PDB-5nnp: Structure of Naa15/Naa10 bound to HypK-THB

ID or keywords:

Entry

Database: PDB / ID: 5nnp

Title

Structure of Naa15/Naa10 bound to HypK-THB

Components

(Putative uncharacterized ...) x 2
N-terminal acetyltransferase-like protein
Ser-Glu-Ser-Ser

Keywords

TRANSFERASE / N-acetylation / NATs /

Naa15 / Naa10 / HypK / NatA / Nat1 / Ard1 / bisubstrate analogue

Function / homology

Function and homology information

NatA complex /

N-terminal protein amino acid acetylation /

peptide alpha-N-acetyltransferase activity /

transferase activity /

cytoplasm
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.602 Å

Authors

Weyer, F.A. / Gumiero, A. / Kopp, J. / Sinning, I.

Funding support

Germany, 3items

Citation

Journal: Nat Commun / Year: 2017
Title: Structural basis of HypK regulating N-terminal acetylation by the NatA complex.
Authors: Weyer, F.A. / Gumiero, A. / Lapouge, K. / Bange, G. / Kopp, J. / Sinning, I.

History

Deposition	Apr 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nnp.cif.gz	744.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5nnp.ent.gz	632.6 KB	Display	PDB format
PDBx/mmJSON format	5nnp.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/nn/5nnp ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnp	HTTPS FTP

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Related structure data

Related structure data	5nnrC C: citing same article (ref.)
Similar structure data	5nnr-1 1h38-1 5ftu-1 6gvi-d 5nnr-2 6gvg-d 2zv3-d 6gvf-d 5ftu-3 4ncf-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) 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #141 - Sep 2011 O-GlcNAc Transferase similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #230 - Feb 2019 Initiation Factor eIF4E similarity (3) #166 - Oct 2013 Proteasome similarity (2)

Deposited unit

A: N-terminal acetyltransferase-like protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

E: N-terminal acetyltransferase-like protein

F: Putative uncharacterized protein

G: Putative uncharacterized protein

I: Ser-Glu-Ser-Ser

L: Ser-Glu-Ser-Ser

hetero molecules

233 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N-terminal acetyltransferase-like protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

I: Ser-Glu-Ser-Ser

hetero molecules

defined by author&software
Evidence: gel filtration, isothermal titration calorimetry, light scattering
117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: N-terminal acetyltransferase-like protein

F: Putative uncharacterized protein

G: Putative uncharacterized protein

L: Ser-Glu-Ser-Ser

hetero molecules

defined by author&software
Evidence: gel filtration, isothermal titration calorimetry, light scattering
117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.319, 106.041, 130.937
Angle α, β, γ (deg.)	90.00, 94.98, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Putative uncharacterized ... , 2 types, 4 molecules BFCG

#2: Protein	Putative uncharacterized protein Mass: 22440.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063490 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SEE8
#3: Protein	Putative uncharacterized protein Mass: 6593.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0058830 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCY6

#2: Protein

Putative uncharacterized protein

Mass: 22440.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063490 / Production host:

Escherichia coli (E. coli) / References: UniProt: G0SEE8

#3: Protein

Putative uncharacterized protein

Mass: 6593.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0058830 / Production host:

Escherichia coli (E. coli) / References: UniProt: G0SCY6

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Protein / Protein/peptide , 2 types, 4 molecules AEIL

#1: Protein	N-terminal acetyltransferase-like protein Mass: 84913.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0031530 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S4M4
#4: Protein/peptide	Ser-Glu-Ser-Ser Mass: 408.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

#1: Protein

N-terminal acetyltransferase-like protein

Mass: 84913.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0031530 / Production host:

Escherichia coli (E. coli) / References: UniProt: G0S4M4

#4: Protein/peptide

Ser-Glu-Ser-Ser

Mass: 408.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 476 molecules

#5: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-CMC / CARBOXYMETHYL COENZYME A Mass: 825.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₈P₃S / Source*: (synth.) synthetic construct (others)
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.82 Å³/Da / Density % sol: 56.42 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5 25 % PEG 3350 protein at 15 mg/ml concentration

