PDB-4jn4: Allosteric opening of the polypeptide-binding site when an Hsp70 ...

ID or keywords:

Entry

Database: PDB / ID: 4jn4

Title

Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP

Components

Chaperone protein DnaK

Keywords

CHAPERONE / DnaK / 70kDa heat shock protein (Hsp70) / Single-wavelength anomalous diffraction (SAD) / native structure determination / multiple crystals

Function / homology

Function and homology information

stress response to copper ion / sigma factor antagonist activity / : / protein unfolding / cellular response to unfolded protein / inclusion body / heat shock protein binding / protein folding chaperone / ATP-dependent protein folding chaperone / ADP binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Native SAD / Resolution: 2.3 Å

Authors

Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. ...

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Allosteric opening of the polypeptide-binding site when an Hsp70 binds ATP.
Authors: Qi, R. / Sarbeng, E.B. / Liu, Q. / Le, K.Q. / Xu, X. / Xu, H. / Yang, J. / Wong, J.L. / Vorvis, C. / Hendrickson, W.A. / Zhou, L. / Liu, Q.

History

Deposition	Mar 14, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2013	Group: Database references
Revision 1.2	Aug 7, 2013	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _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	4jn4.cif.gz	486.7 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4jn4_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4jn4_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4jn4_validation.xml.gz	55.5 KB	Display
Data in CIF	4jn4_validation.cif.gz	82.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jn/4jn4 ftp://data.pdbj.org/pub/pdb/validation_reports/jn/4jn4	HTTPS FTP

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Related structure data

Related structure data	4jneC 4jnfC C: citing same article (ref.)
Similar structure data	4jne-d 6j5a-d 1xo0-d 5erg-1 1pvr-d 3tvw-2 5eqj-1 1pvp-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	#32 - Aug 2002 Chaperones similarity (11)

Deposited unit

A: Chaperone protein DnaK

B: Chaperone protein DnaK

hetero molecules

134 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	291.739, 291.739, 99.500
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-1324- HOH
2	1	A-1584- HOH
3	1	B-1450- HOH
4	1	B-1578- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Chaperone protein DnaK Mass: 65893.344 Da / Num. of mol.: 2 / Fragment: UNP residues 2-610 / Mutation: N432M,Q433G,S434G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8

#1: Protein

Chaperone protein DnaK

Mass: 65893.344 Da / Num. of mol.: 2 / Fragment: UNP residues 2-610 / Mutation: N432M,Q433G,S434G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Plasmid: pSMT / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y8

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Non-polymers , 5 types, 1105 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1086 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

Crystal	Density Matthews: 4.02 Å³/Da / Density % sol: 69.37 %
Crystal grow	Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8-2.0 M ammonium sulfate, 0.1 M Hepes-NaOH, 2-3% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.7432 Å
Detector	Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 15, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7432 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. all: 182234 / Num. obs: 182234 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.3→2.36 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure: Native SAD / Resolution: 2.3→39.85 Å / SU ML: 0.3 / σ(F): 1.22 / Phase error: 17.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1972	9119	5 %	Random
R_work	0.1621	-	-	-
obs	0.1639	182212	99.97 %	-
all	-	182234	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.52 Å² / k_sol: 0.37 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.4035 Å²	0 Å²	-0 Å²
2-	-	1.4035 Å²	-0 Å²
3-	-	-	-2.807 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→39.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9100	0	143	1086	10329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9338
X-RAY DIFFRACTION	f_angle_d	0.889	12630
X-RAY DIFFRACTION	f_dihedral_angle_d	13.922	3548
X-RAY DIFFRACTION	f_chiral_restr	0.055	1466
X-RAY DIFFRACTION	f_plane_restr	0.004	1652

