PDB-6g5z: Choline sulfatase from Ensifer (Sinorhizobium) meliloti

ID or keywords:

Entry

Database: PDB / ID: 6g5z

Title

Choline sulfatase from Ensifer (Sinorhizobium) meliloti

Components

Choline-sulfatase

Keywords

HYDROLASE / Choline-sulfatase

Function / homology

Function and homology information

choline biosynthetic process / choline-sulfatase / choline-sulfatase activity / iduronate-2-sulfatase activity / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Sinorhizobium meliloti CECT 4857 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.98 Å

Authors

Martinez-Rodriguez, S. / Camara-Artigas, A.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.
Authors: Gavira, J.A. / Camara-Artigas, A. / Neira, J.L. / Torres de Pinedo, J.M. / Sanchez, P. / Ortega, E. / Martinez-Rodriguez, S.

History

Deposition	Mar 30, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 10, 2019	Provider: repository / Type: Initial release
Revision 2.0	Apr 24, 2019	Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1	Mar 8, 2023	Group: Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_conn_type Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2	Feb 7, 2024	Group: Data collection / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn Item: _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6g5z.cif.gz	1.1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6g5z_validation.pdf.gz	463.5 KB	Display	wwPDB validaton report
Full document	6g5z_full_validation.pdf.gz	468.8 KB	Display
Data in XML	6g5z_validation.xml.gz	73.6 KB	Display
Data in CIF	6g5z_validation.cif.gz	104.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g5/6g5z ftp://data.pdbj.org/pub/pdb/validation_reports/g5/6g5z	HTTPS FTP

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Related structure data

Related structure data	6g60C 7pthC 7ptjC 2vqrS 2w8sS 3b5qS 3ed4S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6g60-d 5tls-1 2ols-2 1tez-d 3vti-d 5xs8-d 1eak-d 6ssa-d 5u1s-d 2wp5-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	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: Choline-sulfatase

B: Choline-sulfatase

C: Choline-sulfatase

D: Choline-sulfatase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: light scattering

Unit cell

Length a, b, c (Å)	128.197, 206.452, 116.673
Angle α, β, γ (deg.)	90.000, 110.280, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Choline-sulfatase Mass: 58148.066 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti CECT 4857 (bacteria) Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69787*PLUS, choline-sulfatase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 861 / 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: 3.11 Å³/Da / Density % sol: 60.49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M Lithium Sulfate, 0.1M Hepes

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.9778 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2014 / Details: Silicon (1 1 1) channel-cut

Radiation

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

Radiation wavelength

Wavelength: 0.9778 Å / Relative weight: 1

Reflection

Resolution: 1.98→109.44 Å / Num. obs: 197246 / % possible obs: 100 % / Redundancy: 8.5 % / B_iso Wilson estimate: 31.92 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.086 / Net I/σ(I): 12.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
1.98-2.01	8	0.8	9738	0.847	1	100
10.84-109.44	8.7	0.042	1234	0.999	1	99.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
Aimless	0.5.27	data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.24	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2VQR,2W8S,3ED4, 3B5Q

Resolution: 1.98→19.976 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 22.3

	R_factor	Num. reflection	% reflection
R_free	0.2	9987	5.07 %
R_work	0.1706	-	-
obs	0.1721	196983	99.64 %

Solvent computation

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

Displacement parameters

B_iso max: 216.73 Å² / B_iso mean: 45.6141 Å² / B_iso min: 14.21 Å²

Refinement step

Cycle: final / Resolution: 1.98→19.976 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16015	0	74	861	16950
B_iso mean	-	-	59.34	39.93	-
Num. residues	-	-	-	-	2022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	16557
X-RAY DIFFRACTION	f_angle_d	0.809	22596
X-RAY DIFFRACTION	f_chiral_restr	0.045	2382
X-RAY DIFFRACTION	f_plane_restr	0.005	2980
X-RAY DIFFRACTION	f_dihedral_angle_d	11.511	9814

