PDB-5nek: Crystal structure of the polysaccharide deacetylase Bc1974 from B...

ID or keywords:

Entry

Database: PDB / ID: 5nek

Title

Crystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with acetazolamide

Components

Peptidoglycan N-acetylglucosamine deacetylase

Keywords

HYDROLASE / CE4 domain / polysaccharide deacetylase / PgdA / Bacillus cereus

Function / homology

Function and homology information

peptidoglycan-N-acetylglucosamine deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Bacillus cereus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.057 Å

Authors

Andreou, A. / Giastas, P. / Eliopoulos, E.E.

Citation

Journal: Biochemistry / Year: 2018
Title: Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.
Authors: Giastas, P. / Andreou, A. / Papakyriakou, A. / Koutsioulis, D. / Balomenou, S. / Tzartos, S.J. / Bouriotis, V. / Eliopoulos, E.E.

History

Deposition	Mar 10, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5nek.cif.gz	349.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5nek_validation.pdf.gz	482.1 KB	Display	wwPDB validaton report
Full document	5nek_full_validation.pdf.gz	494.8 KB	Display
Data in XML	5nek_validation.xml.gz	35.3 KB	Display
Data in CIF	5nek_validation.cif.gz	45.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ne/5nek ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5nek	HTTPS FTP

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Related structure data

Related structure data	5n1jC 5n1pC 5nc6C 5nc9C 5ncdC 5nelC C: citing same article (ref.)
Similar structure data	5nc6-d 5n1j-d 5nel-d 2o54-2 2o59-2 2o54-1 6bgc-d 3rr5-d 2o19-2 7cy7-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	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1)

Deposited unit

A: Peptidoglycan N-acetylglucosamine deacetylase

B: Peptidoglycan N-acetylglucosamine deacetylase

C: Peptidoglycan N-acetylglucosamine deacetylase

D: Peptidoglycan N-acetylglucosamine deacetylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	49.388, 118.211, 98.265
Angle α, β, γ (deg.)	90.00, 102.09, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Peptidoglycan N-acetylglucosamine deacetylase Mass: 27884.674 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The 42 N-terminus residues were not detected in the electron density Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_1974 / Production host: Escherichia coli (E. coli) References: UniProt: Q81EJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

#1: Protein

Peptidoglycan N-acetylglucosamine deacetylase

Mass: 27884.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The 42 N-terminus residues were not detected in the electron density
Source: (gene. exp.)

Bacillus cereus (bacteria) / Gene: BC_1974 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q81EJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 5 types, 35 molecules

#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE Mass: 222.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆N₄O₃S₂ / Comment: medication*YM
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.51 Å³/Da / Density % sol: 51.09 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 100 mM sodium citrate, 10% ethanol, 30% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.05→48.29 Å / Num. obs: 20563 / % possible obs: 98.05 % / Redundancy: 4.8 % / Net I/σ(I): 8.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.057→48.29 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 29.75

	R_factor	Num. reflection	% reflection
R_free	0.2525	1990	5.03 %
R_work	0.1779	-	-
obs	0.1818	39561	96.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.057→48.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6536	0	48	26	6610

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	6788
X-RAY DIFFRACTION	f_angle_d	1.201	9188
X-RAY DIFFRACTION	f_dihedral_angle_d	4.167	4386
X-RAY DIFFRACTION	f_chiral_restr	0.055	955
X-RAY DIFFRACTION	f_plane_restr	0.007	1201

