PDB-5u5f: MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQ...

ID or keywords:

Entry

Database: PDB / ID: 5u5f

Title

MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQFDA(PH)2STRRLRCGGSK

Components

(MEMAB TRASTUZUMAB FAB ...) x 2
5-DIPHENYL LONG MEDITOPE
Immunoglobulin G binding protein A
Protein L

Keywords

IMMUNE SYSTEM

Function / homology

Function and homology information

IgG binding / immunoglobulin binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Finegoldia magna (bacteria)

Staphylococcus aureus (bacteria)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.81 Å

Authors

Bzymek, K.P. / Avery, K.N. / Zer, C. / Williams, J.C.

Citation

Journal: To Be Published
Title: Meditope Enabled Trastuzumab I83E Variant In Complex With (Ac)Cqfda(Ph)2Strrlrcggsk
Authors: Bzymek, K.P. / Avery, K.N. / Zer, C. / Williams, J.C.

History

Deposition	Dec 6, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2018	Provider: repository / Type: Initial release
Revision 1.1	Mar 28, 2018	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_ref / struct_ref_seq / struct_ref_seq_dif Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name ..._entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2	Apr 18, 2018	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3	Oct 4, 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 1.4	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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Download

PDBx/mmCIF format	5u5f.cif.gz	262.2 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	5u5f.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5u5f_validation.pdf.gz	464.5 KB	Display	wwPDB validaton report
Full document	5u5f_full_validation.pdf.gz	467.4 KB	Display
Data in XML	5u5f_validation.xml.gz	30.9 KB	Display
Data in CIF	5u5f_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u5/5u5f ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u5f	HTTPS FTP

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Related structure data

Related structure data	4ioiS 5u3d 5u5m 5u6a S: Starting model for refinement
Similar structure data	4ioi-d 6b9z-d 6b9y-d 4hjg-d 4hkz-d 6bah-d 5u6a-d 6bae-d 1jec-d 2ziw-d 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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E

B: MEMAB TRASTUZUMAB FAB HEAVY CHAIN

E: Protein L

D: 5-DIPHENYL LONG MEDITOPE

C: Immunoglobulin G binding protein A

hetero molecules

62.4 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.430, 105.380, 117.000
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 3 types, 3 molecules ABC

#1: Antibody	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E Mass: 23518.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	MEMAB TRASTUZUMAB FAB HEAVY CHAIN Mass: 23774.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody	Immunoglobulin G binding protein A Mass: 6037.530 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UW42, UniProt: P02976*PLUS

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Protein / Protein/peptide , 2 types, 2 molecules ED

#3: Protein	Protein L Mass: 6994.734 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918
#4: Protein/peptide	5-DIPHENYL LONG MEDITOPE Mass: 1967.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 799 molecules

#6: Chemical	ChemComp-MRY / MESO-ERYTHRITOL Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.65 Å³/Da / Density % sol: 53.62 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 7.2

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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: Apr 10, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.81→33.64 Å / Num. obs: 60655 / % possible obs: 99.4 % / Redundancy: 3.9 % / R_merge(I) obs: 0.085 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.81→1.86 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.784 / Mean I/σ(I) obs: 1.66 / Num. unique all: 4170 / % possible all: 93.7

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	dev_1839	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4IOI

4ioi

Resolution: 1.81→33.64 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.44

	R_factor	Num. reflection	% reflection
R_free	0.192	2938	4.84 %
R_work	0.163	-	-
obs	0.164	60648	99.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.81→33.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4340	0	8	798	5146

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4669
X-RAY DIFFRACTION	f_angle_d	1.075	6379
X-RAY DIFFRACTION	f_dihedral_angle_d	13.589	1739
X-RAY DIFFRACTION	f_chiral_restr	0.046	705
X-RAY DIFFRACTION	f_plane_restr	0.005	838

