PDB-5iop: Cetuximab Fab in complex with 4-bromophenylalanine meditope variant

ID or keywords:

Entry

Database: PDB / ID: 5iop

Title

Cetuximab Fab in complex with 4-bromophenylalanine meditope variant

Components

Cetuximab Fab, heavy chain
Cetuximab Fab, light chain
Meditope variant

Keywords

IMMUNE SYSTEM / antibody / anti-EGFR

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

HOMO SAPIENS (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.499 Å

Authors

Bzymek, K.P. / Williams, J.C.

Citation

Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.

History

Deposition	Mar 8, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Dec 13, 2017	Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5iop.cif.gz	355.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5iop.ent.gz	290.4 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/io/5iop ftp://data.pdbj.org/pub/pdb/validation_reports/io/5iop	HTTPS FTP

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Related structure data

Related structure data	5etuC 5eukC 5f88C 5ff6C 5i2iC 5ir1C 5itfC 5iv2C 5ivzC 5t1kC 5t1lC 5t1mC 5th2C 4gw1S 5hpm 5hyq 5icx 5icy 5icz 5id0 5id1 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5id1-2 5esq-1 4gaj-d 5opy-d 5ivz-2 6w73-d 5i2i-2 1u6a-d 5icx-1 3g6j-4 4jzn-1 6xul-5 6z3k-7 2gfb-1 2uyl-1 5euk-1 6mfj-2 5t1k-1 5icz-2 1ruq-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 - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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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

A: Cetuximab Fab, light chain

B: Cetuximab Fab, heavy chain

C: Cetuximab Fab, light chain

D: Cetuximab Fab, heavy chain

E: Meditope variant

F: Meditope variant

hetero molecules

97.2 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cetuximab Fab, light chain

B: Cetuximab Fab, heavy chain

E: Meditope variant

hetero molecules

defined by author&software
48.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Cetuximab Fab, light chain

D: Cetuximab Fab, heavy chain

F: Meditope variant

hetero molecules

defined by author&software
48.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.050, 83.160, 212.260
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Cetuximab Fab, light chain Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#2: Antibody	Cetuximab Fab, heavy chain Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#3: Protein/peptide	Meditope variant Mass: 1459.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.92 Å³/Da / Density % sol: 57.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 15, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.499→33.132 Å / Num. obs: 39836 / % possible obs: 99.2 % / Redundancy: 6.26 % / Net I/σ(I): 20.5
Reflection shell	Resolution: 2.5→2.56 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.3 / % possible all: 92.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1

Resolution: 2.499→33.132 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2261	1992	5 %
R_work	0.1772	-	-
obs	0.1797	39829	99.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.499→33.132 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6707	0	15	414	7136

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6911
X-RAY DIFFRACTION	f_angle_d	0.729	9425
X-RAY DIFFRACTION	f_dihedral_angle_d	11.312	4113
X-RAY DIFFRACTION	f_chiral_restr	0.048	1060
X-RAY DIFFRACTION	f_plane_restr	0.004	1207