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9784-2.0009	0.3259	680	0.272	12314	12994	100
2.0009-2.0244	0.2858	694	0.2553	12245	12939	99
2.0244-2.049	0.2741	593	0.2428	12392	12985	100
2.049-2.0749	0.268	664	0.2331	12378	13042	100
2.0749-2.1022	0.2766	667	0.2297	12330	12997	100
2.1022-2.131	0.2737	573	0.2262	12480	13053	100
2.131-2.1614	0.2563	671	0.2238	12293	12964	100
2.1614-2.1936	0.2412	602	0.2059	12337	12939	100
2.1936-2.2279	0.2482	682	0.2001	12308	12990	100
2.2279-2.2643	0.2215	628	0.189	12314	12942	100
2.2643-2.3033	0.2171	713	0.1789	12356	13069	100
2.3033-2.3451	0.2196	666	0.1784	12365	13031	100
2.3451-2.3902	0.2209	659	0.1793	12294	12953	100
2.3902-2.4389	0.2276	716	0.173	12256	12972	100
2.4389-2.4918	0.2224	730	0.1834	12298	13028	100
2.4918-2.5497	0.1903	677	0.166	12360	13037	100
2.5497-2.6133	0.1991	700	0.1698	12281	12981	100
2.6133-2.6838	0.2235	606	0.1763	12407	13013	100
2.6838-2.7626	0.2215	677	0.1836	12374	13051	100
2.7626-2.8515	0.2327	605	0.1735	12370	12975	100
2.8515-2.9531	0.2227	644	0.1878	12391	13035	100
2.9531-3.0709	0.2193	724	0.1871	12217	12941	99
3.0709-3.2102	0.2257	639	0.1947	12381	13020	100
3.2102-3.3786	0.2229	683	0.1792	12407	13090	100
3.3786-3.5892	0.1814	613	0.1649	12348	12961	100
3.5892-3.8645	0.1597	642	0.1472	12359	13001	100
3.8645-4.25	0.1473	639	0.1268	12388	13027	100
4.25-4.8572	0.1556	642	0.1261	12334	12976	99
4.8572-6.0907	0.163	672	0.1464	12359	13031	100
6.0907-19.9768	0.1829	651	0.1724	12258	12909	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	0.0467	-0.0252	-0.0114	0.0044	-0.0034	-0.0016	-0.1175	-0.042	0.0422	0.0323	0.0631	0.036	0.0722	-0.07	-0	0.2648	0.0183	-0.0218	0.2292	0.0016	0.17	21.0061	0.5726	60.7211
2	0.0121	0.0002	-0.0025	0.0145	-0.0052	-0.0065	-0.1456	0.034	0.0018	0.0141	0.1112	-0.0001	-0.0171	-0.0046	-0	0.2496	0.0272	-0.0686	0.2534	0.0089	0.205	24.1155	13.2868	52.0855
3	0.0399	-0.0597	-0.0474	0.0004	0.0137	0.0221	-0.1838	0.0055	-0.0637	-0.0454	0.1362	-0.1121	-0.0181	-0.0643	-0	0.3043	-0.0292	-0.0544	0.2407	-0.007	0.0852	31.145	1.9107	48.1731
4	0.0324	-0.072	-0.0075	0.0265	-0.0002	0.0094	-0.0649	-0.0138	-0.0095	0.012	0.0808	-0.0078	0.0306	0.0142	-0	0.2747	0.0152	-0.0514	0.226	-0.0181	0.152	32.7042	-4.2259	56.0551
5	0.011	0.0131	-0.0017	0.0082	-0.0005	0.0183	-0.067	0.0966	-0.0876	-0.0285	0.0285	0.075	0.0303	-0.0939	-0	0.3453	-0.0905	-0.0795	0.3873	-0.0426	0.2567	11.4159	-6.8048	36.3317
6	0.0095	-0.0408	-0.014	0.0007	0.0174	0.0067	-0.1488	0.0708	-0.0524	0.0283	0.0146	-0.0004	0.0985	0.0768	-0	0.3154	-0.0086	-0.0045	0.2223	-0.0177	0.1618	30.2546	-10.9953	49.9928
7	0.0535	-0.0142	-0.0224	0.0969	-0.0268	0.0181	-0.1309	0.0138	-0.0248	0.0633	0.1376	0.116	0.07	0.0187	0	0.2682	0.0245	0.0046	0.2513	0.0182	0.1675	16.4832	-3.4106	64.0925
8	0.0342	0.0035	0.0353	0.0162	0.0098	0.0259	-0.0569	-0.0193	0.0661	0.0015	-0.0033	0.1074	0.0382	-0.082	-0	0.1927	-0.0826	0.0115	0.3393	-0.0125	0.2721	-1.7156	-1.8754	52.7234
9	0.0012	0.0054	-0.0083	0.0234	0.0383	0.0254	0.0105	0.0599	0.0045	-0.0231	0.0165	0.0174	0.0171	0.0272	-0	0.2368	0.0302	-0.0556	0.2895	0.0251	0.2621	19.9434	20.8024	48.3781
10	0.0016	-0.0059	-0.0084	0.0025	-0.009	-0.0017	-0.0214	-0.0926	0.0482	0.0401	-0.0097	-0.0232	0.0104	-0.0112	0	0.3545	0.0288	-0.0486	0.3093	-0.0246	0.269	53.9967	6.0985	70.7082
11	0.0079	-0.0684	-0.0524	0.043	-0.0299	0.1409	-0.0129	-0.0461	0.0235	-0.0523	0.0882	0.0525	0.0442	0.0686	-0	0.2077	0.0137	0.0054	0.2156	-0.022	0.1907	36.1971	-38.0769	90.9197