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 (%)
1.8101-1.8397	0.3022	121	0.2811	2468	X-RAY DIFFRACTION	91
1.8397-1.8715	0.2724	134	0.2341	2708	X-RAY DIFFRACTION	100
1.8715-1.9055	0.2694	133	0.2082	2754	X-RAY DIFFRACTION	100
1.9055-1.9421	0.2202	131	0.189	2714	X-RAY DIFFRACTION	100
1.9421-1.9818	0.2239	129	0.194	2771	X-RAY DIFFRACTION	100
1.9818-2.0249	0.225	140	0.1825	2708	X-RAY DIFFRACTION	100
2.0249-2.072	0.2498	128	0.1881	2749	X-RAY DIFFRACTION	100
2.072-2.1238	0.2355	141	0.1769	2704	X-RAY DIFFRACTION	100
2.1238-2.1812	0.2191	134	0.1646	2752	X-RAY DIFFRACTION	100
2.1812-2.2453	0.182	143	0.1632	2747	X-RAY DIFFRACTION	100
2.2453-2.3178	0.1876	158	0.1616	2728	X-RAY DIFFRACTION	100
2.3178-2.4006	0.2069	151	0.1672	2718	X-RAY DIFFRACTION	100
2.4006-2.4967	0.2076	137	0.1671	2740	X-RAY DIFFRACTION	100
2.4967-2.6103	0.2006	139	0.1662	2762	X-RAY DIFFRACTION	100
2.6103-2.7479	0.1981	115	0.1647	2776	X-RAY DIFFRACTION	100
2.7479-2.9199	0.177	144	0.1632	2781	X-RAY DIFFRACTION	100
2.9199-3.1452	0.1845	167	0.1601	2761	X-RAY DIFFRACTION	100
3.1452-3.4614	0.1868	151	0.1468	2767	X-RAY DIFFRACTION	100
3.4614-3.9617	0.1593	152	0.1402	2796	X-RAY DIFFRACTION	100
3.9617-4.9887	0.1389	143	0.1228	2835	X-RAY DIFFRACTION	100
4.9887-33.6489	0.1762	147	0.1666	2971	X-RAY DIFFRACTION	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	0.6294	0.8322	0.3382	1.2073	0.9795	2.4871	-0.0085	0.0186	0.0168	-0.0457	0.1373	-0.006	-0.2803	0.0938	-0.0629	0.1375	0.0067	0.0014	0.1328	0.0123	0.1585	-7.7144	-17.9489	10.2899
2	1.1719	-0.2327	0.2991	1.1545	0.4865	1.3244	0.0104	0.0548	0.038	0.0182	-0.0001	0.2207	-0.1238	-0.1633	-0.0135	0.0927	0.0162	-0.0049	0.1401	0.012	0.1588	-16.5338	-24.1701	8.2801
3	0.1501	0.0032	0.0947	0.5426	0.656	1.7032	-0.054	0.0127	0.0476	0.0545	0.0084	0.1266	-0.0149	-0.1194	0.011	0.1513	0.0144	0.0094	0.1369	0.0097	0.1416	-10.0394	-22.5984	15.8488
4	1.7714	-0.4732	0.2713	2.9583	-0.0833	1.8699	0.0738	-0.0524	-0.3137	0.5657	0.0298	-0.0495	0.3616	0.2012	-0.1463	0.2477	0.063	-0.0607	0.1708	-0.0285	0.1607	4.7441	-33.2032	48.3967
5	4.1859	-3.361	2.0512	3.8354	-2.035	2.9807	0.0721	0.1539	0.0665	-0.0336	-0.0553	-0.172	0.0977	0.3119	-0.0314	0.1299	0.0219	-0.0078	0.1136	-0.0408	0.0822	4.894	-21.8758	38.7191
6	4.4853	-1.9232	2.5651	2.506	-1.0633	3.5554	0.0548	0.2329	0.1972	-0.0095	-0.0228	-0.3146	-0.0013	0.6631	0.0558	0.1563	0.0271	0.0149	0.2734	-0.0458	0.1902	13.6312	-25.3489	38.9731
