PDB-3sqv: Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, w...

ID or keywords:

Entry

Database: PDB / ID: 3sqv

Title

Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7

Components

Ubiquitin-conjugating enzyme E2 L3
secreted effector protein

Keywords

LIGASE/SIGNALING PROTEIN / effector protein / pentapeptide / HECT domain / HECT E3 ubiquitin ligase / E2 ubiquitin conjugating enzyme / protein-protein complex / ubiquitin transfer / ubiquitin / ubiquitination / LIGASE-SIGNALING PROTEIN complex

Function / homology

Function and homology information

cell cycle phase transition / ubiquitin-protein transferase activator activity / HECT-type E3 ubiquitin transferase / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / cellular response to glucocorticoid stimulus / E2 ubiquitin-conjugating enzyme / cellular response to steroid hormone stimulus / ubiquitin conjugating enzyme activity / ubiquitin ligase complex ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Lin, D.Y. / Chen, J.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions.
Authors: Lin, D.Y. / Diao, J. / Chen, J.

History

Deposition	Jul 6, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 22, 2012	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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3sqv.cif.gz	568.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3sqv_validation.pdf.gz	485.5 KB	Display	wwPDB validaton report
Full document	3sqv_full_validation.pdf.gz	533.3 KB	Display
Data in XML	3sqv_validation.xml.gz	56.9 KB	Display
Data in CIF	3sqv_validation.cif.gz	77.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sq/3sqv ftp://data.pdbj.org/pub/pdb/validation_reports/sq/3sqv	HTTPS FTP

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Related structure data

Related structure data	3sy2C 1c4zS 3nb2S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hex-1 5qd8-d 3kfc-d 4hxi-d 1v00-d 3k5c-d 5grb-1 1i7u-d 1hhk-d 5qct-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 - 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	#60 - Dec 2004 Ubiquitin similarity (11) #234 - Jun 2019 MDM2 and Cancer similarity (10) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: secreted effector protein

B: secreted effector protein

C: Ubiquitin-conjugating enzyme E2 L3

D: Ubiquitin-conjugating enzyme E2 L3

hetero molecules

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

1

A: secreted effector protein

C: Ubiquitin-conjugating enzyme E2 L3

hetero molecules

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

2

B: secreted effector protein

D: Ubiquitin-conjugating enzyme E2 L3

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	302.313, 72.012, 125.669
Angle α, β, γ (deg.)	90.00, 109.22, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	secreted effector protein / NleL Mass: 69700.234 Da / Num. of mol.: 2 Fragment: C-terminal beta-helix domain and HECT-like domain (UNP residues 170-782) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs1560 / Plasmid: pMCSG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q8X5G6, UniProt: A0A0H3JDV8*PLUS, ubiquitin-protein ligase
#2: Protein	Ubiquitin-conjugating enzyme E2 L3 / UbcH7 / L-UBC / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin- ...UbcH7 / L-UBC / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3 Mass: 18033.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBCE7, UBCH7, UBE2L3 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) star / References: UniProt: P68036, ubiquitin-protein ligase
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O
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: 3.68 Å³/Da / Density % sol: 66.58 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.5-1.7 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: mirrors
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97942 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. all: 39210 / Num. obs: 38818 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / B_iso Wilson estimate: 95.13 Å² / R_sym value: 0.138 / Net I/σ(I): 20.3
Reflection shell	Resolution: 3.3→3.42 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3696 / R_sym value: 0.635 / % possible all: 95.2

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3NB2 AND 1C4Z

3nb2

1c4z

Resolution: 3.3→48.08 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 33.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2977	1922	4.99 %	RANDOM
R_work	0.2662	-	-	-
obs	0.2677	38544	99.04 %	-
all	-	38918	-	-

Solvent computation

Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 119.124 Å² / k_sol: 0.306 e/Å³

Displacement parameters

B_iso mean: 128.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	34.2366 Å²	0 Å²	-36.6552 Å²
2-	-	-30.6654 Å²	0 Å²
3-	-	-	-3.5712 Å²

Refinement step

Cycle: LAST / Resolution: 3.3→48.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10910	0	63	14	10987

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	11218
X-RAY DIFFRACTION	f_angle_d	0.87	15318
X-RAY DIFFRACTION	f_dihedral_angle_d	13.846	3706
X-RAY DIFFRACTION	f_chiral_restr	0.057	1688
X-RAY DIFFRACTION	f_plane_restr	0.003	2032