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 (%)
2.3-2.3262	0.2526	303	0.201	5729	X-RAY DIFFRACTION	99
2.3262-2.3535	0.235	330	0.1853	5759	X-RAY DIFFRACTION	100
2.3535-2.3822	0.2156	293	0.1739	5780	X-RAY DIFFRACTION	100
2.3822-2.4124	0.2398	291	0.179	5793	X-RAY DIFFRACTION	100
2.4124-2.4441	0.2286	332	0.1836	5759	X-RAY DIFFRACTION	100
2.4441-2.4776	0.241	264	0.174	5742	X-RAY DIFFRACTION	100
2.4776-2.513	0.2158	269	0.1763	5812	X-RAY DIFFRACTION	100
2.513-2.5505	0.2172	300	0.1664	5810	X-RAY DIFFRACTION	100
2.5505-2.5903	0.229	275	0.1669	5800	X-RAY DIFFRACTION	100
2.5903-2.6328	0.2173	314	0.1675	5750	X-RAY DIFFRACTION	100
2.6328-2.6782	0.2346	318	0.1715	5775	X-RAY DIFFRACTION	100
2.6782-2.7269	0.2084	339	0.1678	5723	X-RAY DIFFRACTION	100
2.7269-2.7793	0.2258	308	0.1728	5731	X-RAY DIFFRACTION	100
2.7793-2.836	0.2542	271	0.1701	5844	X-RAY DIFFRACTION	100
2.836-2.8977	0.2086	280	0.1714	5779	X-RAY DIFFRACTION	100
2.8977-2.965	0.2128	325	0.1688	5747	X-RAY DIFFRACTION	100
2.965-3.0392	0.1936	289	0.1691	5769	X-RAY DIFFRACTION	100
3.0392-3.1213	0.2216	285	0.1686	5834	X-RAY DIFFRACTION	100
3.1213-3.2131	0.2197	331	0.1811	5778	X-RAY DIFFRACTION	100
3.2131-3.3168	0.2081	282	0.1746	5769	X-RAY DIFFRACTION	100
3.3168-3.4353	0.2206	314	0.1694	5742	X-RAY DIFFRACTION	100
3.4353-3.5727	0.1708	325	0.1614	5714	X-RAY DIFFRACTION	100
3.5727-3.7352	0.1779	331	0.1505	5757	X-RAY DIFFRACTION	100
3.7352-3.932	0.1664	333	0.1434	5769	X-RAY DIFFRACTION	100
3.932-4.1781	0.1505	308	0.1408	5759	X-RAY DIFFRACTION	100
4.1781-4.5003	0.168	317	0.1294	5733	X-RAY DIFFRACTION	100
4.5003-4.9524	0.1578	287	0.1282	5793	X-RAY DIFFRACTION	100
4.9524-5.6673	0.1748	331	0.1474	5748	X-RAY DIFFRACTION	100
5.6673-7.1335	0.2171	304	0.1856	5801	X-RAY DIFFRACTION	100
7.1335-39.8556	0.172	270	0.1698	5794	X-RAY DIFFRACTION	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	0.1067	-0.0732	0.006	0.057	-0.002	0.0022	-0.0521	0.0979	0.0187	-0.0533	-0.0307	-0.0261	0.0463	-0.0247	-0.0157	0.1137	0.0028	-0.0063	0.0963	0.0012	0.0519	19.3852	72.4654	15.8136
2	0.0531	-0.0364	0.0303	0.1148	-0.0519	0.2154	-0.0129	-0.0492	0.0537	0.0389	0.0177	-0.0775	-0.0513	-0.0645	0.005	0.1153	0.0263	-0.0505	0.1339	-0.0176	0.1524	11.6749	90.8359	21.7084
3	0.0807	-0.0303	-0.0947	0.036	-0.0155	0.2042	-0.0856	0.0567	0.0109	0.0049	0.0549	0.0288	0.0541	-0.015	-0.0249	0.0864	-0	-0.0345	0.1683	0.017	0.021	9.0199	73.0289	16.3502
4	0.0115	0.0007	0.0004	0.0038	-0.0003	0	-0.0011	0.007	-0.0043	-0.0121	-0.0045	-0.0214	0.0161	0.009	0.007	0.4848	0.095	0.0689	0.3479	0.0672	0.3617	11.3218	51.0607	34.4201
