PDB-6vhe: FphF, Staphylococcus aureus fluorophosphonate-binding serine hydr...

ID or keywords:

Entry

Database: PDB / ID: 6vhe

Title

FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT130 bound

Components

Esterase family protein

Keywords

HYDROLASE / FphF / fluorophosphonate-binding / serine hydrolases / sodium bound / acyl / KT130 / intermediate

Function / homology

Function and homology information

S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / cytosol
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.94 Å

Authors

Fellner, M. / Mace, P.D.

Citation

Journal: Acs Infect Dis. / Year: 2020
Title: Structural Basis for the Inhibitor and Substrate Specificity of the Unique Fph Serine Hydrolases of Staphylococcus aureus .
Authors: Fellner, M. / Lentz, C.S. / Jamieson, S.A. / Brewster, J.L. / Chen, L. / Bogyo, M. / Mace, P.D.

History

Deposition	Jan 9, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 16, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 21, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2	Oct 11, 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 1.3	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vhe.cif.gz	435.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6vhe_validation.pdf.gz	511 KB	Display	wwPDB validaton report
Full document	6vhe_full_validation.pdf.gz	513.9 KB	Display
Data in XML	6vhe_validation.xml.gz	2 KB	Display
Data in CIF	6vhe_validation.cif.gz	14.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhe ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhe	HTTPS FTP

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Related structure data

Related structure data	6vh9SC 6vhdC 6wcxC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vhd-d 1g8j-2 1g8j-1 6vh9-d 6wcx-d 1g8k-1 1g8k-3 1g8k-4 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

Deposited unit

A: Esterase family protein

B: Esterase family protein

C: Esterase family protein

D: Esterase family protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	87.126, 87.126, 454.920
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

#1: Protein	Esterase family protein / Putative esterase / Tributyrin esterase Mass: 29205.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: EP54_00010, EQ90_02595, HMPREF3211_01237, NCTC10654_02801, NCTC10702_04070, RK64_00235 Plasmid: M1366 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0D6GS23, UniProt: Q2FUY3*PLUS, S-formylglutathione hydrolase
#2: Chemical	ChemComp-6WG / (2~{R})-2-phenylpiperidine-1-carbaldehyde Mass: 189.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₂H₁₅NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.34 % / Mosaicity: 0.09 °
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.25 uL ~6.6 mg/ml FphF+KT130 (0.2 mM KT130, 20% DMSO, 8 mM HEPES pH 7.5, 40 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.8 M sodium ...Details: 0.25 uL ~6.6 mg/ml FphF+KT130 (0.2 mM KT130, 20% DMSO, 8 mM HEPES pH 7.5, 40 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.8 M sodium formate, 10% w/v PEG 8000, 10% w/v PEG 1000 and 0.1 M HEPES pH 7.0. Crystals were soaked for ~20 seconds in 75% reservoir solution and 25% glycerol prior to freezing in liquid nitrogen

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.34 % / Mosaicity: 0.09 °

Crystal grow

Temperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.25 uL ~6.6 mg/ml FphF+KT130 (0.2 mM KT130, 20% DMSO, 8 mM HEPES pH 7.5, 40 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.8 M sodium ...

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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: 0.954 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.954 Å / Relative weight: 1

Reflection

Resolution: 1.94→49.24 Å / Num. obs: 77616 / % possible obs: 100 % / Redundancy: 39.3 % / CC_1/2: 1 / R_merge(I) obs: 0.152 / R_pim(I) all: 0.024 / R_rim(I) all: 0.154 / Net I/σ(I): 23.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.94-1.98	32.7	1.957	145969	4466	0.804	0.342	1.987	2.2	99.5
9.69-49.24	31.3	0.033	25358	809	1	0.006	0.033	87.5	99.4

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.29 Å	49.24 Å
Translation	7.29 Å	49.24 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.4	data scaling
PHASER	2.8.3	phasing
PHENIX	dev-3699	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6VH9

6vh9

Resolution: 1.94→49.24 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 21.19

	R_factor	Num. reflection	% reflection
R_free	0.2086	6997	4.88 %
R_work	0.1681	-	-
obs	0.1701	77403	99.93 %

Solvent computation

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

Displacement parameters

B_iso max: 99.45 Å² / B_iso mean: 37.8561 Å² / B_iso min: 15.44 Å²

Refinement step

Cycle: final / Resolution: 1.94→49.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8236	0	70	499	8805
B_iso mean	-	-	48.28	40.88	-
Num. residues	-	-	-	-	1020