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	141	X-RAY DIFFRACTION	POSITIONAL
1	2	B	141	X-RAY DIFFRACTION	POSITIONAL	0.016
2	1	A	919	X-RAY DIFFRACTION	POSITIONAL
2	2	B	919	X-RAY DIFFRACTION	POSITIONAL	0.027
3	1	A	99	X-RAY DIFFRACTION	POSITIONAL
3	2	B	99	X-RAY DIFFRACTION	POSITIONAL	0.025
4	1	A	1092	X-RAY DIFFRACTION	POSITIONAL
4	2	B	1092	X-RAY DIFFRACTION	POSITIONAL	0.026
5	1	A	218	X-RAY DIFFRACTION	POSITIONAL
5	2	B	218	X-RAY DIFFRACTION	POSITIONAL	0.02
6	1	A	698	X-RAY DIFFRACTION	POSITIONAL
6	2	B	698	X-RAY DIFFRACTION	POSITIONAL	0.032
7	1	A	110	X-RAY DIFFRACTION	POSITIONAL
7	2	B	110	X-RAY DIFFRACTION	POSITIONAL	0.018
8	1	A	910	X-RAY DIFFRACTION	POSITIONAL
8	2	B	910	X-RAY DIFFRACTION	POSITIONAL	0.045
9	1	C	285	X-RAY DIFFRACTION	POSITIONAL
9	2	D	285	X-RAY DIFFRACTION	POSITIONAL	0.015
10	1	C	591	X-RAY DIFFRACTION	POSITIONAL
10	2	D	591	X-RAY DIFFRACTION	POSITIONAL	0.017

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
3.3-3.3825	0.3872	116	0.3702	2497	2613	95
3.3825-3.4739	0.3486	149	0.3422	2539	2688	98
3.4739-3.5761	0.3582	140	0.3146	2581	2721	99
3.5761-3.6915	0.3786	130	0.2956	2619	2749	100
3.6915-3.8234	0.3182	160	0.278	2576	2736	100
3.8234-3.9764	0.2836	129	0.26	2645	2774	100
3.9764-4.1573	0.2756	123	0.2435	2623	2746	100
4.1573-4.3763	0.2435	136	0.2222	2616	2752	100
4.3763-4.6503	0.2821	134	0.2141	2647	2781	100
4.6503-5.009	0.2737	138	0.2251	2643	2781	100
5.009-5.5125	0.3349	148	0.2843	2615	2763	100
5.5125-6.3086	0.3884	119	0.302	2663	2663	100
6.3086-7.9424	0.3291	153	0.2657	2662	2662	100
7.9424-48.0851	0.2404	147	0.2634	2696	2696	98

