PDB-6wyr: Crystal structure of anti-Muscle Specific Kinase (MuSK) Fab, MuSK1A

ID or keywords:

Entry

Database: PDB / ID: 6wyr

Title

Crystal structure of anti-Muscle Specific Kinase (MuSK) Fab, MuSK1A

Components

MuSK1A heavy chain
MuSK1A light chain

Keywords

IMMUNE SYSTEM / Human Fab / anti-MuSK

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Vieni, C. / Ekiert, D.

Funding support

United States, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01-AI114780	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R21-AI142198	United States
Muscular Dystrophy Association	MDA575198	United States
Colton Center for Autoimmunity		United States
Brown-Coxe fellowship		United States

Citation

Journal: J.Exp.Med. / Year: 2020
Title: Affinity maturation is required for pathogenic monovalent IgG4 autoantibody development in myasthenia gravis.
Authors: Fichtner, M.L. / Vieni, C. / Redler, R.L. / Kolich, L. / Jiang, R. / Takata, K. / Stathopoulos, P. / Suarez, P.A. / Nowak, R.J. / Burden, S.J. / Ekiert, D.C. / O'Connor, K.C.

History

Deposition	May 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2020	Group: Data collection / Database references / Structure summary Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_entity_branch_descriptor Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 18, 2023	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
Revision 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6wyr_validation.pdf.gz	1014.6 KB	Display	wwPDB validaton report
Full document	6wyr_full_validation.pdf.gz	1019.5 KB	Display
Data in XML	6wyr_validation.xml.gz	39.2 KB	Display
Data in CIF	6wyr_validation.cif.gz	57.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wy/6wyr ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wyr	HTTPS FTP

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Related structure data

Related structure data	6wytC 6dw2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5cd3-3 5cd3-1 6kvf-1 4kjq-3 6m87-3 7lk9-1 1ub6-2 3ejy-4 4at6-3 4r7n-7 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: MuSK1A light chain

H: MuSK1A heavy chain

M: MuSK1A light chain

I: MuSK1A heavy chain

hetero molecules

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

1

L: MuSK1A light chain

H: MuSK1A heavy chain

hetero molecules

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

2

M: MuSK1A light chain

I: MuSK1A heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.870, 71.720, 106.180
Angle α, β, γ (deg.)	90.000, 104.370, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Antibody , 2 types, 4 molecules LMHI

#1: Antibody	MuSK1A light chain Mass: 23179.529 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBacDual / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody	MuSK1A heavy chain Mass: 24925.785 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBacDual / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)

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Sugars , 2 types, 2 molecules

#3: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

#4: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source

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Non-polymers , 2 types, 618 molecules

#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 602 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.52 Å³/Da / Density % sol: 51.28 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 8.5 / Details: 20% PEG6000, 0.1 M bicine, pH 8.5

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Data collection

Diffraction

Mean temperature: 80 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-B / Wavelength: 1.0332 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.8→49.04 Å / Num. obs: 88524 / % possible obs: 99.5 % / Redundancy: 3.465 % / B_iso Wilson estimate: 35.047 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.086 / Χ²: 1.007 / Net I/σ(I): 9.68 / Num. measured all: 306753 / Scaling rejects: 8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.8-1.85	3.238	1.089	0.87	20730	6500	6403	0.4	1.304	98.5
1.85-1.9	3.555	0.873	1.26	22619	6399	6362	0.576	1.027	99.4
1.9-1.95	3.556	0.657	1.75	21962	6204	6176	0.685	0.773	99.5
1.95-2.01	3.517	0.502	2.28	21048	6005	5984	0.804	0.593	99.7
2.01-2.08	3.487	0.383	2.99	20409	5889	5853	0.871	0.452	99.4
2.08-2.15	3.398	0.304	3.67	19060	5621	5609	0.908	0.361	99.8
2.15-2.23	3.33	0.244	4.52	18186	5478	5461	0.931	0.291	99.7
2.23-2.32	3.399	0.206	5.29	17822	5257	5243	0.953	0.244	99.7
2.32-2.43	3.555	0.18	6.28	17908	5050	5037	0.967	0.212	99.7
2.43-2.55	3.606	0.154	7.45	17406	4841	4827	0.974	0.181	99.7
2.55-2.68	3.574	0.126	8.86	16321	4572	4567	0.982	0.148	99.9
2.68-2.85	3.515	0.1	11.16	15266	4349	4343	0.987	0.118	99.9
2.85-3.04	3.35	0.075	14.18	13681	4104	4084	0.992	0.089	99.5
3.04-3.29	3.384	0.059	18.08	12849	3814	3797	0.995	0.07	99.6
3.29-3.6	3.432	0.044	23.9	12000	3510	3496	0.997	0.052	99.6
3.6-4.02	3.645	0.038	28.56	11551	3175	3169	0.998	0.045	99.8
4.02-4.65	3.564	0.031	33.59	10064	2834	2824	0.998	0.037	99.6
4.65-5.69	3.342	0.03	32.15	7951	2387	2379	0.999	0.036	99.7
5.69-8.05	3.39	0.032	31.16	6313	1872	1862	0.998	0.038	99.5
8.05-49.04	3.442	0.021	40.19	3607	1068	1048	0.999	0.025	98.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.25	data extraction
Coot	0.8.9.2	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6DW2

