PDB-4elk: Crystal structure of the Hy19.3 type II NKT TCR

ID or keywords:

Entry

Database: PDB / ID: 4elk

Title

Crystal structure of the Hy19.3 type II NKT TCR

Components

Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)
Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

Keywords

IMMUNE SYSTEM / antigen presentation / type II NKT cells

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / FORMIC ACID / MALONATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Girardi, E. / Maricic, I. / Wang, J. / Mac, T.T. / Iyer, P. / Kumar, V. / Zajonc, D.M.

Citation

Journal: Nat.Immunol. / Year: 2012
Title: Type II natural killer T cells use features of both innate-like and conventional T cells to recognize sulfatide self antigens.
Authors: Girardi, E. / Maricic, I. / Wang, J. / Mac, T.T. / Iyer, P. / Kumar, V. / Zajonc, D.M.

History

Deposition	Apr 10, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 9, 2013	Group: Database references
Revision 1.2	Sep 13, 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 27, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4elk.cif.gz	502.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4elk.ent.gz	422.1 KB	Display	PDB format
PDBx/mmJSON format	4elk.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/el/4elk ftp://data.pdbj.org/pub/pdb/validation_reports/el/4elk	HTTPS FTP

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Related structure data

Related structure data	4elmC 2q86S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6dfq-3 5d5m-3 3skn-4 3rev-d 3vxt-1 6cph-d 3qh3-2 2eys-d 6dfq-1 2eyt-2 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

Deposited unit

A: Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

B: Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

C: Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

D: Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

hetero molecules

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

1

A: Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

B: Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

hetero molecules

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

2

C: Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

D: Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.220, 101.530, 134.490
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

non-covalent dimer of TCR alpha and beta chains

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Hy19.3 TCR alpha chain (mouse variable domain, human constant domain) Mass: 23209.518 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: Valpha1 (mouse variable domain, human constant domain) Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein	Hy19.3 TCR beta chain (mouse variable domain, human constant domain) Mass: 27993.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Gene: Vbeta16 (mouse variable domain, human constant domain) Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

#1: Protein

Hy19.3 TCR alpha chain (mouse variable domain, human constant domain)

Mass: 23209.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse)
Gene: Valpha1 (mouse variable domain, human constant domain)
Plasmid: pET22b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

#2: Protein

Hy19.3 TCR beta chain (mouse variable domain, human constant domain)

Mass: 27993.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse)
Gene: Vbeta16 (mouse variable domain, human constant domain)
Plasmid: pET30a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 422 molecules

#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.44 Å³/Da / Density % sol: 49.61 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 18% PEG 4000, 0.2M ammonium citrate dibasic, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2010
Radiation	Monochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→49 Å / Num. all: 59820 / Num. obs: 59222 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / R_merge(I) obs: 0.079 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.1→2.15 Å / R_merge(I) obs: 0.563 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2Q86

2q86

Resolution: 2.1→38.233 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2265	2857	5.05 %	RANDOM
R_work	0.1884	-	-	-
obs	0.1904	56586	95.55 %	-

Solvent computation

Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.882 Å² / k_sol: 0.412 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.0702 Å²	0 Å²	-0 Å²
2-	-	2.9957 Å²	0 Å²
3-	-	-	-4.066 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→38.233 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6761	0	48	409	7218

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7102
X-RAY DIFFRACTION	f_angle_d	1.037	9666
X-RAY DIFFRACTION	f_dihedral_angle_d	13.414	2427
X-RAY DIFFRACTION	f_chiral_restr	0.069	1046
X-RAY DIFFRACTION	f_plane_restr	0.004	1272

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 (%)
2.1-2.1362	0.2943	139	0.2439	2514	X-RAY DIFFRACTION	91
2.1362-2.1751	0.3116	122	0.2351	2467	X-RAY DIFFRACTION	90
2.1751-2.2169	0.2693	137	0.2293	2574	X-RAY DIFFRACTION	91
2.2169-2.2621	0.2635	122	0.2262	2541	X-RAY DIFFRACTION	92
2.2621-2.3113	0.2816	147	0.2224	2557	X-RAY DIFFRACTION	92
2.3113-2.3651	0.2729	123	0.2124	2654	X-RAY DIFFRACTION	94
2.3651-2.4242	0.2774	137	0.2203	2617	X-RAY DIFFRACTION	95
2.4242-2.4898	0.2857	154	0.2197	2622	X-RAY DIFFRACTION	95
2.4898-2.563	0.2529	140	0.2187	2650	X-RAY DIFFRACTION	95
2.563-2.6457	0.2846	147	0.2091	2688	X-RAY DIFFRACTION	97
2.6457-2.7402	0.2583	149	0.2139	2704	X-RAY DIFFRACTION	97
2.7402-2.8499	0.2479	142	0.2012	2729	X-RAY DIFFRACTION	97
2.8499-2.9796	0.2518	134	0.1889	2722	X-RAY DIFFRACTION	97
2.9796-3.1366	0.213	162	0.1766	2741	X-RAY DIFFRACTION	98
3.1366-3.333	0.2376	141	0.1829	2808	X-RAY DIFFRACTION	99
3.333-3.5902	0.2114	130	0.1818	2794	X-RAY DIFFRACTION	99
3.5902-3.9512	0.1877	165	0.1672	2787	X-RAY DIFFRACTION	99
3.9512-4.5221	0.1619	156	0.134	2802	X-RAY DIFFRACTION	98
4.5221-5.6944	0.1804	158	0.1514	2832	X-RAY DIFFRACTION	98
5.6944-38.2393	0.2566	152	0.2333	2926	X-RAY DIFFRACTION	97

