PDB-5m7v: Translation initiation factor 4E in complex with (RP)-m2(7,2'O)Gp...

ID or keywords:

Entry

Database: PDB / ID: 5m7v

Title

Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D1)

Components

Eukaryotic translation initiation factor 4E

Keywords

TRANSLATION / Protein-ligand complex / translation initiation factor / eIF4E / m2(7 / 2'O)GppSpG / beta-S-ARCA / phosphorothioate / mRNA 5' cap analog

Function / homology

Function and homology information

Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Warminski, M. / Nowak, E. / Kowalska, J. / Jemielity, J. / Nowotny, M.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Translation initiation factor 4E in complex with (RP)-m2(7,2'O)GppSpG mRNA 5' cap analog (beta-S-ARCA D1)
Authors: Warminski, M. / Nowak, E. / Kubacka, D. / Kowalska, J. / Nowotny, M. / Jemielity, J.

History

Deposition	Oct 28, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5m7v.cif.gz	294.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5m7v.ent.gz	239 KB	Display	PDB format
PDBx/mmJSON format	5m7v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5m7v_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	5m7v_full_validation.pdf.gz	1.3 MB	Display
Data in XML	5m7v_validation.xml.gz	31.3 KB	Display
Data in CIF	5m7v_validation.cif.gz	44 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m7/5m7v ftp://data.pdbj.org/pub/pdb/validation_reports/m7/5m7v	HTTPS FTP

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Related structure data

Related structure data	1l8bS S: Starting model for refinement
Similar structure data	6u06-1 6u09-2 6u06-4 6gkj-4 5m7z-1 5m80-3 5j5o-1 5j5o-3 5m7w-2 5m7x-4 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1l8bS

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	#230 - Feb 2019 Initiation Factor eIF4E similarity (17)

Deposited unit

A: Eukaryotic translation initiation factor 4E

B: Eukaryotic translation initiation factor 4E

C: Eukaryotic translation initiation factor 4E

D: Eukaryotic translation initiation factor 4E

hetero molecules

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

1

A: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author&software
22.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author&software
22.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Eukaryotic translation initiation factor 4E

hetero molecules

defined by author&software
22.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Eukaryotic translation initiation factor 4E

defined by author&software
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.049, 38.057, 146.942
Angle α, β, γ (deg.)	88.60, 95.40, 103.61
Int Tables number	1
Space group name H-M	P1

#1: Protein	Eukaryotic translation initiation factor 4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit Mass: 22145.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical	ChemComp-WZO / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl)phosphoryl] hydrogen phosphate Mass: 568.307 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₂₁N₅O₁₃P₃S
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.32 Å³/Da / Density % sol: 47.08 % / Description: Thin plates
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18% Jeffamine, 0.1M HEPES pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.918 Å / Relative weight: 1
Reflection	Resolution: 1.74→50 Å / Num. obs: 77683 / % possible obs: 94.6 % / Redundancy: 1.776 % / CC_1/2: 0.997 / R_merge(I) obs: 0.054 / Net I/σ(I): 9.68
Reflection shell	Resolution: 1.74→1.84 Å / Redundancy: 1.724 % / R_merge(I) obs: 0.347 / Mean I/σ(I) obs: 2 / CC_1/2: 0.716 / % possible all: 93.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b

Resolution: 1.74→36.988 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 29.85

	R_factor	Num. reflection	% reflection
R_free	0.2876	2100	2.7 %
R_work	0.2363	-	-
obs	0.2376	77679	94.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.74→36.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5333	0	108	417	5858

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5595
X-RAY DIFFRACTION	f_angle_d	0.975	7639
X-RAY DIFFRACTION	f_dihedral_angle_d	14.384	3242
X-RAY DIFFRACTION	f_chiral_restr	0.057	822
X-RAY DIFFRACTION	f_plane_restr	0.005	963