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	0.2077	-0.2248	0.1451	0.7643	0.0755	0.2055	-0.0885	-0.0351	0.0842	0.4074	-0.0143	-0.0093	-0.0357	0.0178	0.0446	0.8279	-0.1046	-0.0536	0.6072	0.1059	0.6428	41.9755	31.6443	65.0687
2	0.102	-0.056	0.0574	0.0509	-0.0166	0.5236	-0.0107	0.0277	-0.034	-0.0367	-0.112	-0.2476	0.3886	-0.0715	0.005	1.0001	-0.1392	-0.1093	0.5861	0.0066	0.718	28.3776	17.3057	36.9499
3	0.3555	-0.2389	0.2898	0.5522	-0.4201	0.4595	0.0509	0.3339	-0.1459	-0.3871	0.0209	0.0032	0.406	0.0614	-0.0877	0.4821	0.0188	-0.0323	0.4833	0.0708	0.2398	29.7774	28.7381	5.5295
4	0.5168	-0.4657	-0.4914	1.0214	-0.7412	2.8761	0.2463	0.418	0.1951	-0.1969	0.1105	-0.0505	0.4497	-0.3725	-0.2762	1.1662	0.4588	0.1109	1.2808	0.3812	1.1053	19.0847	58.3365	-12.8076
5	0.0744	-0.3786	-0.0707	1.5693	0.2633	2.6339	0.0643	0.1127	0.0631	-0.1635	-0.4887	-0.7334	0.0254	-0.6457	0.1461	0.2723	0.181	0.0874	0.2512	1.2582	0.0894	32.9453	55.0343	-7.7922
6	0.0725	-0.1401	-0.0219	0.8188	0.3238	0.1453	-0.0635	0.1176	-0.0432	0.2418	0.0187	-0.3722	0.1128	-0.0015	0.005	0.6805	-0.066	-0.2311	0.63	0.0932	1.0079	62.2642	30.2662	46.8942
7	0.7683	-0.3421	-0.3177	0.5893	-0.1592	0.8361	0.1657	0.1766	0.3523	0.1756	-0.1003	-0.3053	-0.0334	-0.1462	-0.0238	0.7444	0.0217	-0.0322	0.6719	0.1466	0.8047	35.9017	44.6917	30.0179
8	0.9684	0.1673	-0.2282	0.3323	0.1388	0.2375	0.2213	-0.2535	0.1842	-0.0029	-0.2115	-0.036	-0.0635	-0.3479	-0.0021	0.0099	-0.1135	0.1542	1.0053	-0.0332	0.4225	4.5271	33.0114	28.5804
9	0.6216	0.2254	-0.2313	0.3853	0.4783	1.1481	-0.5999	0.1447	0.16	-0.1848	-0.041	0.0755	0.031	-0.2841	0.4954	1.5984	-0.3572	-0.1695	1.1384	-0.3016	1.0853	-13.1244	3.0351	17.9352
10	0.3838	-0.2488	-0.116	0.5318	0.145	0.0227	0.2512	0.2221	0.0027	0.6404	-0.2125	0.1579	0.0048	-0.4763	0.1612	0.5793	-0.839	0.3276	0.5988	-0.209	0.2682	-8.9853	6.9849	31.3392
11	0.0594	-0.0017	-0.1124	-0.0001	0.0033	0.2104	0.011	-0.1289	0.0942	0.0184	0.0591	0.0617	-0.0274	-0.2185	-0.1001	1.2284	0.1182	0.1622	1.68	0.5427	1.7248	48.4875	26.974	-3.9362
12	0.2922	0.0079	0.0128	0.4586	0.3642	0.4255	0.0886	0.2019	0.0803	-0.0853	0.0226	-0.0201	-0.1185	0.065	-0.1063	1.8127	0.1086	0.1941	2.0157	0.0696	1.7808	53.7906	23.6131	-18.0293
13	0.8925	-0.3648	-0.3741	0.3389	-0.0916	0.5899	0.1791	0.1086	-0.184	0.0673	0.004	0.2042	-0.1104	0.0742	-0.1654	1.7616	-0.1497	0.1443	1.8685	-0.3375	2.0977	54.0729	34.1677	-12.9988
14	0.058	0.0135	-0.0212	0.0166	-0.0214	0.012	-0.2853	0.0549	0.2311	0.0261	-0.1925	0.1459	0.1302	-0.1086	0.4443	1.2658	0.3305	0.2322	1.5128	-0.0502	1.3309	46.2416	34.821	-17.4334
15	0.3392	0.2116	-0.0728	0.2724	0.2151	0.4993	0.0113	0.3489	0.1368	0.0349	0.1234	0.0862	-0.1159	0.2977	-0.0868	1.2629	0.3128	-0.029	1.4049	0.3078	0.9052	40.5506	38.0945	-20.4823
16	0.7165	0.0536	0.1638	0.1633	-0.2129	0.3479	-0.0413	0.2437	0.1584	-0.0736	0.2625	-0.2053	-0.1695	-0.1889	-0.1958	0.4226	-0.025	0.2592	0.3292	0.0502	0.5567	41.749	28.3846	-21.1955
17	0.1728	0.1438	-0.1395	0.1243	-0.1165	0.1113	0.024	0.0096	0.0462	-0.0424	0.0048	-0.0092	0.0126	-0.0137	-0.0189	2.0555	0.1285	0.1958	1.9307	0.1437	2.0092	35.2082	42.3315	-32.47
18	0.037	0.013	-0.0069	0.0526	0.038	0.1466	0.0524	0.0181	0.0522	-0.0079	0.0146	-0.0001	-0.2011	-0.1709	-0.0745	2.5838	-0.0949	0.0314	2.0721	0.29	1.8662	46.0344	39.1752	-39.262
19	0.0007	0.0016	-0.0022	0.0068	-0.0205	0.0686	-0.0906	0.0066	-0.0521	-0.0864	0.1411	-0.0124	0.0556	0.0477	0.0022	1.4443	-0.559	-0.0945	1.8417	0.1807	1.0516	-5.5404	35.8117	47.4959
20	0.9923	0.0986	0.2062	0.6409	-0.3232	0.2278	0.0457	-0.0748	-0.0348	0.0659	-0.1815	0.0153	0.0553	-0.1112	0.1204	1.0659	-0.2996	0.0338	1.4188	-0.0275	0.9779	-20.5417	37.5275	51.1673
21	0.0986	-0.0206	0.1443	0.3641	-0.1944	0.2866	0.0074	-0.014	-0.0214	0.0667	0.0047	0.0229	0.0974	-0.1576	-0.0061	1.8138	-0.169	-0.0596	1.4989	0.227	1.3459	-8.1653	27.0722	54.1068
22	1.2773	-0.5069	0.5908	0.3321	-0.2492	0.2802	-0.0014	0.0515	0.0539	0.0342	-0.1784	0.1853	0.1311	-1.1321	0.1462	1.1516	-0.0817	0.0982	1.9533	-0.0552	1.0074	-25.5505	26.6834	49.572
23	0.656	0.681	-0.6288	0.7217	-0.6659	0.6124	0.0177	0.0215	0.0079	0.0688	0.0961	0.0246	0.0104	0.2434	-0.0925	1.0653	-0.016	0.4548	1.3662	0.0033	1.0923	-7.5727	26.2424	40.1015
24	0.1805	-0.2313	0.0486	0.311	-0.0327	0.6018	0.0551	-0.0601	-0.1603	0.1852	0.0712	0.0366	0.1643	-0.0789	-0.088	1.45	-0.2263	0.0197	1.5579	0.0732	1.2422	-21.0702	22.6655	38.7635
25	0.042	-0.1125	0.0037	0.3068	-0.0414	0.786	-0.0719	0.1582	-0.0973	-0.0674	-0.169	-0.0645	-0.1635	-0.0044	0.2192	0.9314	-0.0326	0.1874	0.9822	0.1202	0.2381	-23.3538	31.2429	39.3565
26	0.0363	0.0392	-0.0735	0.0353	-0.0726	0.1375	-0.0753	-0.0249	-0.0638	-0.0633	-0.0781	0.0015	0.2699	-0.2217	0.1432	1.7619	-0.3496	0.4331	1.7236	-0.1947	1.4868	-36.8843	18.315	41.8727