7	3.8641	-2.9278	2.7568	4.2294	-2.0607	4.2381	0.1636	0.0027	-0.2616	0.0093	0.06	0.035	0.2471	0.1841	-0.2387	0.1423	0.0201	-0.0215	0.1166	-0.0177	0.1125	3.5045	-27.3695	39.1933
8	2.5624	-2.2309	1.8727	4.9179	-2.1156	3.6299	-0.0757	-0.1744	0.0115	0.4748	0.2052	-0.3572	0.1049	0.1471	-0.0498	0.1829	0.0316	-0.0569	0.1432	-0.0293	0.1272	8.4541	-20.5576	48.484
9	3.8789	-0.7189	1.678	2.2065	-0.4603	2.4574	-0.3408	-0.4865	0.0056	0.3817	0.337	0.0825	0.0393	-0.1873	0.037	0.149	-0.0072	0.0199	0.0901	-0.0021	0.1036	-7.464	-48.2574	17.9883
10	6.2864	-3.821	0.7328	3.3569	-2.0793	2.7274	0.0737	0.0585	-0.2654	-0.026	0.1214	0.4132	0.1504	-0.3443	-0.2109	0.1184	-0.0301	-0.0018	0.1156	-0.0074	0.2085	-18.5633	-48.8276	11.3386
11	3.0427	2.3213	2.1753	4.7592	3.0442	4.5956	-0.0025	0.1978	-0.0111	-0.2187	0.1076	-0.0853	-0.1166	0.0233	-0.0993	0.098	0.039	-0.0098	0.1041	0.0167	0.0986	-8.2198	-40.4281	7.626
12	7.3044	0.306	1.9239	1.8348	-0.4818	3.3272	0.1952	0.6537	-0.0543	-0.2272	-0.1363	0.0583	0.2048	0.319	-0.0616	0.1627	0.0589	-0.0001	0.1428	-0.0213	0.1038	-7.3865	-47.2362	0.0298
13	1.331	-1.4796	0.9198	2.972	0.7714	3.0658	0.0962	0.1583	-0.2204	-0.0298	0.0725	0.0783	0.1375	0.0168	-0.1663	0.1165	0.021	0.0063	0.0652	-0.0022	0.0959	-7.7785	-51.0491	10.2984
14	5.9523	-1.5225	1.5824	3.6325	-0.1261	3.842	0.032	0.4347	0.245	-0.0503	-0.0684	0.4538	-0.0927	-0.4296	0.0407	0.1025	0.006	0.0211	0.1702	0.0209	0.195	-17.0627	-38.0337	9.5498
15	0.5262	0.2454	-1.0047	1.2509	0.9427	3.6796	0.0938	-0.0094	-0.1082	0.3107	0.0729	-0.1745	0.2963	0.4165	-0.1709	0.1947	0.0339	-0.0462	0.102	-0.0325	0.1452	0.6762	-46.3544	24.4642
16	0.9503	-0.8358	-0.4896	2.7392	1.8158	3.2369	0.0581	0.0223	-0.0172	0.1113	0.0012	-0.0395	0.2293	0.0424	-0.0518	0.152	0.005	0.0069	0.0837	-0.0027	0.1012	-3.0763	-33.913	40.5573
17	2.9236	-1.3844	-2.4388	2.6323	1.1152	5.0515	-0.2155	-0.1951	-0.2339	0.8111	0.1254	0.2273	0.9272	0.1253	0.012	0.3218	0.0013	0.0313	0.1317	0.0197	0.138	-6.9397	-41.068	45.5618
18	7.7764	-5.4179	-1.7987	3.8709	1.0093	4.8434	0.0737	-0.345	0.1701	0.2394	0.159	-0.0654	-0.3248	0.4571	-0.2238	0.1959	-0.0567	0.0236	0.1759	-0.0395	0.3664	-0.822	-8.8563	15.1514
19	7.259	-1.4672	-2.0507	4.6396	0.0667	4.2153	0.0345	0.4305	0.2723	-0.2717	-0.0751	-0.0817	-0.1154	0.2368	0.0552	0.1263	-0.0488	-0.0016	0.1355	0.0343	0.1487	-1.302	-11.3626	8.3571
20	5.2297	-2.3563	0.254	1.8229	-0.0717	4.7549	-0.0158	-0.0851	0.6363	0.1959	0.0243	-0.3664	-0.7167	0.9818	0.1429	0.4476	-0.1606	0.0468	0.4061	0.1834	0.5062	2.0795	-1.5765	10.1321