12	-0.0073	-0.0279	-0.0437	0.0051	-0.0198	0.0326	0.0393	-0.0536	-0.1236	0.0182	0.0965	0.0529	0.0759	-0.0792	-0	0.1944	-0.0013	-0.0173	0.2886	-0.0052	0.1982	22.7933	-35.9838	94.7144
13	0.1072	0.045	-0.0949	0.0028	0.0065	0.0515	0.0294	-0.0193	0.0299	-0.0051	0.0806	0.0011	-0.0075	-0.0639	0	0.1666	0.0326	-0.0069	0.25	0.0069	0.156	24.145	-28.7031	84.3157
14	0.0401	-0.0538	-0.0357	0.0057	-0.079	0.2541	0.0277	-0.046	0.0259	-0.0631	0.0708	-0.0281	-0.0727	0.0264	-0	0.1595	-0.0145	0.0196	0.2073	-0.0403	0.1683	38.495	-29.2943	83.5406
15	-0.0012	-0.2756	0.0922	0.1416	-0.1313	0.0413	0.0423	0.0399	0.1116	-0.0284	0.1945	0.2622	0.1077	0.1233	0	0.1771	0.0144	0.0635	0.0511	-0.0248	0.2014	34.5416	-46.0556	89.8089
16	0.0397	-0.076	-0.0528	0.059	0.0017	-0.0474	-0.0131	0.0171	0.1113	0.0201	0.0464	0.0381	0.0846	0.0074	-0	0.2059	0.053	-0.0352	0.2248	0.0017	0.3129	21.7783	40.8616	57.7331
17	0.0335	-0.0307	0.0186	0.0172	0.0086	0	-0.0299	-0.0041	0.2308	0.0075	0.1293	-0.03	0.1164	-0.0447	-0	0.236	0.0371	-0.0319	0.282	-0.0249	0.287	33.7307	43.1849	64.7448
18	0.0179	0.0507	0.005	0.0116	0.006	-0.0022	0.0506	0.0233	0.2112	-0.0611	-0.0039	-0.0034	0.0178	0.0215	-0	0.2331	0.019	-0.0149	0.2768	-0.021	0.3492	32.7808	49.274	56.7575
19	0.0102	-0.0168	-0.0005	0.0019	0.0001	-0.0081	0.0654	-0.159	0.1858	0.0616	0.1659	0.0011	0.0803	-0.0387	0	0.3177	0.1214	0.0259	0.3069	-0.2062	0.3814	18.213	51.6345	82.0487
20	0.01	-0.0019	0.0038	0.0022	-0.0098	0.0033	-0.076	-0.044	0.317	-0.0454	-0.086	0.0608	0.0125	0.0498	0	0.2595	0.023	-0.0187	0.2897	-0.0705	0.4323	32.2357	56.0341	63.2696
21	0.0197	-0.0504	-0.0256	0.059	-0.007	0.023	-0.0022	0.0242	0.1774	0.0094	0.0269	0.1097	0.0498	0.0389	-0	0.195	0.0608	-0.0165	0.2385	0.0312	0.3805	15.0863	48.3209	53.9131
22	0.0026	-0.0296	-0.0347	0.0056	0.021	0.0284	0.0032	-0.0087	0.11	0.0825	0.0527	0.0935	0.0773	0.0547	-0	0.2183	0.0866	0.0195	0.2459	-0.0138	0.4022	0.9041	46.773	70.2352
23	-0.0067	-0.0058	-0.0315	0.1588	0.0629	-0.0462	-0.0326	-0.0433	0.183	0.0803	0.078	-0.0165	-0.0628	0.0684	-0	0.2563	0.0399	-0.0239	0.2934	0.0181	0.2892	32.8722	29.6242	55.8708
24	0.0408	0.0414	0.0741	0.0236	-0.0056	0.0512	-0.0564	-0.078	0.0129	-0.1365	0.0257	0.0206	0.0415	0.0183	0	0.3775	0.0368	0.0835	0.219	0.0177	0.3402	33.9142	-76.2798	89.5854
25	-0.0136	0.008	-0.0348	0.0076	-0.0071	-0.0167	-0.0361	-0.0996	0.077	0.0132	0.0285	0.0019	-0.04	0.0444	-0	0.3647	0.1032	-0.0343	0.4172	-0.016	0.4707	50.304	-71.433	101.7943
26	0.0049	0.0395	0.0022	0.0533	-0.0454	-0.0227	-0.0596	-0.1453	0.0268	-0.0098	-0.0199	0.1166	0.2096	-0.012	-0	0.3483	0.0061	0.0814	0.2885	0.0567	0.378	27.862	-81.3557	101.6718
27	-0.0246	0.0037	0.0393	0.1181	-0.094	-0.0273	-0.1774	-0.165	-0.008	-0.2371	-0.0474	-0.0579	0.4438	-0.0409	0	0.3646	0.1413	0.1233	0.2144	0.075	0.4062	43.2912	-86.8794	94.4645
28	0.0177	0.0151	-0.0577	0.0597	-0.012	-0.0226	-0.2278	-0.2143	0.034	-0.247	0.0983	-0.0632	0.1639	-0.0194	-0	0.4619	0.0039	0.0889	0.2269	-0.0143	0.3198	39.6241	-77.454	77.2126
29	0.0115	-0.0019	0.0244	-0.0056	0.0209	0.0024	-0.4037	0.1133	-0.0466	-0.1617	0.1331	-0.0173	-0.0363	0.0875	0	0.1443	0.4454	0.6089	-0.2026	-0.43	0.137	57.3501	-82.8938	74.2653
30	-0.005	-0.0266	-0.023	0.1134	-0.0143	-0.0235	-0.0994	-0.0364	-0.0602	0.0908	0.0955	-0.0261	0.1002	-0.0167	-0	0.3522	0.0846	0.0371	0.3392	-0.0302	0.3126	29.432	-63.6648	99.6819

