PDB-6jss: Structure of Geobacillus kaustophilus lactonase, Y99P mutant

ID or keywords:

Entry

Database: PDB / ID: 6jss

Title

Structure of Geobacillus kaustophilus lactonase, Y99P mutant

Components

Phosphotriesterase

Keywords

HYDROLASE / Alpha-Beta Barrel

Function / homology

Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase / zinc ion binding / : / HYDROXIDE ION / Phosphotriesterase

Function and homology information

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.16 Å

Authors

Xue, B. / Yew, W.S.

Funding support

Singapore, 1items

Citation

Journal: Structure / Year: 2020
Title: Directed Computational Evolution of Quorum-Quenching Lactonases from the Amidohydrolase Superfamily.
Authors: Go, M.K. / Zhao, L.N. / Xue, B. / Supekar, S. / Robinson, R.C. / Fan, H. / Yew, W.S.

History

Deposition	Apr 8, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2020	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 17, 2020	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3	Nov 22, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/6jss ftp://data.pdbj.org/pub/pdb/validation_reports/js/6jss	HTTPS FTP

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Related structure data

Related structure data	6jstC 6jsuC 4h9uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6bhl-d 4ha0-d 2r1k-2 6jst-2 2r1l-2 6bh7-d 4xay-d 6jst-1 4ker-1 4kes-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #158 - Feb 2013 Proton-Gated Urea Channel similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Phosphotriesterase

B: Phosphotriesterase

C: Phosphotriesterase

D: Phosphotriesterase

hetero molecules

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

1

A: Phosphotriesterase

B: Phosphotriesterase

hetero molecules

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

2

C: Phosphotriesterase

D: Phosphotriesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	51.491, 51.648, 135.291
Angle α, β, γ (deg.)	91.830, 91.490, 95.780
Int Tables number	1
Space group name H-M	P1

#1: Protein	Phosphotriesterase Mass: 36813.867 Da / Num. of mol.: 4 / Mutation: Y99P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Strain: HTA426 / Gene: GK1506 / Plasmid: modified pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical	ChemComp-FE / FE (III) ION Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-OH / HYDROXIDE ION Mass: 17.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HO
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.43 Å³/Da / Density % sol: 49.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 17.00% w/v PEG 20000, 0.10 M TRIS-HCl, pH 8.5, 0.10 M MgCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX1 / Wavelength: 0.9537 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 21, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.9537 Å / Relative weight: 1

Reflection

Resolution: 2.16→19.714 Å / Num. obs: 74284 / % possible obs: 94.3 % / Redundancy: 1.134 % / CC_1/2: 0.997 / R_merge(I) obs: 0.061 / R_rim(I) all: 0.086 / Χ²: 1.509 / Net I/σ(I): 9 / Num. measured all: 159053

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.16-2.29	1.154	0.437	1.72	24584	23884	21302	0.737	0.618	89.2
2.29-2.45	1.15	0.331	2.23	24430	22722	21245	0.828	0.469	93.5
2.45-2.64	1.144	0.214	3.28	22534	20924	19697	0.922	0.303	94.1
2.64-2.89	1.134	0.14	4.89	20929	19406	18451	0.962	0.198	95.1
2.89-3.23	1.127	0.071	8.88	18959	17568	16823	0.988	0.1	95.8
3.23-3.73	1.122	0.038	14.84	16587	15350	14786	0.996	0.053	96.3
3.73-4.56	1.117	0.022	21.54	14125	13030	12644	0.998	0.031	97
4.56-6.43	1.109	0.02	22.67	10991	10184	9913	0.998	0.029	97.3
6.43-19.714	1.101	0.016	29.38	5914	5582	5371	0.999	0.022	96.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.07 Å	48.57 Å
Translation	4.07 Å	48.57 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.7.17	phasing
PHENIX	1.11.1_2575	refinement
PDB_EXTRACT	3.24	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4H9U

4h9u

Resolution: 2.16→19.714 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 25.04

	R_factor	Num. reflection	% reflection
R_free	0.2291	6980	4.97 %
R_work	0.1751	-	-
obs	0.1777	72731	94.7 %