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 (%)
1.7379-1.7783	0.3147	132	0.2943	4745	X-RAY DIFFRACTION	91
1.7783-1.8228	0.34	143	0.2813	5154	X-RAY DIFFRACTION	95
1.8228-1.8721	0.3118	140	0.27	5042	X-RAY DIFFRACTION	96
1.8721-1.9272	0.3204	141	0.2644	5073	X-RAY DIFFRACTION	95
1.9272-1.9894	0.3201	142	0.2587	5132	X-RAY DIFFRACTION	96
1.9894-2.0605	0.301	141	0.2504	5066	X-RAY DIFFRACTION	95
2.0605-2.143	0.3175	141	0.2446	5085	X-RAY DIFFRACTION	95
2.143-2.2405	0.2643	142	0.2482	5114	X-RAY DIFFRACTION	96
2.2405-2.3586	0.3313	140	0.2409	5039	X-RAY DIFFRACTION	96
2.3586-2.5063	0.2845	142	0.2409	5094	X-RAY DIFFRACTION	96
2.5063-2.6998	0.2959	141	0.2385	5084	X-RAY DIFFRACTION	95
2.6998-2.9714	0.281	141	0.2332	5088	X-RAY DIFFRACTION	96
2.9714-3.4011	0.2662	141	0.2184	5042	X-RAY DIFFRACTION	95
3.4011-4.284	0.2607	137	0.2089	4947	X-RAY DIFFRACTION	92
4.284-36.9966	0.277	136	0.2297	4874	X-RAY DIFFRACTION	92

