PDB-5uu6: The crystal structure of nitroreductase A from Vibrio parahaemoly...

ID or keywords:

Entry

Database: PDB / ID: 5uu6

Title

The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633

Components

NADPH-flavin oxidoreductase

Keywords

OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Vibrio parahaemolyticus serotype O3:K6

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Tan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of nitroreductase A from Vibrio parahaemolyticus RIMD 2210633
Authors: Tan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Feb 16, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	5uu6_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	5uu6_full_validation.pdf.gz	1.6 MB	Display
Data in XML	5uu6_validation.xml.gz	39.4 KB	Display
Data in CIF	5uu6_validation.cif.gz	55.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/5uu6 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/5uu6	HTTPS FTP

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Related structure data

Related structure data	2bkjS S: Starting model for refinement
Similar structure data	3nsy-d 1pf3-d 2fqg-d 5b7m-2 6im7-d 5b7f-d 3nsd-d 5b7m-1 4ef3-d 2bkj-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
Other databases	TargetTrack: CSGID-IDP07628

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NADPH-flavin oxidoreductase

B: NADPH-flavin oxidoreductase

C: NADPH-flavin oxidoreductase

D: NADPH-flavin oxidoreductase

hetero molecules

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

1

A: NADPH-flavin oxidoreductase

B: NADPH-flavin oxidoreductase

hetero molecules

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

2

C: NADPH-flavin oxidoreductase

D: NADPH-flavin oxidoreductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.004, 71.609, 110.450
Angle α, β, γ (deg.)	90.00, 93.15, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	NADPH-flavin oxidoreductase Mass: 27061.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria) Strain: RIMD 2210633 / Gene: VPA1601 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q87FS7
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.1 Å³/Da / Density % sol: 41.57 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Magnesium Chloride, 0.1 M Bis-Tris:HCl, 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2017 / Details: Mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97919 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 64115 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / B_iso Wilson estimate: 17.3 Å² / R_merge(I) obs: 0.104 / R_pim(I) all: 0.067 / Χ²: 0.741 / Net I/σ(I): 10.3
Reflection shell	Resolution: 1.95→1.98 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.819 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 3042 / CC_1/2: 0.593 / R_pim(I) all: 0.572 / Χ²: 0.892 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2BKJ

2bkj

Resolution: 1.95→43.689 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.02

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2098	2863	5.06 %	random
R_work	0.1627	-	-	-
obs	0.1652	56535	87.16 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→43.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7111	0	134	383	7628

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	7471
X-RAY DIFFRACTION	f_angle_d	1.155	10172
X-RAY DIFFRACTION	f_dihedral_angle_d	4.779	6099
X-RAY DIFFRACTION	f_chiral_restr	0.067	1155
X-RAY DIFFRACTION	f_plane_restr	0.007	1328

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 (%)
1.95-1.9836	0.2857	69	0.1866	1518	X-RAY DIFFRACTION	49
1.9836-2.0197	0.239	95	0.1911	1642	X-RAY DIFFRACTION	54
2.0197-2.0586	0.2449	81	0.1918	1657	X-RAY DIFFRACTION	54
2.0586-2.1006	0.2707	89	0.19	2015	X-RAY DIFFRACTION	65
2.1006-2.1463	0.2536	127	0.1879	2279	X-RAY DIFFRACTION	75
2.1463-2.1962	0.2646	124	0.1836	2521	X-RAY DIFFRACTION	82
2.1962-2.2511	0.246	131	0.1893	2809	X-RAY DIFFRACTION	91
2.2511-2.312	0.2525	155	0.1797	2938	X-RAY DIFFRACTION	95
2.312-2.38	0.208	154	0.183	2982	X-RAY DIFFRACTION	97
2.38-2.4568	0.1971	185	0.1805	2941	X-RAY DIFFRACTION	97
2.4568-2.5446	0.2579	174	0.1752	3006	X-RAY DIFFRACTION	98
2.5446-2.6465	0.246	171	0.1641	3024	X-RAY DIFFRACTION	99
2.6465-2.7669	0.1874	165	0.1653	3051	X-RAY DIFFRACTION	99
2.7669-2.9127	0.22	165	0.1681	3030	X-RAY DIFFRACTION	99
2.9127-3.0952	0.2168	173	0.1728	3044	X-RAY DIFFRACTION	99
3.0952-3.3341	0.2116	146	0.1645	3031	X-RAY DIFFRACTION	98
3.3341-3.6695	0.1984	148	0.1413	3070	X-RAY DIFFRACTION	99
3.6695-4.2001	0.1792	165	0.1327	3075	X-RAY DIFFRACTION	99
4.2001-5.2902	0.1717	145	0.1279	3036	X-RAY DIFFRACTION	97
5.2902-43.7004	0.1835	201	0.1771	3003	X-RAY DIFFRACTION	96

