PDB-4gxz: Crystal structure of a periplasmic thioredoxin-like protein from ...

ID or keywords:

Entry

Database: PDB / ID: 4gxz

Title

Crystal structure of a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium

Components

Suppression of copper sensitivity protein

Keywords

ISOMERASE / thiol-disulfide oxidoreductase / Thioredoxin fold / OXIDOREDUCTASE / thiol-disulfide oxidation reduction / periplasmic space

Function / homology

Function and homology information

disulfide oxidoreductase activity
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

Shepherd, M. / Heras, B. / King, G.J. / Argente, M.P. / Achard, M.E.S. / King, N.P. / McEwan, A.G. / Schembri, M.A.

Citation

Journal: Antioxid Redox Signal / Year: 2013
Title: Structural and functional characterization of ScsC, a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium
Authors: Shepherd, M. / Heras, B. / Achard, M.E. / King, G.J. / Argente, M.P. / Kurth, F. / Taylor, S.L. / Howard, M.J. / King, N.P. / Schembri, M.A. / McEwan, A.G.

History

Deposition	Sep 4, 2012	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 17, 2013	Provider: repository / Type: Initial release
Revision 1.1	Mar 12, 2014	Group: Database references
Revision 1.2	Nov 8, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gxz.cif.gz	292.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4gxz.ent.gz	240.4 KB	Display	PDB format
PDBx/mmJSON format	4gxz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gx/4gxz ftp://data.pdbj.org/pub/pdb/validation_reports/gx/4gxz	HTTPS FTP

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Related structure data

Related structure data	3gykS 3l9s 3l9u S: Starting model for refinement
Similar structure data	6pw7-1 5w7o-d 1n5n-1 1hlm-d 6e3b-18 4iou-3 6ifv-2 1qa7-2 4c76-2 4h79-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) 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: 3L9VCrystal Structure of Salmonella enterica serovar Typhimurium SrgA

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (2) #91 - Jul 2007 Thymine Dimers similarity (2)

Deposited unit

A: Suppression of copper sensitivity protein

B: Suppression of copper sensitivity protein

C: Suppression of copper sensitivity protein

D: Suppression of copper sensitivity protein

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

1

A: Suppression of copper sensitivity protein

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

2

B: Suppression of copper sensitivity protein

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

3

C: Suppression of copper sensitivity protein

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

4

D: Suppression of copper sensitivity protein

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

Unit cell

Length a, b, c (Å)	53.107, 90.998, 83.309
Angle α, β, γ (deg.)	90.00, 102.23, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Suppression of copper sensitivity protein Mass: 21229.330 Da / Num. of mol.: 4 / Fragment: lack the signal sequence 1-17 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: scsC, STM1115 / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pLysS / References: UniProt: H9L4C1, protein disulfide-isomerase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Suppression of copper sensitivity protein

Mass: 21229.330 Da / Num. of mol.: 4 / Fragment: lack the signal sequence 1-17
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: scsC, STM1115 / Plasmid: pETLIC / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) pLysS / References: UniProt: H9L4C1, protein disulfide-isomerase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 411 / 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: 46.91 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 8.2 Details: 18-27% (w/v) PEG 4000, 0.1M Tris buffer pH 8.2 , VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.541 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 31, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.541 Å / Relative weight: 1
Reflection	Resolution: 1.98→48.69 Å / Num. all: 106172 / Num. obs: 106150 / % possible obs: 99.97 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.45 % / B_iso Wilson estimate: 35.41 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 13
Reflection shell	Resolution: 1.98→2.05 Å / Redundancy: 7.29 % / R_merge(I) obs: 0.479 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10617 / % possible all: 100

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
CrystalClear		data reduction
CrystalClear		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3GYK

3gyk

Resolution: 2.04→48.689 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.7881 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.76 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2526	2506	5.09 %	RANDOM
R_work	0.1992	-	-	-
all	0.2018	49333	-	-
obs	0.2018	49220	99.77 %	-

Solvent computation

Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.165 Å² / k_sol: 0.346 e/Å³

Displacement parameters

B_iso max: 117.24 Å² / B_iso mean: 44.5163 Å² / B_iso min: 17.46 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.5202 Å²	-0 Å²	-1.0006 Å²
2-	-	-2.7511 Å²	0 Å²
3-	-	-	12.2714 Å²