6dw2

Resolution: 1.8→49.04 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2135	2005	2.27 %	RANDOM
R_work	0.1804	86485	-	-
obs	0.1812	88490	99.55 %	-

Solvent computation

Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 380.67 Å² / B_iso mean: 46.7505 Å² / B_iso min: 17.16 Å²

Refinement step

Cycle: final / Resolution: 1.8→49.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6589	0	286	602	7477
B_iso mean	-	-	88.79	43.74	-
Num. residues	-	-	-	-	873

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 (%)
1.8-1.84	0.3856	137	0.347	6034	6171	98
1.84-1.89	0.3219	141	0.2949	6155	6296	99
1.89-1.95	0.2942	145	0.2514	6135	6280	100
1.95-2.01	0.2477	147	0.2286	6122	6269	100
2.01-2.09	0.2377	137	0.2031	6179	6316	100
2.09-2.17	0.2201	139	0.196	6182	6321	100
2.17-2.27	0.2194	145	0.1874	6178	6323	100
2.27-2.39	0.2307	144	0.1795	6157	6301	100
2.39-2.54	0.2002	137	0.1772	6184	6321	100
2.54-2.73	0.2082	154	0.1741	6200	6354	100
2.73-3.01	0.2082	138	0.1693	6192	6330	100
3.01-3.44	0.2141	147	0.1675	6210	6357	100
3.44-4.34	0.1865	142	0.1546	6222	6364	100
4.34-49.04	0.1973	152	0.1716	6335	6487	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	2.3612	1.1723	-2.5112	4.3623	-1.1077	8.2208	-0.3941	-1.1789	0.8691	-0.0014	-0.4397	-0.2112	-0.2586	0.0349	-1.1016	0.2886	0.1084	0.0248	0.6942	-0.2059	0.2367	6.1055	51.6594	32.1363
2	4.9722	-0.6681	-0.2654	3.3879	1.1881	3.8303	-0.0035	-0.9443	0.3172	-0.1671	-0.0394	0.3644	-0.272	-0.5734	0.0716	0.2362	0.0803	0.0096	0.521	-0.0068	0.3365	-0.9534	46.1637	25.1421
3	5.9753	0.4391	-2.005	5.7928	-0.2542	5.6081	0.2846	-1.086	0.3192	0.0338	0.0514	0.3849	0.1741	-0.3511	-0.1809	0.1866	0.0123	-0.0175	0.5447	-0.0201	0.2859	4.4748	44.389	28.3731
4	2.9672	0.8364	-0.8976	3.9054	0.3691	0.3745	-0.0785	-1.1652	0.6582	-0.1179	0.0379	0.0877	-0.5178	0.0106	-0.6402	0.1396	0.107	0.0318	0.6575	-0.0745	0.3512	8.2899	48.3427	26.0755
5	7.1001	1.1876	-3.5203	1.2827	-0.3613	4.6626	0.0502	-0.5246	0.1948	0.1587	0.0347	-0.1652	0.0979	0.3399	-0.0564	0.2774	0.0129	-0.0132	0.179	-0.0488	0.2581	35.2856	48.1274	37.7455
6	5.2337	0.4749	-1.7622	1.8702	0.1381	4.1757	-0.1576	0.1355	0.073	-0.01	0.0725	-0.0976	0.0612	-0.4877	-0.0079	0.2899	0.0282	-0.0295	0.3037	-0.0326	0.2668	25.4842	49.4631	35.2976
7	6.5498	1.5276	-2.0297	3.8472	-0.366	4.4199	-0.1347	0.5334	0.2979	-0.1334	0.2479	-0.5569	-0.342	-0.038	-0.1936	0.2971	-0.0181	0.0061	0.1898	-0.0013	0.346	37.872	53.3894	30.1658
8	5.9634	1.4916	-2.1903	4.0382	-0.5457	4.3897	0.8256	-0.7021	1.0156	0.3622	-0.2549	-0.0774	-0.7092	0.2543	-0.2666	0.4756	-0.0487	0.0193	0.2522	-0.083	0.4519	33.819	57.8809	40.5049
9	4.583	0.6798	-0.1813	1.2875	0.0517	0.3127	-0.2265	0.2378	-0.1357	-0.1806	0.1222	0.0263	0.0263	-0.0076	0.0853	0.2701	-0.0138	-0.0043	0.2029	0.0139	0.1905	13.939	32.3423	8.3857
10	2.5935	-0.2193	-1.23	2.1385	0.2763	1.0886	-0.0512	0.1741	0.2772	-0.267	0.0902	0.2009	-0.1855	-0.1231	-0.0354	0.2437	-0.0083	-0.0316	0.2023	0.0783	0.1942	10.2073	41.7053	6.3596
