PDB-3r8y: Structure of the Bacillus anthracis tetrahydropicolinate succinyl...

ID or keywords:

Entry

Database: PDB / ID: 3r8y

Title

Structure of the Bacillus anthracis tetrahydropicolinate succinyltransferase

Components

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

Keywords

TRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / 2 domains- 3-Layer(aba) Sandwich and 3 Solenoid

Function / homology

Function and homology information

tetrahydrodipicolinate N-acetyltransferase / tetrahydrodipicolinate N-acetyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Structure of the Bacillus anthracis tetrahydropicolinate succinyltransferase
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 24, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3r8y.cif.gz	496 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3r8y_validation.pdf.gz	469.4 KB	Display	wwPDB validaton report
Full document	3r8y_full_validation.pdf.gz	483.6 KB	Display
Data in XML	3r8y_validation.xml.gz	63.7 KB	Display
Data in CIF	3r8y_validation.cif.gz	96.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/3r8y ftp://data.pdbj.org/pub/pdb/validation_reports/r8/3r8y	HTTPS FTP

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Related structure data

Related structure data	3cj8S S: Starting model for refinement
Similar structure data	6hff-1 4ubu-4 4h6d-4 6hfl-1 6hfe-1 4ubu-1 4h6d-1 4ubt-1 6hfd-1 3rhf-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
Other databases	TargetDB: IDP01143

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#165 - Sep 2013 Designed Protein Cages similarity (4) #49 - Jan 2004 Carbonic Anhydrase similarity (4) #39 - Mar 2003 lac Repressor similarity (5)

Deposited unit

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

B: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

C: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

D: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

E: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

F: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

hetero molecules

155 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

B: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

C: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

hetero molecules

defined by author&software
77.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

E: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

F: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

hetero molecules

defined by author&software
77.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.421, 52.219, 134.550
Angle α, β, γ (deg.)	97.41, 93.19, 115.71
Int Tables number	1
Space group name H-M	P1

#1: Protein	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase / Tetrahydrodipicolinate N-acetyltransferase / THP acetyltransferase / Tetrahydropicolinate acetylase Mass: 25734.873 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: dapH, BA_4194, GBAA_4194, BAS3891 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL References: UniProt: Q81MQ2, tetrahydrodipicolinate N-acetyltransferase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1728 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.83 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, 200mM Calcium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 110 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97857 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 17, 2011 / Details: beryllium lens

Radiation

Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. all: 143723 / Num. obs: 142717 / % possible obs: 99.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.3 / Redundancy: 5.7 % / R_merge(I) obs: 0.099 / Net I/σ(I): 13.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	% possible all
1.7-1.76	4.5	0.624	2.3	98.8
1.76-1.83	5.6	0.474	3.9	100
1.83-1.91	6	0.332	5.6	99.9
1.91-2.02	6	0.235	7.1	99.8
2.02-2.14	5.9	0.169	9.3	99.6
2.14-2.31	5.7	0.138	10.3	99.4
2.31-2.54	5.6	0.115	11.7	99.3
2.54-2.91	5.7	0.095	13.3	99.3
2.91-3.66	5.6	0.08	14.7	98.5
3.66-50	6	0.066	19.2	98.6

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Processing

Software

Name	Version	Classification
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
BLU-MAX		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MrBUMP/MolRep		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3CJ8

3cj8

Resolution: 1.7→29.406 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.23 / σ(F): 1.44 / Phase error: 22.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2209	6928	5.01 %
R_work	0.1862	-	-
obs	0.188	138207	99.31 %
all	-	139167	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 63.432 Å² / k_sol: 0.384 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.8711 Å²	4.2143 Å²	0.7143 Å²
2-	-	1.6205 Å²	-0.098 Å²
3-	-	-	0.2506 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→29.406 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9098	0	9	1728	10835

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9257
X-RAY DIFFRACTION	f_angle_d	1.12	12593
X-RAY DIFFRACTION	f_dihedral_angle_d	11.482	3417
X-RAY DIFFRACTION	f_chiral_restr	0.078	1550
X-RAY DIFFRACTION	f_plane_restr	0.004	1622

