0037	0.0912	-0.0744	-0.0281	0.3328	0.0473	0.1421	92.6627	51.2909	13.7162
8	3.3361	0.8607	-0.6196	1.8959	-0.2628	2.9742	-0.0958	-0.1618	-0.0726	0.1548	0.1347	-0.2913	0.1066	0.3081	0.1014	0.2444	0.0577	0.0393	0.1466	-0.0167	0.2661	109.726	-5.1189	20.9922
9	2.5202	0.8935	-0.8717	1.6454	-0.6126	2.3408	0.1082	-0.6138	0.0989	0.4394	-0.1305	-0.1415	0.0906	0.3875	-0.0048	0.2093	-0.0067	0.026	0.1434	0.0248	0.2196	108.5358	-2.6063	27.8555
10	1.7373	-0.3133	-0.2281	1.1472	0.3667	2.3151	-0.1826	0.2254	-0.5844	-0.2067	-0.0269	-0.5269	0.6493	0.5592	-0.2126	0.4362	0.0758	0.1793	0.0564	-0.0289	0.5076	110.6449	-12.6775	16.6999
11	1.7602	-0.4839	-0.5081	0.8906	0.6818	3.2477	0.3169	0.2846	-0.3099	-0.377	-0.1876	0.2555	-0.4139	-0.7519	0.0573	0.5846	0.0893	-0.0196	0.2759	-0.1424	0.23	91.2712	-4.5914	1.3255
12	1.6843	-0.625	1.2446	1.1484	0.1955	3.2525	0.3853	0.5972	-0.5863	-0.2714	-0.1807	0.2567	-0.0064	0.192	-0.0023	0.3385	-0.0248	0.0373	0.2289	-0.1156	0.2648	101.6427	-7.7441	3.298
13	1.5593	0.4969	0.3245	1.0029	0.3518	3.1744	0.1896	0.2089	0.244	-0.3141	-0.2084	0.1615	-0.5793	-0.3104	0.1082	0.4672	0.0419	0.0097	0.2118	-0.0438	0.3566	94.4428	-0.6098	-3.3049
14	1.544	-1.0892	0.2929	1.3262	1.3014	4.5825	0.2189	0.0538	-0.0564	-0.335	-0.1499	0.1455	-0.2817	-0.4215	-0.1564	0.3054	-0.071	0.0416	0.2652	-0.0227	0.238	95.3291	-1.7976	17.5432
15	1.0894	0.5924	0.3243	1.4205	1.8513	4.7542	-0.0996	0.1079	-0.2315	-0.4235	-0.1039	0.3516	0.0152	-1.2204	0.0907	0.3063	-0.0317	-0.0302	0.6623	-0.1685	0.4374	82.617	-7.2339	10.4184
16	1.0118	-0.1779	0.1624	1.286	-0.3109	2.945	-0.0398	0.0098	0.0864	0.2959	0.1474	0.5043	-0.2391	-0.6148	0.1293	0.2083	-0.0323	0.0386	0.1088	0.04	0.2431	68.0187	24.945	40.7705
17	1.7453	0.1626	0.6751	1.5641	0.2401	3.3084	0.0938	-0.0741	-0.0402	-0.0215	-0.0151	0.3153	-0.4331	-0.7706	0.0927	0.1356	0.0086	0.0339	0.1552	0.0395	0.2068	65.3766	26.9795	34.1979
18	1.5921	-0.0135	0.0419	1.1667	-0.0579	2.0053	0.0685	-0.5633	-0.122	0.7262	0.0717	0.2262	0.4819	-0.5411	0.0716	0.3508	-0.1158	0.0392	0.2188	0.119	0.248	68.3084	17.5927	45.5353
19	1.4179	0.2775	-0.3499	1.1591	0.4181	2.4213	-0.1141	-0.2088	0.2611	0.1653	-0.0155	0.0134	-0.4284	0.2298	0.0175	0.333	-0.0187	-0.0904	0.2576	-0.0352	0.2477	93.3285	27.5854	48.8436
20	1.7929	-0.1948	0.1427	2.9119	1.0297	2.9474	-0.1902	-0.2692	-0.0351	0.5289	-0.1503	0.484	-0.1774	0.2863	0.0692	0.2747	-0.0557	0.0339	0.2611	0.0671	0.2612	96.1225	12.6703	38.5161
21	4.8885	-0.1158	-0.2382	0.5256	-0.0236	1.3166	-0.0598	-0.1433	-0.495	0.2207	0.0472	0.0029	-0.1893	0.0087	0.1752	0.375	-0.0698	0.0292	0.2096	0.0044	0.1888	86.0421	20.5816	49.3222
22	1.6771	-0.7553	-0.3364	1.9016	1.0861	3.0048	-0.2932	-0.1678	0.2271	0.3096	0.3506	-0.2174	-0.1997	0.5691	0.297	0.3003	-0.0363	-0.0244	0.1833	-0.0122	0.14	96.3881	24.7202	49.7718
23	0.8909	-0.2999	0.9586	0.2679	-0.3833	1.1193	0.0989	0.0939	-0.0727	0.4684	-0.0556	0.2416	-0.1167	0.0796	0.0583	0.2253	-0.0179	-0.0019	0.1787	-0.0268	0.2239	83.0073	27.4313	33.1015
24	3.0335	-2.5345	-0.1972	3.0717	0.369	1.29	-0.1807	0.1136	-0.2511	0.2614	0.0621	0.0762	-0.0787	-0.0134	0.1156	0.2315	-0.01	-0.0099	0.2554	0.0211	0.1669	95.5367	15.1088	32.5047
25	3.2738	0.2983	1.0387	2.5216	-0.0271	4.1478	0.1102	0.4542	-0.3307	-0.5895	0.04	-0.3646	0.2313	0.8763	0.0067	0.3196	-0.1475	0.0283	0.3768	-0.064	0.0862	105.8527	69.6578	26.3513
26	1.0308	0.2191	-0.2821	2.5682	0.029	1.2876	-0.2981	0.8382	0.4599	-1.1019	-0.0884	0.2598	-0.6318	0.9317	0.1715	0.4158	-0.2313	0.1591	0.5236	0.1705	-0.1485	103.8842	74.4275	15.7204