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 (%)
3.0567-3.1331	0.3627	107	0.3052	1976	X-RAY DIFFRACTION	72
3.1331-3.2178	0.3345	143	0.2859	2733	X-RAY DIFFRACTION	99
3.2178-3.3125	0.3456	146	0.2581	2770	X-RAY DIFFRACTION	99
3.3125-3.4194	0.3118	145	0.2387	2756	X-RAY DIFFRACTION	99
3.4194-3.5415	0.3035	144	0.2181	2764	X-RAY DIFFRACTION	98
3.5415-3.6833	0.2993	144	0.2154	2699	X-RAY DIFFRACTION	98
3.6833-3.8509	0.3184	146	0.196	2753	X-RAY DIFFRACTION	98
3.8509-4.0538	0.2415	143	0.174	2700	X-RAY DIFFRACTION	98
4.0538-4.3076	0.2623	148	0.1521	2729	X-RAY DIFFRACTION	97
4.3076-4.64	0.2343	144	0.1383	2722	X-RAY DIFFRACTION	98
4.64-5.1064	0.2199	148	0.1374	2769	X-RAY DIFFRACTION	99
5.1064-5.8443	0.187	145	0.1438	2718	X-RAY DIFFRACTION	98
5.8443-7.359	0.2425	148	0.1584	2766	X-RAY DIFFRACTION	98
7.359-48.2984	0.1757	139	0.1468	2716	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	5.8377	-1.6076	-1.2242	4.3062	-3.1102	3.4656	1.3177	-0.5401	-0.3748	-1.1998	0.2223	0.1153	0.8884	0.3295	-1.2864	0.8788	0.0448	0.0257	0.4714	-0.204	0.5934	19.8829	-1.708	88.4172
2	3.9618	0.4585	0.6399	6.5885	-1.6533	4.1686	0.3502	0.9196	-0.7942	-0.8048	0.0533	-0.1625	1.3065	0.2358	-0.3311	0.9962	0.0731	-0.1649	0.474	-0.1567	0.6734	15.2681	-8.7267	86.4181
3	2.8083	-0.0586	1.3138	3.5595	1.1427	1.8912	0.6627	-0.2754	-0.6502	0.1533	-0.1332	0.4081	1.4921	0.0531	-0.2673	0.9327	0.0361	-0.2598	0.3195	-0.0692	0.6159	12.1928	-4.6423	101.382
4	5.653	-1.4069	1.1927	1.2133	0.1342	4.1865	0.2483	-0.5316	-0.0517	-0.5354	-0.0898	0.65	0.4079	0.0814	-0.1408	0.5757	0.1195	-0.1333	0.3025	0.013	0.5299	17.7127	3.5677	110.5373
5	1.5007	-0.9091	0.6612	3.7995	-4.0166	4.7408	-0.2503	0.1053	0.1103	0.4901	0.5108	-0.4018	-0.6422	-0.1878	-0.1254	0.7843	0.0209	-0.0441	0.4476	-0.1306	0.6412	19.0901	6.4402	92.0864
6	3.0699	-1.5342	3.4367	6.613	0.5238	7.9926	0.0806	0.344	0.4156	-0.4429	0.0282	-0.3783	-1.0567	1.3312	-0.1603	0.7847	0.0454	0.2165	0.7107	-0.1327	0.5424	24.4715	6.4639	85.2434
7	2.8425	-1.8096	0.7991	2.8481	0.1236	4.3999	0.1426	0.8233	-0.5304	-0.2654	0.1782	-1.1499	0.8941	1.3446	-0.3851	0.7913	0.0287	-0.0465	0.706	-0.3384	0.9008	27.4783	-0.9575	93.2193
8	0.3723	-1.0718	-0.8743	5.1095	0.5178	3.9182	0.4337	-0.9048	0.0777	1.2106	-0.4158	-0.7106	0.112	-0.2974	0.0756	1.1501	0.0308	-0.2775	0.5622	-0.0334	0.4476	33.6923	12.0071	133.128
9	3.9706	1.4221	-1.7147	7.3316	1.6807	9.1313	0.391	0.4472	-0.369	0.0377	0.2117	-0.9687	1.4097	0.8428	-0.5999	0.9537	0.2161	-0.2042	0.5019	-0.0244	0.5762	31.8903	2.2808	128.8497
10	1.8213	0.4024	-0.0299	3.1837	1.5209	5.0616	0.7235	-0.2726	-2.0218	-0.0474	-0.0109	0.2975	1.3874	0.5635	-0.6448	1.0275	-0.0341	-0.2515	0.4227	0.1463	0.7334	23.3321	-2.7978	133.9786
11	1.3294	-0.0925	2.2671	9.3037	-2.4421	4.2913	0.5373	-0.4994	-0.4002	1.7032	0.1538	1.2238	0.3592	-0.5595	-0.4989	0.9049	-0.026	-0.072	0.4308	0.1046	0.4812	17.4564	11.183	137.7499
12	2.5865	1.9096	0.5398	8.3002	-0.5775	2.0564	0.4883	-0.1572	-0.1898	1.0869	-0.2895	0.6432	-0.2152	0.1882	-0.1407	1.1674	0.0018	-0.1046	0.4256	0.0762	0.698	20.2223	7.0562	142.3183