11	4.8059	1.3538	1.383	0.3199	0.6019	3.9488	-0.1668	0.2236	0.3922	-0.1143	0.1905	-0.0298	-0.4306	0.2246	0.0759	0.2732	-0.0129	-0.0146	0.2179	0.0621	0.2373	19.8574	40.9277	6.4828
12	3.5558	1.3359	-0.8815	1.8378	0.6763	3.0706	-0.2022	0.1099	0.1246	-0.0987	0.0426	0.3611	-0.0779	-0.3894	0.073	0.2556	0.0169	-0.0302	0.247	0.0508	0.3077	5.4633	37.9618	14.4135
13	2.4453	0.0795	0.7561	1.1199	0.2727	2.3067	-0.005	-0.1948	0.2052	0.1892	0.0799	-0.1382	-0.0625	0.2027	0.0089	0.2793	0.004	0.006	0.2011	-0.0182	0.2898	37.8338	42.4063	28.9336
14	1.4379	-0.1613	-0.0528	1.5514	1.1696	3.7711	-0.0526	-0.2147	-0.001	0.3633	0.1391	-0.1007	0.2345	0.0945	-0.1381	0.3113	0.0182	-0.0382	0.2206	-0.0293	0.2668	38.0989	36.8824	33.946
15	1.6529	0.6061	0.9642	1.8207	1.127	2.6338	-0.3105	-0.3648	0.1406	0.3959	0.4591	-0.0718	0.1446	0.8215	-0.5889	0.3432	0.1114	-0.1304	0.4075	-0.1394	0.3619	47.6879	36.2513	34.5443
16	4.0947	1.1168	0.3596	1.979	-0.6982	2.1557	0.1683	-1.7055	-0.8331	0.1411	-0.2481	-0.2748	0.1524	0.1795	0.0522	0.2582	-0.017	-0.0502	0.7521	0.1889	0.3742	51.9493	8.5712	31.977
17	5.4249	1.2718	2.0102	1.4385	0.8231	4.6124	-0.0766	-0.3792	-0.2646	0.1197	0.1017	0.0945	-0.3629	-0.0257	0.0568	0.2477	-0.0046	0.0022	0.1711	0.0562	0.2008	17.1422	7.0028	36.9373
18	6.5488	4.6718	4.0213	8.1481	5.82	6.8969	-0.1157	-0.062	-0.1887	0.4241	0.2342	-0.1211	-0.0022	1.0467	-0.2535	0.315	0.01	-0.0262	0.4861	0.0878	0.2707	28.5969	4.6995	39.1297
19	3.3804	1.0699	0.6423	3.2761	0.5312	4.0193	-0.0084	-0.3017	-0.2819	0.2182	-0.0698	-0.0844	-0.0277	0.1894	0.0406	0.2841	0.0274	-0.0063	0.2342	0.0786	0.3142	21.0097	2.3672	36.5309
20	3.0694	0.6757	-0.0708	1.3941	-0.33	0.6361	-0.0296	0.0505	-0.021	-0.0257	0.0281	-0.1726	-0.013	0.0001	0.035	0.2431	-0.007	-0.0003	0.2038	-0.0332	0.2125	44.5665	20.2199	12.1756
21	2.0285	-2.0738	-0.298	2.9781	1.3021	3.0177	-0.3416	-0.2817	-0.7425	-0.0702	-0.0098	-0.2805	0.1145	-0.0785	0.2532	0.2393	-0.0035	-0.0345	0.2318	-0.0181	0.2877	45.4685	10.0606	16.0419
22	8.6323	3.1355	-1.3167	4.6995	-0.1427	3.2527	0.0426	-0.1369	-0.5113	0.0676	-0.1201	-0.2321	0.1475	0.0976	0.1478	0.2833	0.0104	0.0297	0.2068	-0.0716	0.2536	48.7964	9.2612	6.4041
23	2.7727	0.9487	-0.5306	2.1875	0.106	2.432	-0.0696	0.1498	-0.2272	-0.1733	0.0252	-0.1926	0.0758	0.0902	-0.0181	0.2486	0.0085	0.0089	0.1781	-0.0291	0.2457	45.5159	15.4714	10.5198
24	1.9465	0.062	-0.5855	0.7435	-0.2097	1.0464	0.0115	-0.0353	-0.0893	0.1287	0.0115	0.0151	0.0693	0.0016	0.043	0.2762	-0.0014	-0.0231	0.137	-0.0186	0.1827	27.5589	14.1535	25.5979
25	1.3782	-0.0644	-0.5165	0.9939	-0.6125	1.938	0.074	-0.1365	0.0334	0.2182	0.0096	0.0716	-0.2708	0.0038	-0.0916	0.2821	-0.0212	0.0151	0.1985	0.0207	0.2338	15.2502	18.5915	32.4966
26	5.5567	2.0728	-3.5227	2.8291	-0.1304	4.1139	0.0558	0.0092	-0.0854	0.3136	0.2523	0.6001	0.0792	-0.6127	-0.7251	0.2239	0.0101	0.0507	0.2461	0.0458	0.2986	5.5531	17.9041	31.8988