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 (resid 5 through 101 )	A	5 - 101
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 102 through 135 )	A	102 - 135
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 182 )	A	136 - 182
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 214 )	A	183 - 214
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 215 through 251 )	A	215 - 251
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 252 through 282 )	A	252 - 282
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 283 through 378 )	A	283 - 378
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 379 through 450 )	A	379 - 450
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 451 through 487 )	A	451 - 487
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 488 through 512 )	A	488 - 512
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 5 through 135 )	B	5 - 135
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 136 through 182 )	B	136 - 182
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 183 through 251 )	B	183 - 251
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 252 through 431 )	B	252 - 431
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 432 through 509 )	B	432 - 509
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 5 through 135 )	C	5 - 135
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 136 through 182 )	C	136 - 182
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 183 through 214 )	C	183 - 214
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 215 through 251 )	C	215 - 251
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 252 through 282 )	C	252 - 282
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 283 through 378 )	C	283 - 378
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 379 through 450 )	C	379 - 450
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 451 through 510 )	C	451 - 510
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 5 through 121 )	D	5 - 121
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 122 through 159 )	D	122 - 159
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 160 through 214 )	D	160 - 214
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 215 through 338 )	D	215 - 338
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 339 through 404 )	D	339 - 404
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 405 through 450 )	D	405 - 450
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 451 through 510 )	D	451 - 510

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