Refinement step

Cycle: LAST / Resolution: 2.04→48.689 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5462	0	0	411	5873

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5627
X-RAY DIFFRACTION	f_angle_d	1.003	7665
X-RAY DIFFRACTION	f_dihedral_angle_d	15.653	2153
X-RAY DIFFRACTION	f_chiral_restr	0.07	898
X-RAY DIFFRACTION	f_plane_restr	0.005	984

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.04-2.0792	0.4798	142	0.4369	2562	2704	100
2.0792-2.1217	0.4084	131	0.3204	2591	2722	99
2.1217-2.1678	0.2938	153	0.245	2521	2674	100
2.1678-2.2183	0.3034	139	0.2295	2638	2777	100
2.2183-2.2737	0.3148	150	0.2474	2526	2676	99
2.2737-2.3352	0.3378	148	0.2217	2572	2720	100
2.3352-2.4039	0.2878	138	0.2104	2611	2749	100
2.4039-2.4815	0.2862	138	0.2037	2524	2662	100
2.4815-2.5702	0.2956	119	0.2148	2639	2758	100
2.5702-2.6731	0.3181	139	0.2114	2614	2753	100
2.6731-2.7947	0.254	145	0.2108	2595	2740	100
2.7947-2.9421	0.2739	117	0.2039	2616	2733	100
2.9421-3.1264	0.2739	159	0.2073	2569	2728	100
3.1264-3.3677	0.2467	134	0.1969	2609	2743	100
3.3677-3.7065	0.252	143	0.1934	2610	2753	100
3.7065-4.2426	0.2256	131	0.1687	2620	2751	100
4.2426-5.3441	0.1831	149	0.1512	2618	2767	100
5.3441-48.7033	0.2057	131	0.1997	2679	2810	100