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 (%)
2.4994-2.5618	0.2804	130	0.2199	2467	X-RAY DIFFRACTION	92
2.5618-2.6311	0.293	140	0.2056	2666	X-RAY DIFFRACTION	100
2.6311-2.7085	0.2915	140	0.201	2658	X-RAY DIFFRACTION	100
2.7085-2.7958	0.292	142	0.2041	2705	X-RAY DIFFRACTION	100
2.7958-2.8957	0.2657	141	0.2051	2683	X-RAY DIFFRACTION	100
2.8957-3.0116	0.2585	143	0.1926	2700	X-RAY DIFFRACTION	100
3.0116-3.1485	0.2284	141	0.1849	2695	X-RAY DIFFRACTION	100
3.1485-3.3144	0.259	143	0.1865	2708	X-RAY DIFFRACTION	100
3.3144-3.5218	0.2192	141	0.1848	2686	X-RAY DIFFRACTION	99
3.5218-3.7934	0.2183	142	0.1809	2699	X-RAY DIFFRACTION	98
3.7934-4.1745	0.1934	143	0.1525	2711	X-RAY DIFFRACTION	100
4.1745-4.777	0.17	145	0.1258	2756	X-RAY DIFFRACTION	100
4.777-6.0126	0.1705	147	0.1518	2783	X-RAY DIFFRACTION	100
6.0126-33.1354	0.2498	154	0.2047	2920	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	2.1838	-2.1597	1.7564	4.3587	-3.5587	4.5091	0.153	-0.0671	-0.1111	-0.3286	0.2127	0.0621	0.4861	-0.2343	-0.3757	0.3681	-0.0852	-0.0212	0.3076	-0.0038	0.2541	19.2995	23.734	19.3488
2	1.2484	0.0597	-0.7823	2.4828	-0.6744	2.2587	0.0909	-0.0409	-0.104	-0.2003	0.0346	0.0317	0.5396	-0.0253	-0.1726	0.2951	-0.0186	-0.0593	0.1915	-0.024	0.148	27.1931	27.5894	14.6662
3	0.0911	-0.3113	0.647	1.3145	-2.5084	4.7387	0.0694	0.0092	-0.0143	-0.5383	0.2036	0.3233	0.4024	0.0061	-0.1579	0.3306	0.0077	-0.0987	0.1739	-0.013	0.1962	24.8291	18.3591	35.2515
4	1.8255	0.909	-0.4461	9.7079	2.1478	2.9551	0.1014	-0.368	0.2064	0.3062	-0.0237	-0.2514	-0.3315	0.5574	-0.0484	0.239	-0.028	-0.0213	0.2429	-0.0602	0.2185	34.3243	36.6489	57.9258
5	1.1479	-0.0264	-0.4853	3.9557	3.6036	3.5247	-0.1165	0.0626	0.0198	-0.161	0.01	0.3323	-0.078	-0.1656	0.1188	0.1276	0.0379	-0.0536	0.1962	-0.0136	0.2593	24.6277	27.5102	50.753
6	1.3137	-0.4735	-1.9921	1.5955	1.5998	3.5191	-0.0379	0.0537	-0.1758	-0.0803	-0.2104	0.5237	0.0862	-0.7193	0.1901	0.1843	0.0737	0.0152	0.3348	-0.026	0.3212	19.792	33.9195	55.4577
7	3.3045	-2.5037	-2.9544	7.5665	3.206	2.8425	0.1996	0.2726	-0.2172	-0.596	-0.4114	0.0506	-0.1808	-0.0717	0.1381	0.1977	-0.0303	-0.0525	0.2426	-0.008	0.1797	30.1506	22.8972	37.138
8	2.3653	1.3374	0.1238	4.9802	1.8595	2.7952	0.2558	-0.4035	0.0582	0.4052	-0.3169	0.1608	0.0426	-0.0981	0.1319	0.1192	-0.0032	0.0182	0.2306	-0.0176	0.1995	25.54	30.5228	59.9903
9	2.6595	-0.8677	-1.8062	1.4718	0.8611	4.7297	0.1287	-0.0904	0.1843	-0.0793	-0.0315	-0.0717	-0.1847	0.3138	-0.0937	0.169	-0.0424	-0.0145	0.1852	0.0134	0.1915	38.519	48.1159	19.9311
10	3.267	1.1741	-2.1644	1.7532	-1.7034	6.1029	-0.1069	0.3005	0.1738	-0.1996	0.1291	0.1518	0.1003	-0.1243	-0.0807	0.206	-0.0166	-0.0153	0.1047	-0.0145	0.1743	29.0309	45.2653	14.8289
11	0.9802	0.3166	-0.0629	0.9094	-0.3214	2.5633	0.032	0.0856	0.1313	0.0257	0.0678	0.035	-0.253	-0.0264	-0.1172	0.237	0.03	-0.0101	0.2063	-0.0154	0.1851	32.1747	47.6592	16.412
12	1.5676	-0.0538	0.0167	0.0847	0.4681	2.0153	0.1248	-0.027	-0.113	0.2769	-0.0545	0.2154	-0.5051	-0.0146	-0.0246	0.143	-0.0302	-0.0445	0.1419	-0.0822	0.2545	35.3094	42.6747	48.4919
13	1.1809	-0.5868	0.9135	1.953	-1.1296	1.7127	-0.0828	0.1089	-0.0726	-0.0503	0.0451	0.0076	-0.1077	0.1573	0.0145	0.1151	0.0024	0.0027	0.1898	-0.0321	0.2047	37.2052	38.7656	43.8793
14	0.5316	-0.2117	-0.2424	1.6894	-0.3382	1.2784	-0.0732	0.0615	-0.0283	0.0284	-0.0433	0.098	0.0265	-0.0943	0.1489	0.1021	0.0072	-0.0299	0.2037	-0.0533	0.2007	34.9618	33.9175	44.9863
15	3.8836	-3.0764	1.7559	7.6679	-3.7079	4.4767	-0.0211	0.3206	0.1681	0.0336	-0.3225	-0.3265	-0.0619	0.6041	0.3697	0.1324	-0.0439	-0.0279	0.1545	0.0419	0.2253	44.9849	37.8244	45.21
16	3.6826	-0.5009	0.3329	9.2002	-5.669	6.7316	-0.0337	0.1802	0.1123	0.2044	0.2251	0.3224	-0.442	0.3449	-0.0302	0.1329	-0.0422	-0.0279	0.2409	0.0005	0.2955	44.836	40.3592	50.0539
17	3.2856	-2.4556	-1.3402	5.0104	3.2899	5.6101	0.1555	-0.1585	0.2196	0.267	0.0291	-0.3409	-0.3058	0.392	-0.2119	0.3193	-0.134	0.0048	0.2685	0.0356	0.2961	11.7118	17.0045	17.9747
18	0.8493	-0.2201	1.0722	2.1977	0.1654	2.7697	-0.0183	0.12	0.1951	-0.04	0.1448	0.0532	-0.2826	-0.2166	-0.1365	0.3072	-0.0234	-0.0004	0.2061	0.0257	0.1827	2.9101	14.4135	11.9178
19	0.4657	0.1644	0.3441	0.3499	0.4941	1.8432	-0.0316	-0.0472	0.0312	-0.154	0.0516	0.025	-0.2787	0.0973	-0.0464	0.197	-0.0078	0.0062	0.1699	0.0089	0.2321	3.3803	9.8903	31.0923