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 (%)
1.94-1.96	0.332	186	0.2717	4456	4642	99
1.96-1.98	0.2672	194	0.2557	4606	4800	100
1.98-2.01	0.2903	223	0.2369	4527	4750	100
2.01-2.03	0.318	226	0.2394	4576	4802	100
2.03-2.06	0.2799	222	0.2285	4518	4740	100
2.06-2.09	0.2567	232	0.2232	4551	4783	100
2.09-2.12	0.297	216	0.2014	4621	4837	100
2.12-2.15	0.2296	251	0.1985	4480	4731	100
2.15-2.18	0.2799	216	0.2021	4608	4824	100
2.18-2.22	0.2507	214	0.187	4562	4776	100
2.22-2.26	0.2338	204	0.1839	4555	4759	100
2.26-2.3	0.2229	251	0.1802	4532	4783	100
2.3-2.34	0.2412	233	0.1785	4556	4789	100
2.34-2.39	0.2131	233	0.1755	4502	4735	100
2.39-2.44	0.2508	249	0.1788	4525	4774	100
2.44-2.5	0.2345	243	0.1727	4599	4842	100
2.5-2.56	0.2075	249	0.1785	4556	4805	100
2.56-2.63	0.2253	232	0.1738	4487	4719	100
2.63-2.71	0.2135	264	0.1753	4541	4805	100
2.71-2.8	0.2349	259	0.1788	4502	4761	100
2.8-2.9	0.2123	274	0.1775	4517	4791	100
2.9-3.01	0.2416	193	0.1783	4574	4767	100
3.01-3.15	0.245	256	0.1779	4519	4775	100
3.15-3.31	0.1937	234	0.1686	4531	4765	100
3.31-3.52	0.1929	234	0.1566	4560	4794	100
3.52-3.79	0.1827	207	0.1463	4596	4803	100
3.79-4.17	0.1886	240	0.1382	4537	4777	100
4.18-4.78	0.1393	267	0.1184	4476	4743	100
4.78-6.02	0.1658	265	0.1463	4521	4786	100
6.02-49.24	0.1995	230	0.1626	4549	4779	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	1.2358	0.1278	0.2841	1.6523	0.2165	3.3321	0.0739	0.0247	-0.0639	-0.0492	-0.096	0.0674	0.3642	-0.0309	0.0226	0.1425	0.0195	-0.0015	0.1609	0.0227	0.1915	-34.2697	25.8529	-10.1819
2	0.377	0.7166	-0.2346	6.2743	1.254	2.8889	0.1677	-0.3762	-0.1644	1.0385	-0.1305	-0.1928	0.6519	0.3434	-0.0423	0.4187	0.0276	-0.0279	0.3648	0.0798	0.2426	-28.9385	20.2389	8.3522
3	2.8903	0.8176	0.1687	4.3754	-2.3009	4.9899	0.1437	-0.1075	-0.4169	0.14	-0.2056	-0.1818	0.8483	0.2957	0.0554	0.4363	0.1007	-0.016	0.2045	0.0262	0.3006	-24.982	9.9793	-2.9588
4	4.6242	3.6044	-3.6388	4.4384	-1.0026	4.8776	-0.0206	0.2301	-0.0115	-0.2431	0.396	0.2554	-0.0029	-0.191	-0.3744	0.0875	0.0213	0.0105	0.2305	-0.0119	0.1926	-20.5056	43.4729	-10.1604
5	8.3922	-5.1764	-6.9722	7.4511	4.7796	8.0021	0.3427	0.648	0.9735	-0.9078	0.3763	-0.7956	-1.154	0.9873	-0.7634	0.4966	-0.2277	0.0605	0.5759	0.0305	0.3945	-10.2399	57.0384	-22.6715
6	2.1609	-0.321	1.1089	1.6481	-1.0471	5.0482	0.0678	0.0009	0.0472	0.0335	-0.0829	-0.0819	-0.3111	0.3108	0.0258	0.1264	-0.0135	0.012	0.1654	-0.0212	0.1826	-24.554	49.598	-5.2929
7	2.8468	-0.1173	-1.4416	3.1294	0.8563	4.9883	0.1144	-0.0811	0.2464	0.0879	0.0015	-0.2111	-0.7877	0.5074	-0.1145	0.2608	-0.0809	-0.0327	0.2149	0.0118	0.2143	-21.6715	58.234	-0.0552
8	4.3958	2.3735	2.81	5.8543	7.1687	8.8497	-0.2037	-0.6955	0.4745	0.1313	-0.3284	0.7795	-0.2211	-1.0683	0.5392	0.2993	-0.0279	0.0127	0.5189	-0.0552	0.3112	-35.8788	45.6259	11.1616
9	4.6488	6.839	-0.7876	2.147	-2.4457	2.1414	0.3819	-0.5526	-0.1459	0.9931	-0.3846	-0.5646	-0.4385	0.4921	-0.0012	0.4186	-0.0409	0.015	0.3321	-0.0454	0.3298	-24.8432	55.9384	16.8753
10	2.0553	0.4551	4.2228	4.8615	-1.2161	5.6546	-0.4102	-0.2406	0.6214	0.1611	0.1001	0.0162	-1.1184	0.2001	0.3291	0.5386	-0.0079	0.0354	0.2801	-0.0796	0.2334	-28.7443	64.3539	3.939
11	9.174	6.7665	5.9141	8.6623	1.4782	6.1156	-0.1191	-1.1909	1.2554	0.9265	-0.2565	0.6832	-1.0748	-0.8729	0.3674	0.6869	0.1629	0.0386	0.3709	-0.0992	0.4654	-33.25	67.6477	10.9202