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	1.2345	0.7843	0.9688	0.6695	0.0572	2.8798	0.1274	0.3086	-0.4639	-0.374	0.1718	0.1175	0.256	0.3991	-0.2301	0.2982	0.03	-0.0687	0.1338	-0.0869	0.2311	16.0801	-14.0907	4.8575
2	4.4434	0.6955	1.3311	6.2058	3.083	6.643	0.5143	-0.2863	-0.5166	0.3544	-0.2444	0.5551	0.9001	-0.4556	-0.1313	0.235	-0.0688	-0.074	0.2161	0.0828	0.2518	5.7354	-13.0011	15.8831
3	1.384	-0.2157	0.4004	1.6317	-0.182	1.2446	0.0335	-0.1355	-0.0201	-0.1275	0.0301	0.3877	0.036	-0.1905	-0.0445	0.0979	-0.007	-0.0023	0.129	0.0029	0.176	4.2885	1.7153	10.1104
4	1.2998	0.5606	0.9811	1.3657	0.0592	0.8408	0.073	0.1609	-0.1121	-0.3205	0.1718	0.0621	0.1168	0.1594	-0.0831	0.1465	0.015	-0.0176	0.1534	-0.0493	0.1484	10.4034	-2.7396	3.9496
5	1.117	-0.3225	0.0242	1.051	0.0173	0.8014	-0.0431	0.1546	-0.0581	-0.1869	-0.0981	-0.3676	-0.0475	0.2562	-0.2102	0.0263	-0.1178	0.1588	0.6096	-0.057	0.2394	35.726	8.4078	7.8841
6	1.8816	0.5444	-0.9492	1.2377	0.0008	1.7112	-0.154	0.3831	-0.2302	-0.3466	0.0603	-0.1891	0.1542	0.0197	-0.0186	0.3824	-0.0687	0.2791	0.743	-0.1714	0.2882	31.0158	1.2219	-7.7834
7	2.1559	-1.8232	-0.963	2.7676	0.0228	0.9395	0.0796	0.465	0.0066	-0.5133	-0.051	-0.1342	0.0998	0.1757	0.0157	0.4135	-0.0424	0.0663	0.6688	-0.0045	0.1874	23.3386	8.7445	-8.5696
8	4.183	-0.0634	-0.6905	3.1434	1.0249	2.4364	-0.1271	0.1256	0.4671	-0.2848	0.0029	0.1842	-0.2354	-0.1655	0.0887	0.1336	-0	-0.0817	0.089	0.0098	0.2213	5.6289	16.8256	6.7175
9	3.7295	-0.6766	0.8781	1.1844	1.551	3.3221	0.3174	-0.1302	-0.4629	0.2377	-0.0141	-0.2512	0.5679	0.0913	-0.2002	0.1981	0.0368	-0.0526	0.1099	0.0486	0.1811	23.3186	-9.7483	24.3733
10	1.2323	0.2095	0.0221	1.3271	0.1177	1.6906	-0.0846	0.2814	0.0045	-0.052	0.1832	-0.2027	-0.0792	0.3854	-0.0473	0.0897	-0.0104	0.0449	0.2139	-0.0396	0.1449	28.2163	6.8348	13.1602
11	2.2716	-1.6879	1.4174	5.6789	-2.6301	3.3891	0.0275	0.1883	0.0297	-0.0554	-0.0036	-0.1953	0.027	0.1348	-0.0373	0.0863	-0.0078	0.025	0.1348	-0.0409	0.0828	19.7452	1.1404	12.3012
12	1.5641	0.0572	0.7993	1.2897	0.5297	0.9376	-0.081	-0.2522	-0.0944	0.2272	0.1249	0.1001	0.1153	-0.2917	-0.0503	0.0998	-0.0062	0.0582	0.2188	0.0363	0.0621	13.0397	2.5711	23.4444
13	0.9442	-0.3576	-0.5426	2.3859	-0.3677	0.5995	0.077	-0.3748	0.0814	0.4261	0.0147	0.164	-0.0627	-0.0014	0.1695	0.2474	-0.006	0.1512	0.5795	-0.0146	0.214	5.018	6.6804	34.056
14	2.8384	0.2491	1.3749	3.4638	-1.4299	3.6283	-0.2581	0.0588	0.4264	0.0072	-0.0427	0.1319	-0.2716	-0.1842	0.1919	0.1132	-0.0084	-0.0334	0.0748	-0.0058	0.1662	16.461	20.7591	15.4387
15	2.978	0.0096	2.1381	1.5871	-0.6342	2.9179	0.1191	0.3944	-0.2906	-0.3235	-0.0044	-0.0047	0.2192	0.3049	-0.0794	0.1826	-0.0011	0.0503	0.1138	-0.0317	0.1135	12.983	-14.6004	58.9019