Solvent computation

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

Displacement parameters

B_iso max: 80.67 Å² / B_iso mean: 30.0952 Å² / B_iso min: 5.08 Å²

Refinement step

Cycle: final / Resolution: 2.16→19.714 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10152	0	12	712	10876
B_iso mean	-	-	25.2	34	-
Num. residues	-	-	-	-	1292

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	10424
X-RAY DIFFRACTION	f_angle_d	0.868	14060
X-RAY DIFFRACTION	f_chiral_restr	0.051	1516
X-RAY DIFFRACTION	f_plane_restr	0.006	1860
X-RAY DIFFRACTION	f_dihedral_angle_d	3.735	6196

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 (%)
2.1598-2.1844	0.3702	227	0.2813	3473	3700	77
2.1844-2.21	0.3303	238	0.2706	4354	4592	92
2.21-2.2369	0.3512	234	0.2693	4468	4702	93
2.2369-2.2652	0.3298	201	0.2693	4297	4498	93
2.2652-2.295	0.2966	243	0.2464	4380	4623	93
2.295-2.3264	0.3093	233	0.2382	4414	4647	94
2.3264-2.3596	0.2923	201	0.2283	4488	4689	93
2.3596-2.3947	0.2779	260	0.2316	4335	4595	94
2.3947-2.4321	0.3028	263	0.2383	4391	4654	94
2.4321-2.4719	0.3033	239	0.2211	4497	4736	94
2.4719-2.5144	0.2819	210	0.2157	4294	4504	94
2.5144-2.56	0.2702	280	0.2181	4559	4839	95
2.56-2.6092	0.3163	217	0.2099	4371	4588	95
2.6092-2.6623	0.2559	241	0.2113	4469	4710	95
2.6623-2.72	0.2914	178	0.2017	4563	4741	95
2.72-2.7832	0.2985	215	0.2047	4378	4593	95
2.7832-2.8526	0.2696	223	0.1983	4658	4881	95
2.8526-2.9294	0.2568	242	0.203	4426	4668	96
2.9294-3.0153	0.2502	177	0.186	4577	4754	96
3.0153-3.1123	0.2568	219	0.1748	4499	4718	96
3.1123-3.2231	0.2117	265	0.1767	4576	4841	96
3.2231-3.3515	0.2162	218	0.1662	4529	4747	97
3.3515-3.5033	0.2177	282	0.1716	4512	4794	97
3.5033-3.6868	0.201	262	0.1561	4593	4855	97
3.6868-3.9161	0.2048	220	0.1405	4490	4710	97
3.9161-4.2158	0.1953	255	0.1287	4560	4815	97
4.2158-4.635	0.1543	241	0.1175	4664	4905	98
4.635-5.2944	0.1573	202	0.123	4573	4775	98
5.2944-6.628	0.1946	231	0.1474	4610	4841	98
6.628-19.7148	0.1578	263	0.1424	4571	4834	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	0.0211	-0.0088	-0.0079	0.008	0.0005	0.0028	-0.0108	-0.0475	-0.0054	0.0059	0.0046	-0.0219	-0.006	-0.0023	0.0005	0.0697	-0.0143	0.0227	0.0656	-0.0324	0.1844	-16.7447	1.3925	-3.4787
2	0.0104	-0.0072	-0.0088	0.012	-0.0042	0.0173	0.0224	-0.012	0.0098	0.036	-0.0343	0.0043	0.0194	-0.0047	0.0012	0.0882	0.003	0.0256	0.1781	-0.0559	0.1354	-30.4534	-12.804	-0.1147
3	0.0172	-0.0284	0.0274	0.1223	-0.1067	0.1218	0.0451	-0.049	0.0392	-0.0314	0.0239	0.0023	0.0174	-0.0323	0.0631	0.044	-0.0104	0.0152	0.111	-0.0118	0.1015	-22.2354	-8.3027	-6.5974
4	0.0178	0.0063	-0.004	0.0123	-0.0113	0.0192	0.0078	0.0287	0.0303	-0.0277	0.0116	-0.0039	0.0452	-0.014	0.0241	0.0889	-0.0133	0.0973	0.0422	0.0262	0.0829	-16.1502	-14.2781	-24.5762
5	0.0322	-0.046	-0.0243	0.0679	0.0251	0.0168	-0.0005	0.0228	0.0317	-0.0078	0.0697	-0.1148	0.0104	0.0333	0.0828	-0.2354	0.0667	0.1614	0.0526	-0.0479	0.0927	-8.442	-12.3744	-14.1208