20	1.4283	0.1852	0.0748	4.3082	-3.1145	2.2837	-0.254	-0.051	0.151	0.0261	0.1202	-0.3007	-0.0233	-0.0176	0.0668	0.1689	0.0468	0.0121	0.1382	-0.0446	0.1966	7.0181	10.4005	48.9458
21	1.7537	-0.7726	0.6632	1.2344	-0.9163	0.6242	-0.1372	-0.4409	0.4282	0.0322	0.0412	-0.2745	-0.2465	-0.2867	-0.0205	0.1465	0.0424	-0.0826	0.275	-0.0031	0.2318	12.0675	3.8682	53.1189
22	1.7004	-0.6398	0.8023	2.6741	-1.4055	2.6853	-0.2046	-0.1887	0.0928	0.2787	0.1592	-0.0916	-0.2708	-0.1406	0.0378	0.1234	0.0238	-0.0318	0.2262	-0.0418	0.1641	5.2005	8.9285	53.161
23	2.5398	-0.7346	1.3779	1.5889	-1.0472	4.1213	0.0061	0.1107	-0.0785	-0.1279	0.0062	0.0668	0.2441	-0.2683	0.0404	0.2453	-0.0715	-0.023	0.2667	-0.0167	0.2183	-6.564	-8.25	16.9126
24	2.6648	1.0534	2.962	1.4819	2.2681	6.2157	0.0397	0.2476	-0.4092	0.0378	0.2576	-0.033	0.0754	0.2506	-0.2887	0.2648	-0.0469	-0.0257	0.1663	-0.0332	0.2101	2.7895	-4.5203	12.0302
25	0.4531	-0.2595	0.8148	1.6015	0.1671	3.9126	0.0619	0.0843	-0.2555	0.0093	0.0989	0.0149	0.6963	0.1052	-0.1679	0.3091	0.0011	-0.0003	0.1879	0.0217	0.2406	1.5218	-12.7038	13.2912
26	1.0821	0.05	-0.7365	0.8436	0.1874	1.8752	-0.0619	0.0319	-0.0269	0.0212	-0.0518	-0.1214	0.1042	-0.2767	0.0632	0.2394	-0.0288	0.012	0.1896	-0.0196	0.2112	-2.3374	-0.4929	13.8089
27	0.7196	0.1832	0.1122	0.8905	-1.0891	1.5129	-0.159	-0.0214	-0.004	0.1751	0.1926	0.0457	0.4566	0.1057	-0.0597	0.1691	-0.0163	0.032	0.1527	0.014	0.2318	-2.6011	-6.6848	44.8538
28	0.7138	-0.4155	-0.4821	1.7701	0.3092	1.1788	0.0546	-0.0676	-0.0467	-0.0393	-0.0226	0.1069	0.105	-0.0478	-0.0632	0.1239	0.0141	-0.011	0.185	0.0333	0.1941	-4.2083	2.2225	42.4752
29	3.0123	-1.7392	-1.4383	4.1728	1.6613	3.8359	0.0179	-0.0881	0.1208	0.07	-0.007	0.0527	0.114	-0.3453	0.0033	0.1083	-0.0232	-0.0096	0.2414	0.0369	0.2138	-12.8847	-1.1233	45.1694
30	2.3741	-0.1081	1.0029	2.0305	0.2079	6.5113	-0.3483	0.2628	0.186	0.795	0.283	0.1698	0.1795	-0.1154	0.0966	0.3706	-0.0337	-0.0739	0.2272	0.011	0.2891	24.0817	35.769	30.5719
31	1.2494	1.4467	-0.559	2.0477	-0.0092	4.6274	-0.4147	0.2137	0.1428	0.7181	0.1186	0.1752	-0.1328	0.3461	0.1986	0.3571	-0.0077	-0.0487	0.2944	-0.0008	0.3821	7.4048	3.8698	28.3211

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 101 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 102 through 113 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 114 through 128 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 129 through 150 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 151 through 163 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 164 through 174 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 175 through 213 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 33 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 34 through 56 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 57 through 117 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 118 through 140 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 141 through 163 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 164 through 194 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 195 through 209 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 210 through 220 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1 through 25 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 26 through 75 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 76 through 128 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 129 through 150 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 151 through 163 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 164 through 213 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1 through 33 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 34 through 56 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 57 through 90 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 91 through 117 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 118 through 140 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 141 through 194 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 195 through 220 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 1 through 12 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 1 through 12 )

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