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	3.5406	-0.6605	1.7027	3.0462	-2.1163	7.1365	0.206	-0.2393	-0.6028	0.0673	-0.2228	-0.3067	0.6233	0.5068	-0.0027	0.1501	0.0284	-0.0656	0.2477	0.0633	0.3711	66.8645	61.5995	0.0545
2	0.9474	-2.35	0.0764	5.9395	-0.317	0.1501	-0.1407	-0.1345	0.3197	0.2239	0.0312	-0.1837	-0.0206	-0.0794	0.076	0.1136	-0.0128	-0.0625	0.1687	-0.0428	0.2496	54.2428	84.8231	-5.5874
3	7.9348	-2.1269	-0.8936	2.2369	-0.9763	2.424	-0.0509	-0.2394	0.0313	0.1548	0.0804	-0.1778	-0.0813	0.1777	-0.0322	0.1075	-0.0244	-0.0493	0.1695	0.0229	0.1536	56.5925	67.7118	1.6368
4	0.865	-0.1881	0.251	1.7579	-0.6672	2.3588	-0.0578	0.067	0.2297	0.0173	-0.0384	-0.0633	-0.2286	0.1286	0.0897	0.1105	-0.0317	-0.0633	0.145	-0.0147	0.1808	54.5008	79.8092	-10.6892
5	0.9901	-0.0953	-0.2932	0.4492	-0.0903	0.9605	-0.1045	0.217	-0.0391	-0.077	0.0068	0.3091	-0.0119	-0.1909	0.0624	0.1395	-0.0326	-0.0735	0.1769	-0.0454	0.259	44.2284	70.0429	-11.8616
6	2.6852	1.7314	0.1154	1.6491	-1.1873	3.0023	-0.0744	0.1725	-0.0804	-0.2785	0.0649	-0.3367	0.2892	0.3127	0.0403	0.1087	-0.0133	-0.0026	0.1413	-0.0122	0.1813	58.2847	68.1838	-16.6172
7	4.9516	-0.9779	-3.0338	1.893	1.3072	3.773	0.0104	0.6439	0.111	-0.2997	-0.0266	0.1394	-0.2795	-0.2251	-0.0084	0.1336	-0.036	-0.0665	0.1754	0.0101	0.1689	50.4675	76.7158	-18.5664
8	1.4803	0.7365	1.0162	3.1507	-0.1259	2.498	-0.058	0.3357	-0.2762	-0.3929	0.123	0.0504	0.1799	-0.1299	-0.0519	0.2002	-0.0485	-0.0484	0.2412	-0.1093	0.1912	49.0752	63.7981	-22.4179
9	2.3863	2.7682	1.0722	5.1092	1.4151	2.849	-0.2621	0.3666	0.146	-0.5455	0.1214	0.3914	-0.4209	-0.0342	0.1238	0.2894	-0.0873	-0.1059	0.312	-0.051	0.1994	50.1338	77.1877	-26.8056
10	5.5396	-1.6699	-3.8749	1.86	1.6799	8.0826	0.1173	0.0588	0.066	-0.3923	0.0625	-0.6692	0.1363	0.7644	-0.1638	0.2257	0.0564	0.1019	0.1766	-0.0274	0.4259	51.9471	45.6394	-59.6539
11	8.2854	-1.2541	-0.9469	0.3261	0.0653	0.4455	0.1178	0.1358	-0.0657	-0.0837	-0.0731	0.0776	-0.0101	-0.1383	-0.0037	0.1563	-0.0117	-0.0216	0.0985	-0.0452	0.2626	26.4186	52.4222	-54.0148
12	2.5059	-0.9379	-0.9071	1.2826	-0.154	1.1572	0.0741	0.127	0.1568	-0.1172	-0.0217	-0.1423	-0.0411	-0.0641	-0.0541	0.1387	-0.0101	0.0056	0.0943	-0.0529	0.1677	37.013	57.4899	-57.8217
13	4.3903	0.0865	-1.428	2.4851	0.5479	8.3992	0.0116	-0.1605	-0.5635	0.3974	-0.0756	0.2852	0.5717	-0.1074	0.021	0.215	-0.045	0.019	0.102	0.0119	0.1953	30.8928	46.1476	-42.8273
14	0.2775	0.1368	-0.2611	1.3195	-0.145	0.9928	-0.0255	-0.1041	0.2114	0.2297	-0.0274	-0.1511	-0.249	0.0257	0.0473	0.1826	-0.0309	-0.0383	0.1134	-0.0468	0.1978	39.3459	64.1377	-47.3222
15	3.4269	-0.9034	1.3812	3.3502	-1.7578	4.1775	0.0603	-0.2576	0.069	0.2769	0.0311	-0.2155	-0.0282	0.0288	-0.0798	0.1368	-0.0311	-0.0342	0.0974	-0.0473	0.143	37.036	55.4417	-41.6362
16	2.0076	1.6585	0.1258	2.7301	0.2789	0.9104	0.1415	-0.358	0.0643	0.506	-0.1495	-0.109	-0.0624	-0.038	-0.0402	0.3454	-0.0675	-0.1048	0.1862	-0.0574	0.1973	39.9591	60.681	-35.3264
17	0.7703	0.2328	-0.9694	1.6451	-3.1437	6.964	0.0854	0.2187	0.0562	-0.3066	0.0529	-0.1514	0.3932	-0.3614	-0.1253	0.4667	0.0776	0.0446	0.173	-0.0273	0.2286	34.2831	61.2218	-71.4301
18	6.1405	0.8418	-0.8488	0.4339	-0.5504	0.7104	0.2458	0.0599	0.6918	-0.1747	0.0071	-0.4462	-0.255	0.2579	-0.2818	0.441	0.0233	0.3154	0.2485	-0.0253	0.5877	52.6482	78.9646	-76.252
19	5.9172	3.5508	-1.2781	2.1529	-0.7103	0.4158	-0.0318	0.3385	0.3845	-0.5015	0.1485	-0.6404	-0.004	0.1435	-0.1002	0.4856	0.0424	0.278	0.2368	0.0302	0.5992	52.8839	75.3225	-75.611
20	0.1929	0.4862	0.1244	3.5057	-0.9402	0.7887	0.242	0.0034	0.3669	-0.1718	0.0397	-0.2842	-0.3209	0.1559	-0.2697	0.3807	0.018	0.1808	0.176	-0.0376	0.3744	40.1456	78.437	-70.0803
21	0.2572	-0.373	-0.5345	0.5556	0.7673	1.1093	0.1315	0.0197	0.1832	-0.2748	0.0951	-0.3785	-0.0925	0.2147	-0.1066	0.6003	0.1057	0.3451	0.2295	0.0425	0.4747	49.8053	74.0555	-82.16
22	0.3696	-0.5594	-0.2616	1.2472	0.8696	0.7552	0.2164	0.1526	0.1335	-0.4431	-0.1249	-0.1879	-0.0722	0.0709	-0.0929	0.7406	0.242	0.2416	0.2063	0.0225	0.2915	38.2082	81.0468	-83.6059