6	0.0617	0.0462	-0.0192	0.0484	0.0066	0.0378	0.0268	-0.0766	-0.0025	0.0728	0.1058	-0.1483	0.0229	0.021	0.1107	0.0589	0.0426	-0.0834	0.1888	-0.0645	0.2621	-3.466	-16.119	3.6615
7	0.0916	-0.0678	0.0315	0.2594	0.1035	0.0892	-0.032	-0.0652	0.0725	0.1457	0.0724	-0.157	0.0925	0.0093	0.0176	0.1146	0.0055	-0.0191	0.1476	-0.0465	0.1173	-12.8357	-11.0607	7.7256
8	0.004	-0.0023	0.0003	0.0031	-0.0011	0.0031	-0.0291	-0.0018	0.0097	0.0281	-0.0897	0.059	-0.0012	0.0142	0	0.1301	0.0167	-0.0451	0.1343	-0.0417	0.2639	-48.2449	-33.5135	-26.387
9	0.1032	-0.0522	-0.1113	0.0281	0.0535	0.1231	0.0816	0.0312	0.0811	-0.2005	0.0302	0.019	-0.0069	0.0307	0.0445	0.2335	0.0335	-0.0657	0.0789	0.0051	0.1442	-35.45	-18.4435	-29.762
10	0.0713	0.0209	-0.0478	0.0078	-0.018	0.071	0.0372	-0.0333	0.0435	-0.1189	-0.051	0.1306	-0.0281	0.0349	0.0117	0.0911	0.022	-0.0393	0.0806	-0.04	0.1629	-39.1963	-27.0922	-23.297
11	0.057	-0.0529	0.0474	0.0902	-0.0706	0.1241	0.0253	-0.096	-0.0271	-0.0315	-0.0525	0.1059	0.0581	0.0648	-0.0041	0.0254	-0.0257	0.0347	0.0784	-0.0083	0.1267	-33.3947	-38.1206	-12.7679
12	0.0476	-0.0355	0.0167	0.0464	-0.0222	0.0768	0.077	0.0527	-0.0368	-0.1128	0.0077	-0.0159	0.0442	0.0492	0.1133	0.2173	0.027	-0.0041	0.1086	-0.034	0.126	-29.5586	-45.1093	-33.5155
13	0.0541	-0.0552	0.0124	0.0753	0.0367	0.1132	0.0454	0.0605	-0.0413	-0.1487	0.0078	0.0234	0.0477	0.1243	0.1108	0.2465	0.001	-0.0318	0.1053	-0.0104	0.0638	-32.4522	-34.0303	-38.7418
14	0.0032	-0.0027	-0.0001	0.0107	0.0036	0.0041	0.0247	0.0097	-0.0219	-0.0349	0.0003	0.0446	0.0058	-0.0002	0.0041	0.2352	-0.0039	-0.1304	0.136	-0.0456	0.3084	-46.471	-44.1515	-33.6993
15	0.0402	0.0315	0.0146	0.0471	-0.0027	0.04	-0.049	-0.0391	0.0538	0.0419	0.0542	-0.0643	-0.0415	0.0726	0	0.1714	-0.0238	-0.0044	0.1711	0.0275	0.1429	-22.0413	1.0541	41.4066
16	0.0966	0.0188	-0.0317	0.0984	-0.0865	0.1665	-0.031	-0.0237	-0.0003	-0.0449	0.0938	0.0562	0.0284	-0.0971	0.0708	0.1356	-0.0184	-0.0273	0.1726	0.0297	0.1123	-35.4649	-5.2621	36.4914
17	0.0029	0.0132	0.0081	0.0816	0.0531	0.0332	-0.0425	-0.0029	0.006	0.0464	-0.068	0.0102	0.0669	0.015	-0.0245	0.161	0.0013	-0.0466	0.2148	0.09	0.1412	3.9542	-14.2519	68.0424
18	0.0045	0.0022	0.0014	0.0043	0.0076	0.0073	0.0006	-0.0034	0.0315	0.0033	-0.0041	-0.0476	-0.0214	-0.046	-0	0.3065	-0.0366	-0.0639	0.2176	-0.0168	0.1882	-8.8377	1.0056	65.3346
19	0.0394	0.0028	0.0079	0.0112	0.0134	0.0182	-0.0738	0.0109	0.0497	0.0355	-0.0595	0.0158	-0.0042	0.0535	0.0001	0.2072	-0.0162	-0.0465	0.1989	0.0332	0.1819	-1.7622	-6.8073	63.5959
20	0.0239	-0.0116	0.0165	0.0092	-0.006	0.0146	-0.0625	0.0013	-0.016	-0.0226	-0.0506	0.039	0.0643	-0.0204	-0.0064	0.1602	0.0064	-0.0268	0.1309	-0.0147	0.0798	-11.1157	-18.6623	52.9931
21	0.0057	-0.0065	0.0094	0.005	-0.0066	0.0108	-0.0126	0.0348	0.0035	-0.0072	0.0479	0.0532	0.0699	0.0445	-0.0001	0.2142	-0.0096	-0.0186	0.183	0.0212	0.1732	-8.7531	-17.8244	58.5271
22	0.0019	0.0015	-0.0015	0.0024	0.0007	0.0014	-0.0294	0.0121	-0.002	-0.0446	-0.0192	-0.0028	0.0512	-0.0042	-0	0.3875	-0.0132	-0.0237	0.1683	0.0073	0.187	-10.6059	-27.2627	55.8052