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 18 )	L	2 - 18
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 19 through 91 )	L	19 - 91
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 92 through 108 )	L	92 - 108
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 109 through 127 )	L	109 - 127
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 128 through 160 )	L	128 - 160
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 161 through 193 )	L	161 - 193
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 194 through 209 )	L	194 - 209
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 210 through 235 )	L	210 - 235
9	X-RAY DIFFRACTION	9	chain 'H' and (resid 2 through 36 )	H	2 - 36
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 37 through 84 )	H	37 - 84
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 85 through 99 )	H	85 - 99
12	X-RAY DIFFRACTION	12	chain 'H' and (resid 100 through 121 )	H	100 - 121
13	X-RAY DIFFRACTION	13	chain 'H' and (resid 122 through 149 )	H	122 - 149
14	X-RAY DIFFRACTION	14	chain 'H' and (resid 150 through 218 )	H	150 - 218
15	X-RAY DIFFRACTION	15	chain 'H' and (resid 219 through 230 )	H	219 - 230
16	X-RAY DIFFRACTION	16	chain 'M' and (resid 3 through 127 )	M	3 - 127
17	X-RAY DIFFRACTION	17	chain 'M' and (resid 128 through 158 )	M	128 - 158
18	X-RAY DIFFRACTION	18	chain 'M' and (resid 159 through 171 )	M	159 - 171
19	X-RAY DIFFRACTION	19	chain 'M' and (resid 172 through 235 )	M	172 - 235
20	X-RAY DIFFRACTION	20	chain 'I' and (resid 2 through 44 )	I	2 - 44
21	X-RAY DIFFRACTION	21	chain 'I' and (resid 45 through 57 )	I	45 - 57
22	X-RAY DIFFRACTION	22	chain 'I' and (resid 58 through 75 )	I	58 - 75
23	X-RAY DIFFRACTION	23	chain 'I' and (resid 76 through 111 )	I	76 - 111
24	X-RAY DIFFRACTION	24	chain 'I' and (resid 112 through 149 )	I	112 - 149
25	X-RAY DIFFRACTION	25	chain 'I' and (resid 150 through 218 )	I	150 - 218
26	X-RAY DIFFRACTION	26	chain 'I' and (resid 219 through 231 )	I	219 - 231

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