23	1.1429	-0.3445	-0.2556	1.0373	0.4508	0.5259	0.1387	0.337	-0.1037	-0.4194	-0.119	-0.0333	0.0349	-0.0186	0.0973	0.8243	0.2567	0.2737	0.3233	0.0152	0.3459	39.6736	76.0933	-89.2293
24	0.2212	0.0033	-0.1672	1.0223	0.769	0.7085	-0.0103	0.7003	0.4651	-0.341	-0.0016	0.021	-0.5969	-0.3851	-0.0099	0.9792	0.3278	0.1895	0.7776	0.1854	0.4051	29.7115	86.105	-93.0652
25	2.5209	-0.6419	-1.1267	3.3188	-4.141	8.2569	-0.0328	-0.3	0.0701	0.398	-0.1952	-0.3416	-0.6744	0.4937	0.2074	0.1481	-0.0514	-0.0384	0.4724	-0.0562	0.2396	47.782	75.7759	10.9011
26	2.2364	1.4902	0.0045	3.3812	0.0597	0.3085	0.0568	-0.2634	-0.6905	0.0206	0.0496	0.243	0.1541	-0.2438	-0.1264	0.2361	0.0335	-0.0489	0.5898	0.2933	0.7718	34.2546	51.6243	16.7883
27	2.4901	0.5066	-0.6957	1.1856	0.4962	1.0942	-0.0243	-0.4057	-0.439	-0.0946	0.142	0.3316	0.0632	-0.1596	-0.0872	0.138	-0.017	-0.0651	0.354	0.0713	0.2858	34.2348	64.0233	11.0327
28	1.5504	-0.0166	0.8881	0.0966	-0.0362	0.5164	0.0545	-0.4029	-0.3371	0.0989	0.0777	-0.0042	0.1185	-0.0646	-0.0884	0.2167	0.0423	-0.0171	0.7978	0.3895	0.4885	39.8715	57.6556	24.1586
29	3.7328	-0.4819	1.0825	0.5121	-0.3203	1.3965	-0.0938	-0.6647	-0.2645	0.1855	-0.0397	0.3016	0.0865	-0.0938	0.1102	0.1998	0.0166	0.0405	0.8483	0.1369	0.5072	20.272	64.3817	24.481
30	3.0421	0.0247	1.1776	1.7398	-0.5774	1.5592	0.0196	-0.5031	-0.0349	0.149	0.0251	-0.1105	-0.0367	0.0276	0.0447	0.1871	0.0699	-0.0286	0.8905	0.0721	0.1904	34.3262	69.4486	23.0326
31	3.0481	0.2072	1.7334	1.1557	0.4475	1.8048	0.1247	-0.5298	-0.2227	0.1116	0.0243	0.0474	0.1237	-0.1267	-0.1688	0.2537	-0.0304	-0.0526	0.9708	0.3187	0.4477	30.7568	60.8009	28.2497
32	3.0819	-1.9389	3.4663	2.0287	-2.2306	3.9016	-0.3452	-0.3274	0.3017	0.2447	-0.0605	-0.1818	-0.3636	-0.0987	0.3777	0.314	0.0824	-0.0634	1.1682	-0.048	0.3494	32.5299	73.8401	31.6442

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 66 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 67 through 78 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 79 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 138 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 139 through 155 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 156 through 172 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 173 through 194 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 195 through 217 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 31 through 42 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 43 through 66 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 67 through 95 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 96 through 110 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 111 through 142 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 143 through 172 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 173 through 217 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 32 through 42 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 43 through 55 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 56 through 66 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 67 through 88 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 89 through 104 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 105 through 142 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 143 through 187 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 188 through 195 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 31 through 42 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 43 through 59 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 60 through 88 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 89 through 110 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 111 through 125 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 126 through 155 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 156 through 172 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 173 through 189 )

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