23	0.0044	-0.0027	0.0274	0.0009	-0.0103	0.1516	0.0243	-0.0194	-0.0474	0.0056	-0.0059	-0.0253	0.0626	-0.0666	0.0004	0.3213	0.0105	0.051	0.1024	0.0145	0.1341	-13.6843	-27.1091	65.7719
24	0.0139	0.0146	0.018	0.0194	0.0194	0.0271	-0.0597	-0.0495	-0.0004	0.0442	-0.0856	0.001	0.0201	0.0106	-0.0028	0.3382	-0.0064	0.0306	0.1274	0.0298	0.132	-12.3507	-24.9708	74.9019
25	0.0015	0.0002	-0.0008	0.002	0.0021	0.0028	0.0158	-0.0066	0.0215	0.036	0.0184	0.0284	0.0152	-0.0162	0	0.4765	-0.0135	0.0445	0.2843	0.0546	0.2154	-16.3763	-18.6592	84.0074
26	0.0221	0.0244	-0.0049	0.0308	0.0053	0.0238	-0.0025	0.0145	0.0217	0.1128	-0.0551	0.0402	-0.0086	0.0026	0.0001	0.3258	0.0289	-0.0175	0.1946	0.0002	0.13	-8.6989	-12.4213	79.3971

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 3 through 26 )	A	3 - 26
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 61 )	A	27 - 61
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 106 )	A	62 - 106
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 107 through 131 )	A	107 - 131
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 201 )	A	132 - 201
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 202 through 254 )	A	202 - 254
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 255 through 325 )	A	255 - 325
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 26 )	B	3 - 26
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 27 through 61 )	B	27 - 61
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 62 through 106 )	B	62 - 106
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 107 through 201 )	B	107 - 201
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 202 through 254 )	B	202 - 254
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 255 through 308 )	B	255 - 308
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 309 through 325 )	B	309 - 325
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 3 through 131 )	C	3 - 131
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 132 through 325 )	C	132 - 325
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3 through 26 )	D	3 - 26
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 27 through 61 )	D	27 - 61
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 62 through 88 )	D	62 - 88
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 89 through 131 )	D	89 - 131
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 132 through 154 )	D	132 - 154
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 155 through 171 )	D	155 - 171
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 172 through 195 )	D	172 - 195
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 196 through 235 )	D	196 - 235
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 236 through 254 )	D	236 - 254
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 255 through 325 )	D	255 - 325

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