16	1.7225	-0.4201	0.6493	4.9669	1.6701	4.0474	-0.0126	-0.2041	-0.0223	0.231	-0.0838	0.2	0.1996	-0.3021	0.1396	0.1127	0.0057	0.0403	0.1253	0.0542	0.0966	4.3953	-8.1514	74.2525
17	1.7416	0.3005	0.1623	1.8313	-0.4151	2.9029	0.0127	0.1103	-0.066	-0.5288	0.1045	0.5873	0.1887	-0.2956	-0.1095	0.2552	-0.0289	-0.1143	0.1368	0.0193	0.214	-6.2262	-2.5788	57.6523
18	2.0773	-0.4008	-1.095	2.6076	0.2466	2.7855	-0.0441	0.1702	-0.0343	-0.3357	-0.0336	0.2459	0.1309	-0.3117	0.0287	0.1704	-0.0371	-0.0364	0.1017	0.0057	0.1268	-0.0092	-3.2442	57.5274
19	1.6831	0.0028	0.0194	2.207	1.0976	1.5761	-0.0407	-0.4656	0.4906	0.5163	0.0566	0.2554	-0.3133	-0.2912	0.0779	0.3139	0.1276	0.0348	0.251	-0.0699	0.213	-3.0402	10.6893	79.7622
20	1.9808	-1.4487	-0.1783	6.0307	1.4716	2.3495	-0.1336	-0.0193	0.1472	0.06	-0.0097	0.1154	-0.1113	-0.0687	0.0334	0.1093	-0.023	-0.0014	0.0861	0.0229	0.0803	9.2437	-1.835	69.0783
21	1.7307	-0.7153	-0.0931	2.2988	0.0419	1.4999	0.0159	0.0187	0.0956	-0.3315	-0.0162	0.1985	-0.1252	-0.1043	0.0369	0.1725	-0.0112	-0.0373	0.0846	0.0086	0.1122	-0.1097	1.5226	60.7131
22	7.0561	6.0983	1.9348	6.1244	1.4265	0.5999	0.0167	0.4708	-0.2264	-0.4272	0.1655	-0.3634	-0.1212	0.2843	-0.0245	0.3155	-0.0373	0.1426	0.3224	-0.0232	0.1451	18.4242	-8.5319	52.2073
23	2.1179	1.0806	-0.7685	3.0927	0.2575	4.3454	-0.061	0.2709	0.3326	-0.0278	-0.1216	-0.4494	-0.4361	0.4791	-0.0338	0.1984	-0.0932	-0.0532	0.267	0.1448	0.5191	32.5527	7.8471	64.1885
24	1.7596	0.6799	0.1422	2.7606	0.493	1.1465	-0.1494	0.5503	0.0367	-0.4842	-0.1494	-0.3891	0.0829	0.2758	0.0238	0.443	-0.0798	0.1925	0.5897	0.145	0.3696	26.719	1.2702	45.9237
25	1.7472	-0.3823	-0.2529	0.7202	0.3377	0.9975	-0.2518	0.2563	0.533	-0.1696	-0.0083	-0.1795	-0.2487	0.2095	-0.0377	0.2874	-0.0178	-0.0535	0.16	0.1045	0.2622	8.0801	14.2834	58.3917
26	4.2907	0.0307	1.2594	1.2935	0.5428	3.2111	0.1659	-0.15	-0.2785	0.2415	-0.1363	-0.3074	0.2482	-0.1148	-0.0341	0.1787	0.0206	-0.0168	0.036	0.051	0.138	19.4459	-12.1421	78.8216
27	2.8212	-1.9435	2.6951	4.6079	-3.0381	4.7243	-0.0654	0.3811	0.1502	-0.1016	-0.1258	-0.3567	-0.0186	0.3459	0.1624	0.1868	-0.0553	0.0609	0.1504	0.0473	0.2375	24.1421	-3.1358	62.9771
28	0.795	-0.1537	-0.1039	1.1753	-0.2683	0.4461	-0.2417	0.044	0.4736	0.1418	-0.0251	-0.4887	-0.2225	0.1713	0.1539	0.217	-0.0604	-0.1108	0.1177	0.0568	0.3554	22.6565	7.0645	72.1274
29	4.4055	-2.3631	3.9163	2.1177	-1.8557	3.5393	0.0266	-0.3807	-0.151	0.2309	0.103	0.029	0.1245	-0.2444	-0.03	0.2128	-0.0025	0.0342	0.198	0.0452	0.1047	11.7688	-9.1947	85.3567