13	4.4203	-2.63	4.6641	3.3001	-0.4339	8.52	0.4544	-0.4856	0.4129	1.0516	-0.8786	0.6721	-0.226	0.1857	0.4546	0.884	-0.1541	-0.0026	0.5571	0.0148	0.5818	17.8733	21.6659	145.9365
14	3.5655	0.892	-1.4972	2.2492	-0.3224	7.847	0.4193	-0.1654	-0.3123	0.6807	-0.289	-0.0373	-0.9493	-0.3571	0.0216	0.6419	0.0237	-0.1744	0.2331	0.053	0.5716	25.8157	16.3511	128.53
15	2.0455	-0.6972	-0.4281	2.2609	-0.6833	5.0378	-0.1807	-0.1118	0.0504	-0.1947	0.1161	-0.3682	-0.03	0.7573	0.0524	0.5208	0.0215	-0.1109	0.418	-0.1024	0.6931	34.8919	13.8949	123.6483
16	5.7511	5.2163	-6.1986	6.4629	-5.4445	8.2347	0.1459	-1.3815	-0.7358	1.5461	-0.1662	-1.7362	0.7359	1.5421	0.4703	1.4763	0.0535	-0.5624	0.6216	0.0397	1.1368	39.5933	11.2635	138.3382
17	4.5287	-2.3666	-2.912	3.1283	0.5877	2.3018	-0.1223	-0.8268	0.3347	1.7019	-0.3009	-0.557	-0.7005	0.4665	0.4205	1.4685	-0.0808	-0.4049	0.4944	-0.0383	0.8087	28.0689	22.3667	144.4132
18	3.0185	0.3348	0.123	3.1612	0.0536	3.3923	-0.2184	-0.8584	-0.1881	0.8854	0.6114	-1.2904	-0.3855	1.2238	-0.4833	0.8798	0.1029	-0.3927	0.8532	-0.2133	0.9109	37.5964	44.9198	143.9542
19	9.2105	3.1498	2.151	5.9772	2.1071	2.2062	-0.4271	-0.5753	0.6647	0.8853	0.4365	0.0812	-0.852	0.1186	0.061	1.132	0.0236	-0.2065	0.5061	-0.1034	0.4801	27.2267	51.2612	146.7432
20	0.1788	0.4964	0.8802	4.2282	0.9938	4.1054	0.3413	-0.2107	0.4181	0.4653	-0.1145	0.0913	-0.6781	-0.0223	-0.2561	0.644	-0.1018	0.1009	0.4405	-0.1282	0.4461	22.3662	40.6525	136.2036
21	1.7429	-2.5497	-1.3558	4.3626	2.7581	2.0143	-0.2955	-0.2806	0.4247	-0.0099	0.4384	-0.0365	-0.8405	-0.0041	-0.2383	1.1199	0.0196	-0.1201	0.3914	-0.1036	0.5036	23.0813	48.3853	134.5927
22	3.3483	-0.6768	-0.597	4.137	0.8218	1.373	-0.3707	-0.0333	-0.1699	0.7742	0.0668	-0.4508	-0.3828	0.3295	0.3593	0.8745	-0.0518	-0.1026	0.3528	-0.0562	0.4879	28.9024	34.8448	133.0855
23	3.6758	-2.2357	3.0053	4.4688	-0.4987	3.762	0.3224	-0.2697	-0.1258	0.8706	0.4661	-1.482	0.7663	1.7148	-0.688	0.8432	0.149	-0.3695	0.9071	-0.2743	1.012	41.722	33.5368	141.827
24	4.1412	-0.0553	4.1975	3.8399	0.1013	4.3432	0.3789	0.7172	-0.3052	1.1067	0.0246	-1.5834	0.528	0.7633	-0.2631	1.2186	0.1558	-0.6219	1.2573	-0.3268	0.9749	44.0568	37.9801	146.9603
25	3.3112	-1.3484	1.3205	6.6117	-1.0561	5.3474	-0.4271	-0.0617	0.6088	-0.4366	0.4271	-1.1456	-0.6416	1.094	0.0518	0.7896	-0.1089	0.0764	0.6092	-0.1577	0.6983	37.6974	42.4351	127.5921
26	7.2414	-4.1648	-4.2326	9.5282	6.3673	6.2779	-0.2879	0.3787	-1.1917	-1.8902	-0.1564	0.0879	-0.3738	-0.6713	0.5326	0.8286	-0.1108	-0.111	0.4467	-0.0485	0.6873	23.4597	27.7751	96.2379
27	2.2489	-0.7686	2.4537	4.0301	2.1161	4.9889	-0.5483	0.4113	0.8085	-0.2161	0.3757	-0.8465	-1.3858	0.3964	-0.0541	1.0998	-0.2045	-0.1768	0.4115	0.0608	0.6796	23.8003	37.5615	101.6684
28	5.3567	3.4078	-5.913	5.5086	-1.6178	8.0376	0.358	0.6486	1.2183	0.1618	-0.0117	0.3786	-2.1024	-0.395	-0.4012	1.307	0.055	-0.2714	0.4661	0.1423	0.7315	14.0102	42.698	102.0771
29	4.5284	-0.226	-0.5739	4.8488	-1.9859	3.8608	-0.202	0.0034	0.0761	-0.6198	0.023	0.8821	-0.7712	0.0242	0.0296	0.9048	-0.0113	-0.1782	0.2989	-0.0484	0.5278	6.7131	31.1429	99.325