12	9.782	5.2444	7.2766	7.331	3.2162	8.7786	-0.6697	-0.3134	1.2127	-0.54	-0.085	0.5549	-1.6564	-0.4214	0.7694	0.5351	0.1133	0.007	0.2986	-0.0527	0.4179	-34.3202	67.2347	1.1743
13	8.6823	4.031	-2.5033	2.0652	-1.7758	10.0053	-0.0343	0.0622	1.0901	-0.1368	-0.0943	0.2417	-1.3073	0.1676	0.097	0.4618	0.0356	-0.0609	0.1695	0.0226	0.3774	-30.5453	63.3459	-9.0463
14	1.6055	0.0724	-0.0478	1.2384	0.3708	1.674	0.0004	-0.0266	-0.0627	0.1624	0.1226	-0.1494	-0.0774	0.812	-0.1326	0.1622	0.0413	0.0105	0.5171	0.0124	0.2696	-14.0561	41.0618	-20.0668
15	8.4179	1.2247	-0.3612	6.942	-1.04	0.2953	-0.048	-0.4235	-0.3083	0.2195	-0.0064	-0.2086	0.2154	0.5539	0.0576	0.2148	0.148	0.0498	0.4553	-0.0008	0.1844	-14.1309	29.7058	-19.253
16	2.6323	-0.842	-0.2191	1.2723	0.0602	0.6139	0.0163	0.3303	0.095	-0.1143	0.082	-0.1717	-0.0527	0.7586	-0.1147	0.1645	0.0222	0.0256	0.6301	0.0168	0.2626	-9.9461	38.3823	-33.272
17	9.3959	1.9766	-8.8312	7.8278	-1.0839	8.4088	-0.7064	0.6483	-1.3096	-0.8128	-0.0821	-0.5044	0.932	0.4004	0.6985	0.3308	0.093	0.0262	0.5715	-0.0733	0.3865	-21.7567	29.2826	-46.6961
18	7.0943	-0.4183	-0.7825	2.6493	0.3661	3.4477	0.0566	1.0722	0.5161	-0.5671	0.0009	0.199	-0.1735	0.0907	-0.0918	0.2778	0.0913	0.1356	1.1115	0.01	0.2314	-6.7225	34.6997	-49.6388
19	6.1207	2.1649	0.7535	4.5366	-0.8711	1.1947	-0.0356	0.1288	-0.2715	-0.4525	-0.0072	-0.4878	0.316	0.7339	0.0007	0.2979	0.1774	0.0807	0.7574	-0.1125	0.2654	-4.4267	25.4997	-37.1271
20	6.7129	0.003	-1.773	1.6036	-0.2797	0.9154	0.3297	0.1859	-0.664	-0.2401	-0.0409	0.1015	0.713	0.5699	-0.0425	0.2921	0.3549	0.0503	0.8773	-0.1419	0.3172	-3.1617	20.2277	-39.3667
21	9.6566	2.5352	0.8848	5.8296	1.0953	3.7636	-0.0183	-0.1166	-0.6614	0.1313	0.1265	-0.6273	0.4318	0.8206	-0.1041	0.3157	0.2674	0.0373	0.7015	-0.0271	0.3022	-7.5366	23.8467	-24.3922
22	-0.0467	0.0814	0.2459	1.7169	-1.2433	2.6738	0.0975	0.0728	-0.012	0.1217	0.0064	0.1164	-0.0506	-0.2969	-0.1121	0.129	0.0524	-0.0159	0.294	0.0086	0.2568	-40.3157	37.7517	-21.7033
23	1.7688	1.4892	1.5724	3.956	1.3444	3.696	-0.003	-0.007	0.0823	0.1371	-0.1951	0.278	-0.3443	-0.3816	0.1948	0.192	0.0874	-0.0357	0.2446	0.0351	0.2569	-40.3835	48.672	-19.0777
24	1.7704	-0.4716	0.1872	1.4207	0.0905	1.6302	0.0213	0.1774	0.0408	-0.1181	-0.0377	0.1953	-0.2187	-0.3915	0.0123	0.1611	0.0926	-0.0324	0.315	0.0057	0.2155	-42.9873	42.2003	-34.6122
25	9.2416	0.6146	6.7795	8.7063	1.1549	5.0673	-0.5727	1.0701	1.0889	-0.8702	0.1243	0.3244	-1.5838	0.3648	0.4427	0.5391	0.0047	-0.0139	0.5811	0.1331	0.3291	-29.5159	52.0118	-45.0028
26	2.0349	2.0069	-5.3339	4.7123	-1.4353	5.0891	-0.0025	1.0668	-0.2189	-0.3568	-0.1159	-0.0471	-0.3468	-0.1505	0.1144	0.3705	0.1602	-0.0872	0.5319	-0.0211	0.2695	-44.2658	48.5968	-50.4214
27	5.4172	2.0758	2.787	7.0612	2.1381	5.4912	-0.0166	0.0495	0.2159	-0.7335	-0.285	0.2849	-0.7129	-0.4127	0.3103	0.3853	0.2214	-0.0601	0.3677	0.0834	0.2697	-49.1277	55.0589	-36.9284
28	9.4077	-0.7879	5.6088	1.0873	-1.5215	4.4695	0.0057	0.252	0.6766	-0.3044	-0.2864	-0.0091	-1.0465	-0.1838	0.3513	0.6509	0.3114	-0.0527	0.3882	0.0572	0.3801	-49.3387	61.0848	-38.4719
29	9.7116	1.6948	-0.0698	7.3213	-0.4947	5.2617	-0.1649	0.1733	0.7985	0.2632	0.0275	0.7764	-0.8209	-0.6392	0.0651	0.3749	0.1737	-0.0586	0.3106	0.0155	0.2609	-46.735	55.0773	-23.8369