21	4.5636	-4.0685	1.2212	5.0115	-1.0444	4.589	0.29	-0.1549	0.5681	0.0105	0.0917	0.032	-0.4241	0.2151	-0.3058	0.3225	-0.082	0.0986	0.1606	0.0377	0.3664	-0.7423	-3.4904	12.4761
22	0.2135	-0.0998	-0.364	7.5599	-6.1659	5.9027	-0.096	-0.3068	0.0396	0.2473	0.0144	-0.3345	-0.0053	0.2569	0.2311	0.2254	0.0251	-0.0367	0.1065	-0.0179	0.1246	-2.0397	-32.4471	21.5572
23	5.3117	0.4608	-2.2278	7.9079	-3.6366	3.6439	0.1782	-0.3402	0.4034	0.6599	-0.2488	-0.8059	-0.7514	0.6714	0.0335	0.2745	-0.0271	-0.0738	0.1768	-0.0085	0.2237	-1.0137	-25.2989	21.5086
24	3.6619	-0.3079	5.6132	5.0124	-0.7228	8.5553	0.2821	0.4636	-0.1658	-0.6395	-0.2914	0.556	0.194	-0.4878	0.0439	0.2548	0.0151	-0.0242	0.2788	-0.0706	0.2058	-2.383	-66.534	-2.0954
25	4.5007	-3.672	0.7521	3.2584	-0.8655	1.927	0.0782	0.041	-0.1432	-0.2422	-0.0493	0.1056	0.0008	-0.0551	-0.0345	0.1546	0.0005	-0.0026	0.0862	-0.0321	0.1286	1.0439	-61.2929	7.5682
26	7.7045	-2.1727	6.5776	4.0599	-1.5077	7.9376	0.4174	0.536	0.2129	-0.669	-0.4101	-0.3461	-0.0596	0.0678	0.0391	0.2541	0.0604	0.0615	0.1706	-0.0054	0.1298	5.4847	-56.3054	1.6572

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 75 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 76 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 188 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 189 THROUGH 214 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 1 THROUGH 17 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 18 THROUGH 32 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 33 THROUGH 52 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 53 THROUGH 67 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 68 THROUGH 91 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 92 THROUGH 110 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 111 THROUGH 126 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 127 THROUGH 195 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 196 THROUGH 223 )
18	X-RAY DIFFRACTION	18	CHAIN 'E' AND (RESID 19 THROUGH 33 )
19	X-RAY DIFFRACTION	19	CHAIN 'E' AND (RESID 34 THROUGH 61 )
20	X-RAY DIFFRACTION	20	CHAIN 'E' AND (RESID 62 THROUGH 72 )
21	X-RAY DIFFRACTION	21	CHAIN 'E' AND (RESID 73 THROUGH 81 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 1 THROUGH 8 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 9 THROUGH 13 )
24	X-RAY DIFFRACTION	24	CHAIN 'C' AND (RESID 1 THROUGH 16 )
25	X-RAY DIFFRACTION	25	CHAIN 'C' AND (RESID 17 THROUGH 35 )
26	X-RAY DIFFRACTION	26	CHAIN 'C' AND (RESID 36 THROUGH 54 )

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