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 171:331)
2	X-RAY DIFFRACTION	2	(chain A and resid 332:470)
3	X-RAY DIFFRACTION	3	(chain A and resid 471:633)
4	X-RAY DIFFRACTION	4	(chain A and resid 634:672)
5	X-RAY DIFFRACTION	5	(chain A and resid 673:782)
6	X-RAY DIFFRACTION	6	(chain B and resid 171:331)
7	X-RAY DIFFRACTION	7	(chain B and resid 332:470)
8	X-RAY DIFFRACTION	8	(chain B and resid 471:633)
9	X-RAY DIFFRACTION	9	(chain B and resid 634:672)
10	X-RAY DIFFRACTION	10	(chain B and resid 673:782)
11	X-RAY DIFFRACTION	11	(chain C and resid 1:13)
12	X-RAY DIFFRACTION	12	(chain C and resid 14:25)
13	X-RAY DIFFRACTION	13	(chain C and resid 26:41)
14	X-RAY DIFFRACTION	14	(chain C and resid 42:67)
15	X-RAY DIFFRACTION	15	(chain C and resid 68:97)
16	X-RAY DIFFRACTION	16	(chain C and resid 98:115)
17	X-RAY DIFFRACTION	17	(chain C and resid 116:128)
18	X-RAY DIFFRACTION	18	(chain C and resid 129:147)
19	X-RAY DIFFRACTION	19	(chain D and resid 1:14)
20	X-RAY DIFFRACTION	20	(chain D and resid 15:24)
21	X-RAY DIFFRACTION	21	(chain D and resid 25:34)
22	X-RAY DIFFRACTION	22	(chain D and resid 35:56)
23	X-RAY DIFFRACTION	23	(chain D and resid 57:68)
24	X-RAY DIFFRACTION	24	(chain D and resid 69:97)
25	X-RAY DIFFRACTION	25	(chain D and resid 98:117)
26	X-RAY DIFFRACTION	26	(chain D and resid 118:147)

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