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	0.3869	-0.121	0.4667	0.6303	-0.2052	0.5814	-0.0442	0.0238	-0.0019	0.0077	-0.0442	-0.0032	0.1542	0.0203	0.0528	0.6983	-0.0495	0.1397	0.7443	-0.1101	0.3207	6.3484	52.8995	28.7896
2	0.3157	-0.2552	0.2464	0.525	-0.0402	0.5737	-0.3011	0.0602	0.334	0.2354	-0.0726	0.2302	-0.2833	-0.0557	0.1564	0.1741	-0.0237	-0.1141	0.1655	-0.028	0.3396	2.8151	44.2413	47.1401
3	0.5647	0.3832	-0.1898	0.2711	-0.0599	0.392	-0.0368	-0.0683	0.0692	-0.0713	-0.0324	0.089	-0.0216	0.0089	0.0369	0.1583	0.0213	-0.035	0.1556	-0.0558	0.188	-8.1307	35.2633	46.1146
4	0.1522	0.3295	0.3804	0.9098	0.2733	1.693	0.2639	-0.1466	-0.072	0.0185	0.1571	0.6377	0.0188	-0.538	0.0731	0.1196	-0.0514	-0.0504	0.0995	-0.1945	0.2806	-22.5648	32.7166	45.8013
5	0.0336	-0.1293	0.1239	0.5203	-0.4188	0.3499	-0.0797	-0.0012	0.1082	0.1668	-0.1427	0.101	-0.082	-0.3677	0.0136	0.1685	0.2136	-0.037	0.229	-0.1225	0.2504	-19.189	47.904	48.683
6	1.1962	0.5756	0.302	0.2859	0.0362	0.6784	-0.1758	0.1191	0.5143	-0.0436	0.0018	0.3301	-0.2816	0.0323	0.1153	0.2333	-0.0113	-0.1851	0.1801	0.0288	0.2869	-6.9121	47.544	36.5627
7	1.4004	-0.5999	0.596	0.8123	-0.1189	0.7711	-0.0882	0.1375	-0.4098	0.0331	0.1519	0.2195	0.0346	0.1663	-0.0346	0.2166	0.0241	0.0306	0.2521	-0.0391	0.3172	5.2448	29.2455	40.6001
8	0.5466	-0.3135	0.0608	0.251	0.0106	0.2274	0.1354	-0.0433	-0.2433	-0.0157	-0.0466	-0.0428	-0.0298	-0.0238	-0.0377	0.1854	-0.0261	-0.0302	0.1347	0.0526	0.1928	6.2789	58.1742	49.0386
9	2.133	-0.1738	0.3694	1.8873	-0.0561	0.9062	-0.2618	-0.3453	0.118	-0.106	-0.0683	-0.202	-0.102	0.0397	0.1577	0.2246	0.0096	-0.0549	0.1723	-0.0106	0.1878	14.2994	69.8453	57.4595
10	0.433	-0.1651	0.3504	0.5048	-0.2045	0.2645	-0.1322	0.0141	-0.0729	-0.1758	0.1795	0.0254	-0.153	0.1085	0.0169	0.1591	-0.0546	0.0702	0.0249	0.3435	-0.2327	14.204	61.584	49.203
11	0.4713	0.2133	0.5098	0.7567	0.2021	0.6899	0.0801	0.0342	-0.1999	0.1148	0.026	-0.249	0.0218	0.0328	-0.0636	0.1888	-0.0067	-0.0349	0.1636	0.0456	0.1875	25.161	57.7826	53.7006
12	0.2894	0.2959	0.0636	0.3145	0.0591	0.399	0.0548	0.0304	0.0114	-0.0737	0.0882	0.1297	-0.0699	0.0121	-0.07	0.1745	0.0079	-0.0321	0.1278	0.0343	0.1709	9.8355	63.364	48.2588
13	1.6878	-0.4477	-0.1249	3.1274	0.4252	0.0588	-0.0816	0.311	-0.1193	0.2986	0.0567	0.1638	0.0023	-0.143	0.0588	0.272	0.038	0.0378	0.2592	0.1605	0.5525	-8.9888	25.359	82.6395
14	0.3257	-0.6541	-0.0208	1.5	0.1405	0.063	-0.1101	0.0825	0.9497	0.2183	0.4092	-0.2755	-0.0745	-0.0336	-0.0323	0.2306	0.0034	0.0231	0.2359	0.3497	0.3764	0.9404	21.9853	70.0299
15	2.6866	0.3506	-1.0934	3.3767	0.5475	0.5876	-0.0439	0.4119	-0.356	0.3993	0.0962	-0.0038	0.3104	-0.1143	0.0212	0.2431	-0.0753	0.0405	0.2914	0.0107	0.2471	5.5862	10.9083	66.0079
16	0.1198	-0.0864	-0.0341	1.1331	0.4573	0.8553	0.1808	0.3011	0.1085	0.1637	0.1967	-0.1946	0.1559	-0.2403	-0.1639	0.2493	0.0261	-0.0347	0.3775	0.1336	0.3753	5.645	19.713	73.806
17	0.2019	0.0657	-0.3506	0.8996	-0.0855	0.6825	0.2834	0.0482	0.7564	0.3138	1.0761	-0.178	0.1715	0.4792	-0.2404	0.2047	-0.2316	-0.0501	-1.1244	0.4717	0.9198	13.6058	27.7493	73.419
18	0.01	0.0078	0.0064	0.2595	-0.0753	0.0328	0.0135	0.5204	0.4505	-0.0573	0.1303	0.1216	0.0576	-0.2266	-0.0588	0.1445	0.0167	-0.1628	0.3237	0.4613	0.3043	12.4804	22.9039	64.1904
19	0.0703	-0.233	-0.175	0.76	0.5953	1.203	0.0868	0.2251	0.0848	0.1974	0.175	-0.4852	-0.0123	0.5927	-0.037	0.1448	-0.0143	0.0114	0.3489	0.1473	0.3645	22.7082	19.6742	68.7947
20	0.1994	0.0007	-0.3573	0.0455	-0.0897	0.783	0.3348	-0.0404	0.4445	-0.0028	0.1777	0.2194	-0.1396	0.0069	-0.2717	0.1542	-0.1923	0.046	0.3794	0.2209	0.8813	16.823	33.8	72.061
21	1.0846	-0.0029	-0.6441	0.0951	0.238	0.9106	0.2417	-0.0623	0.8761	0.1361	0.2563	-0.4595	-0.1702	0.1277	-0.2518	0.2488	0.0641	-0.0227	0.246	-0.0467	0.5813	5.6257	26.8973	83.2607
