PDB-8s02: BzdNO-benzoyl-CoA complex

ID or keywords:

Entry

Database: PDB / ID: 8s02

Title

BzdNO-benzoyl-CoA complex

Components

BzdN
BzdO

Keywords

OXIDOREDUCTASE / Benzoyl-CoA reductase / reductive dearomatization / iron-sulfur clusters

Function / homology

Function and homology information

iron-sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Azoarcus sp. CIB (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Ermler, U. / Boll, M. / Fuchs, J. / Demmer, U.

Funding support

1items

Citation

Journal: To Be Published
Title: X-ray structure of the BzdNO-benzoyl-CoA complex
Authors: Ermler, U. / Boll, M. / Fuchs, J. / Demmer, U.

History

Deposition	Feb 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s02.cif.gz	677.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8s02.ent.gz	559.9 KB	Display	PDB format
PDBx/mmJSON format	8s02.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s02_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8s02_full_validation.pdf.gz	2 MB	Display
Data in XML	8s02_validation.xml.gz	77.2 KB	Display
Data in CIF	8s02_validation.cif.gz	103.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/8s02 ftp://data.pdbj.org/pub/pdb/validation_reports/s0/8s02	HTTPS FTP

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Related structure data

Related structure data	8s1tC 8s2rC C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: BzdO

B: BzdN

C: BzdO

D: BzdN

hetero molecules

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

1

A: BzdO

B: BzdN

hetero molecules

defined by author
Evidence: gel filtration
96.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: BzdO

D: BzdN

hetero molecules

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

Unit cell

Length a, b, c (Å)	208.850, 102.790, 86.820
Angle α, β, γ (deg.)	90.00, 102.48, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-839- HOH

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Protein , 2 types, 4 molecules ACBD

#1: Protein	BzdO Mass: 51272.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q68VL9
#2: Protein	BzdN Mass: 43482.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdN / Production host: Escherichia coli (E. coli) / References: UniProt: Q68VM0

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Non-polymers , 6 types, 886 molecules

#3: Chemical	ChemComp-BYC / benzoyl coenzyme A Mass: 871.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₄₀N₇O₁₇P₃S
#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: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-BJ8 / Double cubane cluster Mass: 735.345 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe₈S₉
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 875 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 19% PEG 3350, 100 mM BTP pH 7.5, 200 mM sodium formate or sodium acetate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.35→50 Å / Num. obs: 388628 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.052 / R_rim(I) all: 0.062 / Net I/σ(I): 11.09

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.35-1.45	1.018	74657	0.473	1.232	1
1.45-1.65	0.404	100714	0.88	0.481	1
1.65-1.95	0.138	83888	0.983	0.165	1
1.95-2.25	0.064	44956	0.994	0.077	1
2.25-2.8	0.045	40572	0.997	0.053	1
2.8-3.5	0.032	21262	0.998	0.038	1
3.5-4.6	0.025	12539	0.998	0.03	1
4.6-5.7	0.027	4753	0.998	0.031	1
5.7-8	0.03	3382	0.998	0.036	1
8-12	0.03	1351	0.998	0.036	1
12-50	0.036	554	0.997	0.044	1

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.35→40.03 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2175	19343	4.98 %
R_work	0.1993	-	-
obs	0.2002	388434	99.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.35→40.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13045	0	198	873	14116

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.718
X-RAY DIFFRACTION	f_dihedral_angle_d	8.106	1888
X-RAY DIFFRACTION	f_chiral_restr	0.085	1918
X-RAY DIFFRACTION	f_plane_restr	0.01	2433