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 (%)
1.7-1.7193	0.3557	232	0.3027	4295	X-RAY DIFFRACTION	98
1.7193-1.7395	0.3168	227	0.2747	4509	X-RAY DIFFRACTION	100
1.7395-1.7608	0.2773	230	0.2565	4254	X-RAY DIFFRACTION	100
1.7608-1.783	0.3166	256	0.2476	4439	X-RAY DIFFRACTION	100
1.783-1.8065	0.2681	214	0.2412	4473	X-RAY DIFFRACTION	100
1.8065-1.8312	0.2818	238	0.2275	4313	X-RAY DIFFRACTION	100
1.8312-1.8574	0.2813	243	0.2088	4490	X-RAY DIFFRACTION	100
1.8574-1.8851	0.2399	216	0.198	4366	X-RAY DIFFRACTION	100
1.8851-1.9146	0.2383	238	0.1929	4358	X-RAY DIFFRACTION	100
1.9146-1.946	0.2538	219	0.1951	4414	X-RAY DIFFRACTION	100
1.946-1.9795	0.2405	251	0.1837	4357	X-RAY DIFFRACTION	100
1.9795-2.0155	0.2305	226	0.1738	4451	X-RAY DIFFRACTION	100
2.0155-2.0542	0.2329	224	0.1711	4360	X-RAY DIFFRACTION	99
2.0542-2.0962	0.1818	243	0.1637	4409	X-RAY DIFFRACTION	100
2.0962-2.1417	0.212	231	0.1716	4330	X-RAY DIFFRACTION	100
2.1417-2.1915	0.2	232	0.1788	4421	X-RAY DIFFRACTION	100
2.1915-2.2463	0.2149	231	0.1748	4339	X-RAY DIFFRACTION	99
2.2463-2.307	0.2137	226	0.1777	4386	X-RAY DIFFRACTION	99
2.307-2.3749	0.2158	230	0.1796	4402	X-RAY DIFFRACTION	99
2.3749-2.4515	0.241	239	0.1906	4314	X-RAY DIFFRACTION	99
2.4515-2.5391	0.2627	234	0.1876	4401	X-RAY DIFFRACTION	99
2.5391-2.6407	0.2329	220	0.1902	4410	X-RAY DIFFRACTION	100
2.6407-2.7608	0.2403	242	0.1934	4397	X-RAY DIFFRACTION	99
2.7608-2.9062	0.1922	241	0.1799	4333	X-RAY DIFFRACTION	99
2.9062-3.0881	0.2147	218	0.1804	4360	X-RAY DIFFRACTION	99
3.0881-3.3263	0.2323	221	0.185	4293	X-RAY DIFFRACTION	98
3.3263-3.6604	0.2126	231	0.1715	4348	X-RAY DIFFRACTION	99
3.6604-4.1888	0.1751	227	0.1561	4346	X-RAY DIFFRACTION	99
4.1888-5.2725	0.1665	231	0.1544	4333	X-RAY DIFFRACTION	98
5.2725-29.4108	0.2338	217	0.2317	4378	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	0.1081	0.1577	0.0207	0.4804	-0.1655	0.1734	0.0767	-0.4237	-0.1148	0.283	0.0465	-0.0035	0.0981	0.1127	-0.0521	0.2898	0.0837	-0.025	0.4572	0.0357	0.1839	-5.3905	25.8652	82.8353
2	0.0456	0.0054	-0.0081	0.1686	0.1107	0.1956	-0.0378	-0.0861	0.0425	0.0531	0.074	-0.1064	-0.0995	0.0708	-0.012	0.0729	-0.0059	-0.0027	0.1001	-0.0049	0.1172	-4.3453	36.3332	51.9515
3	0.1678	0.1573	-0.1208	0.5315	0.0331	0.4853	0.021	0.01	-0.0821	-0.0489	0.0234	-0.0876	-0.0205	0.1733	-0.0078	0.0645	-0.0162	0.0171	0.0902	0.0059	0.1011	-5.4762	31.0155	34.5587
4	0.0677	0.0016	0.0574	0.0852	0.0118	0.0514	-0.0104	-0.0451	-0.0229	0.0278	-0.0466	-0.0182	-0.0041	0.0099	0.022	0.4743	-0.1517	0.1586	0.4323	0.0326	0.3576	-31.1608	12.3851	66.1074
5	0.2576	-0.1038	0.0193	0.0555	-0.0105	0.0699	-0.0434	-0.4155	0.023	0.4647	0.0421	0.081	-0.0101	-0.2103	0.0031	0.3823	0.0531	0.0363	0.3679	0.0129	0.1418	-22.9437	38.3665	82.2613
6	0.0808	0.0443	-0.0613	0.1993	0.1282	0.2551	-0.0482	-0.1741	-0.2035	0.1749	0.063	0.0186	0.1157	0.0811	0.1385	0.143	0.0302	0.0177	0.1017	0.0834	0.1681	-14.4095	17.2546	59.3712
7	0.0383	-0.0163	0.0723	0.4186	-0.115	0.2222	-0.0126	-0.027	-0.1293	-0.0249	-0.0405	0.2483	0.1846	-0.0315	-0.0414	0.1215	0.029	0.0262	-0.0004	0.0371	0.2878	-19.3267	11.2771	43.1666
8	0.1342	0.1392	0.0471	0.1878	0.0437	0.0287	-0.083	-0.3925	0.0496	0.2386	0.1544	-0.0823	-0.3459	0.0823	-0.0101	0.3476	0.0259	-0.054	0.3557	-0.0646	0.1669	-3.8043	46.1623	76.7715
9	0.2966	0.0317	0.1846	0.2451	0.082	0.1493	-0.0524	-0.2009	0.0244	0.0744	0.05	0.1336	-0.0236	-0.0976	-0.0214	0.0829	0.0243	0.0244	0.0954	0.031	0.1147	-26.6268	35.9995	56.1537
10	0.2024	-0.1553	-0.0258	0.2384	-0.0092	0.1445	0.0425	0.0318	0.0109	-0.0069	-0.0432	0.0844	-0.0435	-0.0695	-0.0076	0.0723	0.0021	-0.0024	0.0814	0.0155	0.1367	-29.9492	33.344	38.6887
11	0.1159	0.1394	-0.0521	0.1989	-0.0521	0.0652	0.1103	0.2665	-0.0317	-0.4331	0.0267	0.118	0.0307	-0.1298	-0.0397	0.3913	0.1372	-0.048	0.4036	0.0131	0.1743	-31.1555	36.6938	-31.9656
12	0.1171	0.0131	-0.0361	0.0447	-0.0724	0.2152	0.0805	0.07	0.0811	-0.0422	-0.0401	0.0134	-0.1575	0.0296	0.0138	0.1224	0.0097	0.0045	0.0836	0.0057	0.1077	-22.1279	42.2365	-1.1296
13	0.065	0.0232	-0.1107	0.1	-0.0087	0.1792	0.074	-0.0064	0.018	0.0312	-0.0003	0.0901	-0.1677	-0.0328	0.0246	0.1191	-0.0048	0.0063	0.062	-0.0109	0.0991	-26.6788	39.0499	16.3768
14	0.0034	-0.0058	0.0013	0.0578	0.0206	0.0124	-0.0038	-0.0009	0.0032	0.0052	-0.0243	0.0327	0.011	-0.0095	0.0123	0.6043	-0.1781	0.0574	0.3842	-0.0984	0.4267	-32.3456	7.9193	-15.1529
15	0.3358	-0.0203	-0.0014	0.5001	0.0586	0.0142	-0.0031	0.5611	-0.0155	-0.4862	0.0251	-0.0242	0.1782	0.0299	-0.0001	0.3373	0.0422	0.0035	0.4288	-0.0366	0.1446	-12.2454	26.3592	-31.3958
16	0.049	0.0881	-0.0351	0.2061	-0.016	0.3032	0.0279	0.2088	-0.1123	-0.0623	0.0135	0.3217	-0.0973	-0.2425	0.1605	-0.017	-0.0132	-0.1295	0.1533	-0.0931	0.1416	-35.1786	25.0104	-8.4475
17	0.3285	0.0862	0.2408	0.031	0.0319	0.2805	0.0171	0.0005	-0.3233	-0.0193	-0.0717	0.1221	0.1742	-0.2878	-0.0238	0.0181	-0.0439	-0.0376	0.1213	-0.0378	0.3249	-38.1954	17.7764	7.5245
18	0.0242	0.0149	0.0208	0.027	-0.0129	0.0795	0.1472	0.3164	0.0479	-0.1989	-0.1086	-0.052	-0.1897	0.2024	0.0165	0.2989	0.0316	0.0301	0.3628	0.0687	0.1403	-13.4803	46.8709	-25.7932
19	0.096	-0.015	0.0296	0.1688	-0.0911	0.1925	0.0759	0.1617	-0.1136	-0.0881	-0.0619	-0.0355	0.0428	0.1101	-0.0147	0.0797	0.0167	-0.0148	0.115	-0.0352	0.1283	-12.7825	22.0927	-5.2242
20	0.2514	-0.234	-0.0028	0.2361	0.0335	0.1564	-0.0399	-0.0101	-0.085	0.0851	0.0243	-0.024	0.0436	0.0494	-0.0044	0.0794	0.0144	-0.015	0.0749	-0.0067	0.1607	-13.8738	17.6166	12.3472