22	0.2452	0.0431	-0.0855	0.521	-0.0396	0.1966	0.1051	0.0026	-0.1613	0.0272	0.497	0.1432	0.1237	-0.2297	-0.1691	0.3388	-0.011	0.0289	0.3661	0.1893	0.4301	-1.5644	12.4967	78.253
23	1.4376	-1.3991	0.0412	1.3583	-0.0515	0.8636	0.1687	0.0286	-0.8449	-0.0514	0.1815	0.3964	0.4849	-0.204	-0.3269	0.6827	0.0044	0.0909	0.5636	-0.0358	0.9744	1.045	4.3878	68.3483
24	2.7013	1.8412	-0.397	1.6828	0.4973	1.394	0.0335	0.1549	-0.2384	0.1736	-0.0424	-0.2865	0.1865	-0.1284	0.0047	0.3915	-0.0967	-0.1492	0.4247	-0.013	0.8226	-9.023	9.0232	66.8525
25	1.2788	-0.3582	0.6433	0.3587	0.0192	0.5457	0.0669	-0.0793	-0.3458	-0.0639	-0.0739	0.0986	-0.0408	0.2557	0.0008	0.1647	-0.0013	0.0052	0.2212	0.0064	0.2002	-9.1394	41.0376	75.5675
26	0.9539	0.2614	0.6536	1.266	0.1987	1.3517	-0.3557	0.1995	0.2568	0.0052	-0.322	0.0849	-0.1249	0.1916	0.1878	0.2794	-0.0979	-0.0534	0.3142	0.0358	0.2807	-13.2251	54.6987	74.0871
27	0.296	-0.3756	0.16	0.4824	0.182	0.8036	0.0618	0.0161	-0.1712	-0.0079	-0.1701	0.2016	-0.1694	0.1143	0.063	0.1064	-0.0413	0.0208	0.1543	-0.0323	0.0546	-19.614	43.0345	73.7673
28	0.2056	-0.3891	-0.4719	1.4841	0.2968	1.3314	0.1066	0.1699	-0.2177	0.0461	-0.0771	0.6802	-0.0179	-0.4954	0.103	0.216	0.0389	0.0205	0.2837	-0.1106	0.3552	-31.7059	48.8676	74.5263
29	0.6497	-0.3831	-0.0732	0.9933	-0.4436	0.7298	-0.1671	0.015	-0.4361	0.034	-0.3493	0.5346	0.1044	0.0678	0.0837	0.1826	-0.0179	0.066	0.1536	0.209	0.1575	-19.4835	34.6564	80.3031
30	1.7303	-0.4483	0.395	1.0135	0.4575	0.8465	-0.109	-0.1251	0.6251	0.156	0.0583	-0.2352	0.0039	0.2484	0.0556	0.2257	-0.0741	-0.089	0.3104	-0.0266	0.3082	-3.7945	52.8013	80.2827

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 9:16)	A	9 - 16
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 17:38)	A	17 - 38
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 39:110)	A	39 - 110
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 111:127)	A	111 - 127
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 128:135)	A	128 - 135
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 136:152)	A	136 - 152
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 153:186)	A	153 - 186
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 13:49)	B	13 - 49
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 50:65)	B	50 - 65
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 66:80)	B	66 - 80
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 81:127)	B	81 - 127
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 128:187)	B	128 - 187
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 13:24)	C	13 - 24
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 25:49)	C	25 - 49
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 50:65)	C	50 - 65
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 66:80)	C	66 - 80
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 81:96)	C	81 - 96
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 97:110)	C	97 - 110
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 111:127)	C	111 - 127
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 128:135)	C	128 - 135
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 136:152)	C	136 - 152
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 153:168)	C	153 - 168
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 169:174)	C	169 - 174
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 175:185)	C	175 - 185
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 18:49)	D	18 - 49
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 50:65)	D	50 - 65
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 66:110)	D	66 - 110
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 111:127)	D	111 - 127
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 128:152)	D	128 - 152
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 153:186)	D	153 - 186

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