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8729 Å / Relative weight: 1
Reflection	Resolution: 2.6→49.321 Å / Num. obs: 77910 / % possible obs: 99.7 % / Redundancy: 6.9 % / R_pim(I) all: 0.1 / Net I/σ(I): 8.9
Reflection shell	Resolution: 2.6→2.69 Å / Redundancy: 6.5 % / Num. unique obs: 7407 / % possible all: 97.3

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Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 2.602→49.321 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.87

	R_factor	Num. reflection	% reflection
R_free	0.2199	3925	5.04 %
R_work	0.161	-	-
obs	0.164	77880	99.71 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.602→49.321 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14467	0	182	443	15092

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14926
X-RAY DIFFRACTION	f_angle_d	0.967	20098
X-RAY DIFFRACTION	f_dihedral_angle_d	13.799	5629
X-RAY DIFFRACTION	f_chiral_restr	0.037	2153
X-RAY DIFFRACTION	f_plane_restr	0.004	2550

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 (%)
2.6021-2.6339	0.3174	122	0.2522	2422	X-RAY DIFFRACTION	93
2.6339-2.6672	0.3295	146	0.2465	2670	X-RAY DIFFRACTION	100
2.6672-2.7023	0.3284	144	0.238	2594	X-RAY DIFFRACTION	100
2.7023-2.7393	0.3059	156	0.2342	2618	X-RAY DIFFRACTION	100
2.7393-2.7784	0.2853	145	0.2135	2610	X-RAY DIFFRACTION	100
2.7784-2.8199	0.2874	133	0.2201	2666	X-RAY DIFFRACTION	100
2.8199-2.864	0.2794	120	0.2113	2650	X-RAY DIFFRACTION	100
2.864-2.9109	0.2853	148	0.2106	2656	X-RAY DIFFRACTION	100
2.9109-2.9611	0.3048	132	0.2125	2637	X-RAY DIFFRACTION	100
2.9611-3.015	0.2539	141	0.1967	2656	X-RAY DIFFRACTION	100
3.015-3.0729	0.2169	121	0.1899	2651	X-RAY DIFFRACTION	100
3.0729-3.1356	0.2553	143	0.1953	2618	X-RAY DIFFRACTION	100
3.1356-3.2038	0.2453	139	0.1915	2662	X-RAY DIFFRACTION	100
3.2038-3.2783	0.2653	153	0.1824	2621	X-RAY DIFFRACTION	100
3.2783-3.3603	0.2324	155	0.1786	2639	X-RAY DIFFRACTION	100
3.3603-3.4511	0.2478	156	0.169	2608	X-RAY DIFFRACTION	100
3.4511-3.5527	0.2147	131	0.1676	2633	X-RAY DIFFRACTION	100
3.5527-3.6673	0.2294	144	0.1601	2663	X-RAY DIFFRACTION	100
3.6673-3.7983	0.1901	135	0.1554	2632	X-RAY DIFFRACTION	100
3.7983-3.9503	0.2214	170	0.1444	2623	X-RAY DIFFRACTION	100
3.9503-4.13	0.1964	133	0.1316	2655	X-RAY DIFFRACTION	100
4.13-4.3477	0.1892	131	0.127	2662	X-RAY DIFFRACTION	100
4.3477-4.6199	0.1589	140	0.1205	2663	X-RAY DIFFRACTION	100
4.6199-4.9763	0.1762	149	0.1213	2653	X-RAY DIFFRACTION	100
4.9763-5.4764	0.2066	149	0.1446	2656	X-RAY DIFFRACTION	100
5.4764-6.2675	0.2118	133	0.16	2694	X-RAY DIFFRACTION	100
6.2675-7.8912	0.167	135	0.1379	2682	X-RAY DIFFRACTION	100
7.8912-49.321	0.1694	121	0.1261	2761	X-RAY DIFFRACTION	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	6.6942	1.9561	-1.9467	3.1846	-0.4317	5.0321	-0.3746	0.151	-1.3551	0.2442	0.0648	0.7298	0.9738	-1.0385	0.3724	0.5225	-0.0687	0.1278	0.5319	0.0326	0.8675	-18.4462	25.6475	15.0749