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 -1 through 133 )	A	-1 - 133
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 134 through 189 )	A	134 - 189
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 190 through 253 )	A	190 - 253
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -1 through 24 )	B	-1 - 24
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 25 through 40 )	B	25 - 40
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 41 through 105 )	B	41 - 105
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 106 through 149 )	B	106 - 149
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 150 through 167 )	B	150 - 167
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 168 through 189 )	B	168 - 189
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 190 through 207 )	B	190 - 207
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 208 through 221 )	B	208 - 221
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 222 through 235 )	B	222 - 235
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 236 through 253 )	B	236 - 253
14	X-RAY DIFFRACTION	14	chain 'C' and (resid -1 through 53 )	C	-1 - 53
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 54 through 74 )	C	54 - 74
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 75 through 149 )	C	75 - 149
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 150 through 167 )	C	150 - 167
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 168 through 189 )	C	168 - 189
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 190 through 207 )	C	190 - 207
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 208 through 235 )	C	208 - 235
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 236 through 253 )	C	236 - 253
22	X-RAY DIFFRACTION	22	chain 'D' and (resid -1 through 53 )	D	-1 - 53
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 54 through 74 )	D	54 - 74
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 75 through 149 )	D	75 - 149
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 150 through 167 )	D	150 - 167
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 168 through 189 )	D	168 - 189
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 190 through 207 )	D	190 - 207
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 208 through 235 )	D	208 - 235
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 236 through 253 )	D	236 - 253

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