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 (%)
1.35-1.37	0.4191	615	0.3921	12143	X-RAY DIFFRACTION	99
1.37-1.38	0.3814	643	0.3854	12161	X-RAY DIFFRACTION	98
1.38-1.4	0.36	667	0.3372	12260	X-RAY DIFFRACTION	100
1.4-1.42	0.3128	655	0.3204	12286	X-RAY DIFFRACTION	100
1.42-1.43	0.3398	637	0.3182	12351	X-RAY DIFFRACTION	100
1.43-1.45	0.336	636	0.3089	12266	X-RAY DIFFRACTION	99
1.45-1.48	0.3162	641	0.2986	12242	X-RAY DIFFRACTION	99
1.48-1.5	0.3208	667	0.2824	12279	X-RAY DIFFRACTION	100
1.5-1.52	0.2833	649	0.2602	12230	X-RAY DIFFRACTION	99
1.52-1.55	0.2721	641	0.2506	12256	X-RAY DIFFRACTION	99
1.55-1.57	0.2509	602	0.2277	12328	X-RAY DIFFRACTION	100
1.57-1.6	0.2357	633	0.2137	12408	X-RAY DIFFRACTION	100
1.6-1.63	0.2333	685	0.2034	12297	X-RAY DIFFRACTION	100
1.63-1.66	0.2191	658	0.1983	12351	X-RAY DIFFRACTION	100
1.66-1.7	0.2028	650	0.1843	12372	X-RAY DIFFRACTION	100
1.7-1.74	0.2113	634	0.192	12304	X-RAY DIFFRACTION	100
1.74-1.78	0.2232	648	0.1883	12349	X-RAY DIFFRACTION	100
1.78-1.83	0.2095	645	0.1857	12336	X-RAY DIFFRACTION	100
1.83-1.89	0.2118	624	0.1874	12329	X-RAY DIFFRACTION	99
1.89-1.95	0.2235	639	0.2007	12105	X-RAY DIFFRACTION	98
1.95-2.02	0.2006	657	0.1828	12352	X-RAY DIFFRACTION	100
2.02-2.1	0.2022	627	0.1828	12133	X-RAY DIFFRACTION	98
2.1-2.19	0.1959	625	0.1774	12438	X-RAY DIFFRACTION	100
2.19-2.31	0.1978	664	0.1798	12202	X-RAY DIFFRACTION	99
2.31-2.45	0.1956	613	0.1806	12419	X-RAY DIFFRACTION	100
2.45-2.64	0.2146	690	0.1844	12378	X-RAY DIFFRACTION	100
2.64-2.91	0.2178	658	0.1997	12355	X-RAY DIFFRACTION	99
2.91-3.33	0.2135	644	0.2037	12333	X-RAY DIFFRACTION	99
3.33-4.19	0.1879	648	0.1767	12272	X-RAY DIFFRACTION	98
4.19-40.03	0.2056	648	0.1901	12556	X-RAY DIFFRACTION	99