30	0.6356	-0.0463	-0.756	4.0452	-1.1499	8.7049	0.1602	-0.3937	-0.201	0.4181	-0.0826	0.4093	0.1002	-0.5947	-0.0494	0.1574	-0.0594	0.0225	0.2689	0.0512	0.2063	-8.5579	-3.141	72.269
31	2.9303	-0.5315	0.0845	2.7462	-0.3055	3.1159	0.0403	-0.582	-0.159	0.5294	0.1151	0.1176	0.2872	0.0373	0.0633	0.3874	0.0035	0.1202	0.4734	0.0609	0.1565	-1.6848	-5.3769	88.9906
32	1.6022	-0.2039	0.6972	0.993	-0.0698	0.3689	-0.3262	-0.429	0.4109	0.3545	0.0638	-0.0556	-0.2777	-0.1979	0.0545	0.4124	0.0253	-0.1006	0.1332	-0.0925	0.2669	8.0665	12.9866	79.6437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 36 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 37 through 142 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 143 through 171 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 172 through 185 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 186 through 200 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 201 through 221 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 222 through 240 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 23 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 24 through 97 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 98 through 122 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 199 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 200 through 221 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 222 through 240 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 0 through 23 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 24 through 45 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 46 through 63 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 64 through 82 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 83 through 97 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 98 through 122 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 123 through 159 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 160 through 171 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 172 through 185 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 186 through 211 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 212 through 240 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 0 through 23 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 24 through 45 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 46 through 159 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 160 through 171 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 172 through 185 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 186 through 201 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 202 through 240 )

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