27	1.4563	-0.0061	0.9068	1.2582	0.5469	2.5831	0.0228	0.3894	0.224	-0.701	-0.0491	-0.2274	-0.933	0.3786	0.1266	0.1472	-0.3502	-0.0282	0.165	0.0334	0.1364	105.529	76.3096	29.3176
28	1.8579	0.2198	0.3477	0.2055	0.1066	2.4164	0.0362	0.002	0.021	-0.0175	-0.0298	0.4468	0.1676	-0.881	-0.0547	0.0536	-0.0229	-0.0619	0.5167	-0.0103	0.1467	85.4168	68.6836	41.8557
29	1.4656	-0.0901	0.5517	0.9946	0.707	2.5321	0.1918	0.1111	0.2374	0.1423	0.1048	0.245	-0.4592	-0.054	0.147	0.1627	-0.0587	0.041	0.1645	-0.0181	0.1965	100.9178	74.2157	41.762
30	1.8324	-0.0551	1.2285	1.8147	-0.0242	2.4808	0.1465	-0.2869	-0.1353	-0.1162	-0.0472	0.033	0.0677	-0.3129	0.0089	0.0831	-0.0255	-0.0114	0.1758	0.0095	0.1248	97.7132	66.1287	49.4061
31	1.3727	-0.3246	0.486	1.2217	-0.1633	2.6834	0.121	-0.002	-0.074	-0.1904	-0.1513	0.0098	-0.0699	-0.3922	-0.0692	0.1789	-0.1162	-0.0203	0.2199	0.0193	0.12	93.1763	65.7381	31.3683
32	1.4444	-0.0192	-1.1399	1.0115	0.5202	2.932	-0.0829	0.0269	0.2356	-0.0232	0.0427	0.3072	0.031	-1.0528	0.6153	0.1341	0.0058	-0.0423	0.6679	-0.0045	0.2021	80.3732	69.4289	39.5444

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 59 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 60 through 159 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 160 through 220 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 221 through 252 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 253 through 341 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 342 through 413 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 414 through 464 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 9 through 59 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 60 through 129 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 130 through 181 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 182 through 252 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 253 through 293 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 294 through 355 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 356 through 411 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 412 through 463 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 9 through 59 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 60 through 129 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 130 through 181 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 182 through 220 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 221 through 251 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 252 through 301 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 302 through 355 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 356 through 413 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 414 through 464 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 10 through 45 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 46 through 108 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 109 through 198 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 199 through 252 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 253 through 293 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 294 through 351 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 352 through 418 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 419 through 463 )

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