30	2.3615	0.025	-3.9301	9.0991	-3.1732	7.5826	0.2465	0.3667	-0.3456	-0.0663	-0.0793	1.1562	-0.2679	-0.9791	-0.1691	0.5142	-0.0114	0.0188	0.4105	0.0252	0.5671	2.3445	18.3408	95.268
31	3.6227	2.1046	2.0203	2.1558	1.5715	3.1746	-0.3601	-0.1964	0.1956	-0.0513	0.0514	0.1352	-0.9882	-0.1646	-0.0722	0.5351	0.0455	0.0805	0.3115	0.0401	0.4915	18.8858	23.6015	105.3294
32	2.262	0.1483	2.4306	1.9397	0.5039	5.6337	-0.0119	0.5999	0.177	-0.6148	0.1962	-0.2461	-0.63	1.0704	-0.124	0.4189	-0.1067	0.1134	0.4597	-0.0456	0.5189	27.8732	26.6088	100.5264
33	6.0959	2.0223	2.1298	0.8096	0.3754	1.376	0.0978	0.2598	-0.8379	-0.0465	0.2166	0.0134	0.0347	0.4421	-0.4198	1.0922	-0.0635	-0.1578	0.307	-0.0329	0.6525	11.8598	17.6646	90.9565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 69 through 82 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 83 through 118 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 119 through 166 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 167 through 183 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 184 through 204 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 205 through 233 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 234 through 273 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 68 through 78 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 79 through 102 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 103 through 118 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 119 through 140 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 141 through 168 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 169 through 183 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 184 through 204 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 205 through 249 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 250 through 261 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 262 through 273 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 69 through 102 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 103 through 118 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 119 through 140 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 141 through 166 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 167 through 204 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 205 through 233 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 234 through 248 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 249 through 273 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 68 through 78 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 79 through 102 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 103 through 118 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 119 through 168 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 169 through 183 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 184 through 204 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 205 through 261 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 262 through 273 )

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