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 16:77)
2	X-RAY DIFFRACTION	2	(chain A and resid 78:150)
3	X-RAY DIFFRACTION	3	(chain A and resid 151:220)
4	X-RAY DIFFRACTION	4	(chain B and resid 5:15)
5	X-RAY DIFFRACTION	5	(chain B and resid 16:77)
6	X-RAY DIFFRACTION	6	(chain B and resid 78:150)
7	X-RAY DIFFRACTION	7	(chain B and resid 151:217)
8	X-RAY DIFFRACTION	8	(chain C and resid 16:77)
9	X-RAY DIFFRACTION	9	(chain C and resid 78:150)
10	X-RAY DIFFRACTION	10	(chain C and resid 151:217)
11	X-RAY DIFFRACTION	11	(chain D and resid 17:77)
12	X-RAY DIFFRACTION	12	(chain D and resid 78:150)
13	X-RAY DIFFRACTION	13	(chain D and resid 151:219)
14	X-RAY DIFFRACTION	14	(chain E and resid 4:15)
15	X-RAY DIFFRACTION	15	(chain E and resid 16:77)
16	X-RAY DIFFRACTION	16	(chain E and resid 78:150)
17	X-RAY DIFFRACTION	17	(chain E and resid 151:216)
18	X-RAY DIFFRACTION	18	(chain F and resid 17:77)
19	X-RAY DIFFRACTION	19	(chain F and resid 78:150)
20	X-RAY DIFFRACTION	20	(chain F and resid 151:218)

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