2	1.2277	-0.2878	-0.6268	1.1272	0.7041	1.8495	-0.0407	-0.0387	0.1409	-0.0027	0.245	-0.2665	-0.1026	0.4683	-0.2354	0.2636	-0.0715	-0.0445	0.326	-0.052	0.3572	25.1621	23.9364	0.276
3	5.6316	0.0425	-1.2283	1.1707	0.3209	2.7458	0.1368	0.2305	0.1586	-0.3887	-0.0712	-0.1315	-0.2806	0.1789	-0.0745	0.3792	-0.0171	0.0309	0.3279	-0.0162	0.2456	16.5602	12.5253	-39.8048
4	1.334	0.1273	0.3999	2.3167	0.887	1.776	0.0106	0.2355	0.329	-0.4829	-0.1277	0.3047	-0.5733	-0.2796	0.0892	0.436	0.1215	0.0291	0.3696	0.0198	0.3722	-0.1214	36.1524	-18.4745
5	2.4433	-0.6222	0.07	4.583	1.2624	1.9105	0.1461	0.1751	0.1386	-0.3013	-0.0174	-0.0718	-0.0595	-0.043	-0.1139	0.2225	0.0232	0.0189	0.2936	-0.0133	0.2624	13.6748	16.8676	-14.3369
6	4.8206	-5.0644	5.0911	5.5186	-6.2272	9.3436	-0.5198	-2.2158	-2.6898	2.7471	1.3058	3.682	1.1714	-1.6492	-0.7203	1.1365	0.1448	0.2056	0.9895	0.2621	1.2068	14.6182	-1.3928	3.6274
7	0.6203	-0.1557	2.0074	1.4634	-0.4146	6.7788	0.0585	0.1115	-0.1945	-0.0344	0.1224	-0.0269	-0.0307	0.2201	-0.17	0.2409	-0.0066	0.0001	0.3334	-0.029	0.3127	20.3228	6.562	-15.0387
8	5.7182	0.7725	2.3448	3.663	0.1537	1.3541	0.1167	0.0273	-0.2716	0.0272	-0.0041	-0.0719	0.4629	-0.1263	-0.1862	0.3141	-0.0423	0.0151	0.2783	-0.0303	0.2636	13.5694	-4.9544	-14.1834
9	7.091	3.7351	2.3042	5.8438	2.1073	6.0295	0.612	-0.0945	-0.0028	0.7391	-0.2254	-2.0195	-0.3161	1.4589	-0.3829	0.7078	0.0205	-0.2342	0.6931	-0.0501	1.3284	38.4199	3.085	-1.1645
10	1.4117	2.6392	1.4699	8.1012	4.8366	3.8623	0.2349	-0.1336	-0.242	0.7263	-0.0073	-0.2651	-0.4213	1.0948	-0.2331	0.7422	0.0911	0.0126	0.7028	-0.046	0.6044	4.523	61.9992	4.7186
11	1.8679	-0.51	-0.9033	7.1593	5.3473	4.1329	0.0866	-0.3702	0.5299	-0.5449	-0.6189	0.7043	-0.3062	-0.6722	0.5612	0.5031	0.1215	0.0873	0.5161	-0.0467	0.6391	-2.975	55.8465	-7.0314
12	4.9588	5.8309	-0.6169	7.1898	0.925	8.4537	0.1166	-0.3638	0.2753	0.6932	0.0983	-0.738	0.3578	-0.0008	-0.2551	0.5234	0.1713	0.0577	0.4098	-0.0061	0.5724	4.4237	54.156	-0.9283
13	5.6642	2.0309	-1.1527	6.7004	3.8007	5.7936	0.1622	-0.2138	0.2253	0.0184	0.0141	0.1542	-0.4689	0.4012	-0.1976	0.5445	0.0182	0.1545	0.3245	0.0426	0.6674	8.8595	57.5829	-9.9539
14	2.6865	-0.8952	-0.6358	4.332	1.9799	3.6243	0.1427	0.62	-1.0894	-0.9383	0.2968	0.7163	2.0746	0.352	-0.3707	1.7099	0.0548	-0.4532	0.804	-0.0199	0.8485	-56.4568	-8.5527	-86.3955
15	2.0466	-0.5765	1.2826	1.4089	-0.983	1.7205	-0.0727	-0.2239	0.0805	0.0344	0.1105	0.1529	-0.1785	-0.1859	-0.0317	0.2961	0.0164	0.0336	0.2185	-0.0459	0.2372	-43.6077	-6.6203	-44.754
16	3.2542	-0.4719	-0.8103	2.7524	0.4537	5.0131	-0.0646	0.2922	-0.107	-0.0598	0.083	-0.6059	-0.1139	0.8537	-0.066	0.2674	-0.0861	-0.0558	0.5004	-0.0307	0.4552	-0.1055	-17.33	-39.2343
17	1.8188	-0.9384	-0.011	1.4131	0.1473	1.0488	0.0667	0.3629	0.3844	-0.353	-0.0174	-0.4272	-0.3388	0.361	-0.0301	0.4715	-0.1351	0.0732	0.4528	0.0318	0.3645	-17.7004	-2.1816	-65.5314
18	1.5857	-0.9783	-0.0072	3.5456	-1.0056	3.6933	-0.0807	0.1742	0.0477	-0.0714	0.0184	-0.271	-0.1985	0.2645	0.0253	0.2218	-0.0415	-0.0031	0.2235	-0.0159	0.1919	-25.7446	-15.5042	-52.0114