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	0.0959	0.047	0.125	0.2842	-0.0643	0.218	0.1087	0.0534	0.0241	-0.0167	-0.1278	-0.0573	0.0757	0.1363	0.025	0.1439	0.0299	0.0458	0.1114	0.036	0.1109	-1.2871	-9.2272	-19.7664
2	0.3642	0.1414	0.31	0.0548	0.1195	0.2657	0.0567	0.023	0.0369	-0.0488	-0.1184	-0.2316	0.2844	-0.2122	0.0108	0.345	0.0254	0.0781	0.1408	0.0066	0.2153	-7.843	-12.1503	-13.6494
3	0.2408	0.0697	0.2448	0.2292	0.2681	0.4388	-0.0025	-0.0485	0.0835	-0.064	-0.1032	-0.0123	0.4863	0.0575	-0.0358	0.3593	0.0318	0.0466	0.1719	0.0561	0.2315	-3.8201	-17.2161	-22.9877
4	0.3136	0.1043	0.1354	0.2372	-0.0361	0.4473	0.147	0.0387	0.1287	-0.0595	-0.1835	-0.006	0.3493	0.0253	0.0269	0.2335	0.0147	0.0458	0.1975	0.0241	0.1616	-4.9989	-8.5097	-15.1742
5	1.2352	0.4145	-0.195	0.1413	-0.0634	0.0316	0.0061	-0.0736	-0.1394	-0.405	0.0693	0.0356	-0.2311	-0.1359	0.0394	0.4514	0.0446	-0.0109	0.1349	-0.0268	0.1405	-15.9196	4.9309	-30.1452
6	0.6832	0.2176	-0.4251	0.9105	-0.3189	1.2371	0.0896	-0.0433	0.0209	-0.4062	-0.1047	-0.2443	-0.619	0.0647	-0.0257	0.3742	0.0301	0.068	0.1933	0.0228	0.2761	-16.1395	21.27	-24.4727
7	0.9939	0.1948	-0.4014	1.2791	0.0842	1.0086	-0.1097	0.2306	0.003	-0.2353	-0.1252	0.029	-0.0357	-0.2885	0.0597	0.2634	0.0544	-0.0149	0.2264	-0.039	0.1499	-24.0737	8.6777	-25.0348
8	0.3748	0.032	0.038	0.7207	-0.615	0.5363	0.0138	0.0588	0.1682	-0.2092	0.1144	-0.133	-0.6771	0.1211	-0.0816	0.6062	-0.0822	0.1139	0.2609	0.0769	0.4241	-12.2507	30.6114	-22.8026
9	0.6408	-0.4682	-0.3119	1.2107	0.2179	0.8521	0.4922	0.2073	0.0609	-0.6633	-0.3593	-0.162	-0.3349	0.0963	-0.0353	0.6029	0.1052	0.1241	0.2632	0.039	0.3483	-14.8342	22.8942	-34.1652
10	0.7104	-0.5613	0.2289	0.5289	0.0115	0.819	-0.1535	-0.3443	0.2007	0.1618	0.0475	-0.067	0.018	0.088	0.0799	0.2071	-0.0607	-0.0163	0.2458	-0.0332	0.2505	-8.8141	4.7646	5.2638
11	0.9558	-0.5121	0.2543	0.9067	0.5903	1.0248	-0.0187	-0.2057	0.0924	0.0855	0.1117	-0.2052	0.1671	0.1855	0.0132	0.2286	0.0267	0.0107	0.2824	0.0386	0.2072	-1.4359	-6.7781	3.3595
12	0.8536	-0.6338	0.4513	1.056	0.4166	1.1916	-0.0586	-0.418	-0.0475	0.1129	-0.1293	-0.2456	0.1475	0.0667	-0.0744	0.1393	-0.042	-0.0156	0.3049	0.0547	0.177	-4.2354	-1.3258	5.9763
13	0.8514	-0.2878	0.3496	0.3567	-0.3654	0.3804	-0.0904	-0.1271	-0.0358	0.2033	0.076	0.0073	0.3145	0.0052	-0.0488	0.3069	0.0048	0.0686	0.2695	0.03	0.1103	-7.3045	-14.426	-3.5517
14	0.2687	-0.2319	-0.3474	1.1604	-0.4816	1.0851	-0.0461	-0.0324	0.2851	-0.206	-0.128	-0.0054	-0.1571	0.1955	-0.4065	0.2162	-0.0901	-0.0509	0.163	-0.0194	0.2461	-6.7019	17.4042	2.3172
15	0.6862	-0.111	-0.1971	0.8466	-0.2207	0.8278	0.1198	-0.0156	0.1648	-0.076	-0.0993	-0.0747	-0.2694	-0.2705	0.0429	0.247	0.067	-0.0544	0.1914	-0.0248	0.2149	-23.5676	18.6259	-16.3026
16	0.1966	0.416	0.1926	0.9094	0.1481	1.697	-0.0077	-0.1844	-0.0294	-0.0333	-0.0326	-0.3265	-0.0089	0.1734	-0.0052	0.1789	0.0239	-0.0426	0.2404	-0.0175	0.3417	-15.7	15.144	-12.0764
17	0.5868	0.3242	-0.549	0.7957	-0.2377	0.5802	0.277	-0.0064	-0.0744	0.1426	-0.2551	-0.007	-0.2064	-0.2296	0.1249	0.2259	0.0194	-0.0458	0.2208	-0.0735	0.2087	-24.6248	19.302	-6.9069
18	0.4021	0.2366	0.1286	0.3586	-0.0657	1.674	-0.0865	-0.0394	-0.0323	-0.1255	0.0466	-0.0455	0.3138	-0.2252	0.0325	0.2935	-0.0172	0.0347	0.2009	-0.0217	0.1833	-8.6093	-7.9104	-41.4222
19	0.6324	0.161	0.0728	1.6087	-0.1444	0.0549	-0.1859	0.0426	-0.0769	-0.1611	0.1608	0.21	0.0387	-0.0225	-0.9611	0.2276	0.002	0.0848	0.116	0.0364	0.0993	-6.9193	-5.6998	-46.4487