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	3.4913	-2.7602	3.3429	5.5963	-4.6682	8.1482	0.1449	0.3537	-0.1037	-0.7682	-0.0925	0.1063	0.4693	-0.0659	-0.0552	0.2618	-0.0289	0.0281	0.1798	-0.0328	0.1538	31.7048	-3.921	-7.7219
2	1.0279	0.6911	0.1581	1.3885	-0.0099	0.5942	-0.0038	0.0642	-0.1021	-0.0623	0.0147	-0.0638	0.0496	0.0464	-0.0061	0.1539	0.0104	0.0052	0.123	0.0017	0.1205	31.5516	-10.104	14.9975
3	2.3109	-1.0397	-0.6552	2.9737	0.7941	1.3354	-0.022	-0.1364	0.0651	0.0699	0.0643	-0.2463	-0.0313	0.1945	-0.0408	0.1621	-0.0221	-0.0047	0.1795	0.0038	0.1541	44.7293	1.8026	23.2409
4	1.2528	-0.4927	0.6758	0.7166	-0.1113	1.5295	-0.0039	0.1597	0.0305	-0.1824	-0.0302	-0.0213	-0.0309	0.0069	0.0427	0.2132	-0.017	0.0298	0.1283	0.0099	0.1306	30.9708	7.3561	1.1194
5	1.2259	-0.2695	0.2542	0.898	-0.257	1.2379	-0.0616	-0.0308	0.0677	-0.0506	0.0116	0.0822	-0.1148	-0.1088	0.043	0.1949	0.0071	-0.0028	0.1656	-0.0153	0.1693	16.8283	9.5907	10.559
6	4.0406	-3.4828	2.6011	5.2428	-3.0391	3.7221	0.1295	0.2387	0.174	-0.4605	-0.092	0.1177	0.1171	-0.0794	-0.0527	0.1841	-0.0078	-0.0037	0.2106	-0.0075	0.2042	5.2589	3.8625	-0.2901
7	2.5493	-1.3772	0.4905	6.6582	-3.042	4.6818	-0.0074	-0.3145	0.0547	0.4912	0.2825	0.6822	-0.0518	-0.7171	-0.2615	0.2004	0.0021	0.0687	0.3624	-0.0416	0.2026	2.8086	8.2988	49.3323
8	2.9657	1.1175	1.4207	1.791	0.454	2.3394	-0.0119	-0.0475	0.1257	0.0653	-0.096	0.2702	-0.0653	-0.2255	0.1057	0.1945	0.0182	0.0472	0.1872	-0.0058	0.1726	11.5541	9.6068	37.5654
9	1.5637	-0.2235	0.2789	0.5799	0.0961	0.7536	-0.0111	-0.0304	0.1007	0.0088	-0.0184	0.1041	-0.0731	-0.1388	0.0225	0.1999	0.0135	0.0136	0.1677	0.0001	0.1665	13.6202	8.3211	28.5717
10	3.6889	-1.8846	1.3766	3.3644	-1.6999	1.4393	0.0055	-0.1275	0.3447	0.2696	-0.0427	-0.1406	-0.2803	-0.0166	0.0214	0.1971	-0.024	0.0058	0.1158	-0.0155	0.1114	27.7982	18.7424	38.5623
11	2.194	2.7149	-0.8641	6.102	-1.7835	1.6253	0.2025	-0.2669	0.0038	0.6785	-0.1937	0.0344	0.0555	0.0038	0.0056	0.2867	-0.0028	0.0142	0.2031	-0.0165	0.1134	21.2619	3.7992	52.8495
12	1.6559	0.4211	-0.366	4.1104	-2.3258	1.7686	-0.0566	-0.1228	-0.1288	0.3939	0.0636	0.2397	0.3828	-0.3734	-0.0258	0.3796	-0.0771	0.0675	0.265	-0.0185	0.1512	9.6747	-3.6875	50.4289
13	1.3599	-0.4531	-0.812	2.0562	0.7604	3.8121	-0.002	-0.2615	-0.0469	0.4103	-0.0173	0.2161	0.2257	-0.4652	0.0037	0.2551	-0.0313	0.0382	0.2815	0.0118	0.1618	10.4145	-4.8237	53.3821
14	0.9388	0.3271	0.3439	1.4038	0.348	1.2957	0.0888	-0.1138	-0.1281	0.3019	-0.0762	0.0805	0.3016	-0.1046	-0.0047	0.2327	-0.0145	0.0187	0.1353	0.008	0.1219	20.7312	-8.4336	39.3998
15	7.1295	1.6696	-0.5372	3.4023	-1.082	3.5814	0.1939	-0.1936	-0.2742	-0.0237	0.1281	0.6522	0.8268	-0.5896	-0.3236	0.4239	-0.1537	0.0119	0.3132	-0.0124	0.2738	6.4237	-20.1598	36.188
16	7.4381	4.6395	-4.3574	4.9221	-2.8918	4.866	0.2607	-0.3261	0.2429	0.6528	-0.0853	0.3767	-0.1501	-0.0844	-0.1673	0.325	0.0435	0.0357	0.1597	-0.001	0.1637	21.0303	-46.7062	40.8038
17	1.1471	-0.7449	0.0445	1.9878	-0.2957	0.667	-0.0415	-0.0802	0.094	0.1283	0.0311	-0.0269	-0.0671	0.0101	0.0162	0.1613	-0.0048	0.0021	0.1055	-0.0005	0.1001	30.4496	-40.3584	20.1524
18	1.9208	1.1555	0.3624	2.3608	1.0521	2.1787	-0.0049	0.0097	-0.0647	0.1833	0.077	-0.2619	0.052	0.2056	-0.0579	0.1678	0.0278	-0.0196	0.1464	0.0123	0.1424	45.8846	-52.589	18.1817
19	1.7417	0.5395	-0.4982	0.821	0.0093	0.9804	-0.0012	-0.1553	-0.0483	0.2445	-0.0215	0.0726	0.0502	-0.0751	0.0237	0.2815	0.0046	0.0171	0.1272	0.0141	0.1301	23.9555	-58.2158	32.469
20	1.822	0.7218	0.2476	2.5865	-0.9254	1.5128	0.0228	-0.122	0.0727	0.2883	0.033	0.4992	-0.0421	-0.3367	-0.0507	0.2256	-0.0159	0.0519	0.2018	-0.0248	0.196	9.2349	-55.9984	20.0565