19	6.5668	3.0441	-4.224	6.6355	2.3764	8.7065	-1.0998	3.2237	0.3396	-3.673	1.4528	2.9402	2.0804	-2.6193	-0.4611	1.1435	-0.377	-0.2399	1.2934	0.0359	0.9374	-43.847	-33.5288	-50.6637
20	1.6443	-0.053	-1.2162	2.4185	0.4179	2.3552	0.1633	0.0978	-0.4227	0.076	-0.0435	-0.1487	0.2817	0.0796	-0.118	0.3133	0.0268	-0.0961	0.2847	-0.0455	0.3393	-25.7331	-32.5678	-48.9715
21	2.0845	-1.6667	-0.6429	6.1212	4.8553	4.1145	-0.2616	-0.7379	0.081	1.4818	-0.1462	0.5679	0.4498	-0.3421	0.468	1.3233	-0.0609	0.201	0.6011	0.1214	0.706	-38.5742	-29.1992	-27.0218
22	3.232	-1.4649	2.8828	5.1868	1.1988	3.9575	0.2758	-0.4881	0.1984	0.1081	-0.1561	0.2465	-0.8301	-0.734	-0.135	0.9818	0.1838	-0.0581	0.8195	0.1454	0.772	-45.8773	28.7081	-61.158
23	7.9219	-4.18	1.7771	5.5549	-0.1662	1.9132	0.4598	1.0857	0.4671	-0.7326	-0.4643	-0.186	-0.5521	-0.3099	-0.0016	1.0542	0.0002	-0.1791	0.59	0.112	0.4725	-33.8871	23.1382	-68.7441
24	7.2684	-1.647	-0.4831	6.5936	6.5766	7.0808	0.3438	-0.1039	-0.9618	-0.143	-0.2489	0.6029	-0.7202	-0.5782	-0.1212	0.6904	0.0579	-0.0977	0.4614	0.1458	0.5151	-39.5619	21.3259	-61.1638
25	4.6137	-2.9554	2.022	8.1935	1.6722	5.303	-0.3273	-0.2179	0.4445	-0.0112	-0.0246	0.052	-1.073	-0.3536	0.4685	0.9228	-0.0559	-0.092	0.4042	0.0342	0.473	-30.4792	25.0218	-57.124

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 92 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 93 through 301 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 302 through 466 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 467 through 742 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 69 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 70 through 78 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 79 through 112 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 161 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 162 through 179 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 81 through 85 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 86 through 99 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 100 through 110 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 111 through 125 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 7 through 72 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 73 through 285 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 286 through 402 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 403 through 740 )
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 2 through 69 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 70 through 78 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 79 through 161 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 162 through 178 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 81 through 85 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 86 through 99 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 100 through 110 )
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 111 through 125 )

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