20	1.8285	0.9079	0.9439	0.7952	0.3531	1.3374	-0.2617	-0.1147	-0.2246	-0.1897	-0.0421	-0.184	-0.2192	0.3845	0.016	0.2348	0.0293	0.0371	0.3675	0.0556	0.1768	12.0864	-4.2757	-28.7383
21	1.2424	-0.2734	-0.1466	1.4514	-0.2915	0.2887	-0.324	-0.4088	-0.1043	0.3963	0.1108	0.0006	-0.1379	0.1521	-0.0827	0.2744	0.0897	-0.0526	0.4865	-0.0363	0.1697	22.3558	7.279	-28.7595
22	0.2435	0.2471	0.2069	0.9222	0.2584	0.1858	-0.1719	0.1895	-0.0871	-0.3268	0.1227	-0.1541	-0.0259	0.19	-0.0215	0.1509	-0.0734	0.0699	0.1637	-0.0331	0.1878	2.8056	4.0058	-64.1947
23	0.8862	-0.549	-0.1475	0.6035	-0.2421	0.4438	-0.0478	0.1353	0.0863	0.0967	-0.0349	0.032	-0.0392	-0.1466	0.0566	0.1567	-0.0568	-0.0026	0.1682	-0.0134	0.1493	-9.0632	4.5647	-59.2944
24	1.3922	0.3093	0.4487	0.883	-0.1538	0.9466	-0.1421	0.2406	0.0576	0.1173	0.1078	0.0735	0.1478	0.0417	0.041	0.2024	-0.0535	0.0417	0.1871	-0.0249	0.1925	-3.9421	2.6141	-62.7423
25	0.6561	0.403	0.0765	0.6637	0.3101	0.6403	-0.2404	0.1257	-0.0659	-0.1354	0.0976	0.0641	-0.2639	0.1007	0.0226	0.2075	-0.0889	-0.0608	0.2228	0.0134	0.2522	10.3659	18.1843	-55.6854
26	0.2422	-0.0103	0.1894	0.5935	0.28	0.4219	-0.1537	-0.1413	-0.0138	0.0401	0.1384	-0.038	0.0594	0.2926	0.0515	0.1241	0.0524	-0.0077	0.3974	-0.0095	0.1734	25.2374	5.4748	-40.7806
27	0.402	0.3224	-0.3618	1.0231	0.4423	1.1288	-0.163	-0.1022	-0.0461	-0.0855	0.0051	0.4551	-0.0276	0.2387	0.0968	0.2254	0.0074	0.0016	0.272	-0.0263	0.3124	16.2189	9.1761	-43.6225
28	0.3961	0.138	-0.1611	0.3467	0.3552	0.6427	-0.1592	-0.1018	0.0421	-0.0506	0.0147	-0.105	0.0384	0.6068	-0.1124	0.145	-0.0152	0.0298	0.4482	0.0386	0.2403	26.1158	7.5354	-49.2268

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:39)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 40:54)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 55:77)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 78:107)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 108:121)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 122:161)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 162:178)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 179:188)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 189:204)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 3:19)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 20:69)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 70:96)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 97:109)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 110:124)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 125:162)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 163:188)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 189:244)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 3:77)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 78:107)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 108:121)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 122:207)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 2:31)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 32:65)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 66:109)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 110:124)
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 125:162)
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 163:188)
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 189:244)

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