21	3.5116	2.1263	-1.1978	7.8001	-2.7804	4.3571	-0.0343	0.6336	0.032	-0.8867	0.3109	0.5257	0.2319	-0.6234	-0.2735	0.2758	0.003	-0.0458	0.4151	-0.0488	0.1577	19.2457	-58.6986	-23.3942
22	3.8118	-1.0751	0.1447	1.994	-0.1862	1.5299	-0.0213	0.0279	-0.1227	-0.1688	-0.0241	0.2075	0.0362	-0.1783	0.0498	0.2362	-0.0248	-0.0086	0.1934	-0.0022	0.1524	21.9568	-60.3667	-8.8053
23	1.6528	-0.1104	-0.2937	1.3607	0.4041	1.2101	-0.0018	0.1872	-0.1065	-0.0938	-0.0052	0.1786	0.0801	-0.2161	0.0139	0.1936	-0.0199	-0.0069	0.1867	-0.002	0.1581	15.992	-58.1207	-0.4726
24	2.027	0.287	-0.1554	0.7245	0.0208	0.5102	-0.014	0.0925	-0.1409	-0.0335	0.0029	0.0452	0.0906	-0.0441	-0.0011	0.1505	-0.0086	0.0079	0.1051	-0.0007	0.0984	29.8637	-61.4342	1.7289
25	2.487	0.5722	-0.2406	1.8083	-0.0448	1.0623	0.0227	0.1253	-0.2988	-0.07	0.0165	-0.1283	0.2432	-0.0128	-0.049	0.2358	0.0085	0.0209	0.1434	-0.0005	0.1653	37.0028	-69.5617	-2.8137
26	1.5649	-2.4463	1.0144	9.2222	-4.47	3.1315	0.2409	0.2421	0.1021	-0.7722	-0.2277	-0.2749	0.0905	0.0982	-0.0199	0.2347	0.0113	0.0486	0.2093	-0.0103	0.1221	37.0108	-54.2932	-18.7132
27	1.2176	0.2981	-0.4154	1.4244	0.4983	2.5207	0.1075	0.4055	0.13	-0.4925	-0.0416	-0.0231	-0.3158	-0.2797	-0.051	0.3011	0.0532	0.015	0.2847	0.0322	0.1599	26.8346	-45.8835	-22.8594
28	1.2572	-0.4122	-0.5373	1.3037	0.2186	0.9761	0.1362	0.2166	0.1846	-0.249	-0.0916	-0.0076	-0.2179	-0.11	-0.0325	0.235	0.0147	0.0157	0.149	0.0202	0.1231	31.5189	-44.0019	-8.3145
29	4.5915	-0.8888	1.2914	3.9557	-2.207	4.0387	0.1361	0.306	0.5084	-0.2201	0.0527	0.2771	-0.5701	-0.3853	-0.1686	0.3727	0.1086	0.0646	0.2281	0.0101	0.2351	21.0166	-31.7652	-5.9323

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 160 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 161 through 187 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 188 through 343 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 344 through 397 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 398 through 442 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 2 through 27 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 63 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 64 through 133 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 134 through 158 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 159 through 184 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 185 through 206 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 207 through 243 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 244 through 344 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 345 through 376 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 6 through 31 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 32 through 160 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 161 through 187 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 188 through 343 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 344 through 436 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2 through 27 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 28 through 63 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 64 through 113 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 114 through 133 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 134 through 158 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 159 through 184 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 185 through 243 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 244 through 327 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 328 through 376 )

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