5	0.0753	-0.01	-0.0411	0.0839	-0.0418	0.1142	-0.0719	-0.0183	-0.0069	0.0482	-0.0011	-0.0095	0.0248	0.0255	-0.0639	0.1681	0.0588	-0.0148	0.1251	0.0223	0.0236	6.618	62.8205	34.4946
6	0.1271	0.0955	0.026	0.1456	0.1866	0.3849	-0.0549	-0.1231	0.0431	0.0604	0.0019	-0.0133	0.1111	-0.0842	0.0153	0.1614	0.0745	-0.0245	0.1395	-0.0287	0.1099	11.9851	78.9842	35.2851
7	0.0616	-0.0317	-0.0402	0.1918	0.1197	0.3018	0.0178	-0.0052	0.0119	0.0058	0.0078	-0.0076	-0.0018	0.0315	-0.0135	0.2127	0.0038	-0.0333	0.2106	-0.158	0.2697	26.8566	102.1963	38.583
8	0.0272	-0.0154	-0.0214	0.0167	0.0205	0.0431	0.0215	-0.0116	0.0132	0.0774	0.0804	-0.102	0.0629	0.0922	0.1624	0.1129	0.0598	-0.1534	0.1718	-0.2095	0.1079	28.1702	90.4443	36.5994
9	0.1436	-0.046	-0.0066	0.0417	0.0336	0.0478	-0.1173	-0.1415	-0.0525	0.1405	0.0584	0.049	0.0994	-0.0822	-0.0004	0.1925	0.0729	0.0081	0.1768	-0.0127	0.0329	8.1527	66.7088	35.6636
10	0.0069	0.0067	-0.0075	0.0661	-0.0122	0.0392	-0.0907	-0.0102	0.0349	-0.034	0.0652	-0.001	0.0572	-0.1137	0.0064	0.0962	-0.0277	-0.0274	0.2667	-0.0102	0.0773	-18.218	77.0206	22.9962
11	0.031	-0.0118	0.0571	0.0417	0.0316	0.2272	-0.0018	0.0465	0.0062	-0.0322	-0.007	-0.0086	-0.0585	0.0356	0.0268	0.1269	-0.027	-0.0779	0.1998	0.0451	0.0489	5.1785	83.3403	4.5862
12	0.1732	0.0786	-0.0243	0.2395	0.1005	0.0666	0.0358	-0.0366	-0.0531	0.0427	0.0822	-0.0119	0.0033	-0.1566	0.045	0.1547	-0.0217	-0.0339	0.2462	0.0607	0.0887	40.0443	81.5104	-5.2228
13	0.0398	-0.1592	0.0122	0.8426	0.2878	0.6043	0.1557	0.0308	0.0748	-0.0536	-0.0292	-0.2077	-0.1333	-0.0715	-0.1051	0.2343	-0.0293	0.0037	0.1136	0.0677	0.1948	45.8543	89.1559	-11.2853
14	0.1278	-0.0067	-0.0472	0.1395	-0.1032	0.1085	0.1193	0.0235	0.0759	-0.0784	0.0569	-0.3445	-0.0895	0.073	-0.1632	0.4919	-0.0186	0.0961	0.386	-0.0655	0.5268	52.0547	80.583	-23.5659
15	0.1831	-0.1152	-0.1992	0.0721	0.1254	0.2247	-0.1122	-0.0471	-0.0037	0.0786	-0.0407	0.0337	-0.0481	-0.1124	-0.0327	0.1686	0.009	-0.0411	0.0843	0.0072	0.0704	37.1574	64.506	33.6753
16	0.0271	-0.002	0.007	0.0078	-0.0112	0.0157	-0.0734	0.0313	0.0528	0.0161	-0.0288	-0.0401	-0.1495	0.0641	-0.1922	0.2379	-0.1234	-0.2246	0.1169	0.0564	0.0059	55.3495	72.6178	28.4329
17	0.211	-0.0277	-0.093	0.0447	0.0408	0.079	-0.1021	-0.0009	-0.0314	0.0674	-0.023	-0.0395	-0.0715	-0.0341	-0.0626	0.1265	0.0216	-0.028	0.0878	0.0093	0.0561	45.0889	57.6231	33.3967
18	0.0054	-0.0028	-0.0026	0.0015	0.0014	0.0012	-0.0002	0.0012	0.001	-0.0041	0.0008	0.0033	0.0001	0.0036	0.0002	0.3598	-0.1433	0.0079	0.5162	-0.1094	0.3791	26.8241	45.4541	18.8119
19	0.0714	0.036	0.0613	0.098	0.0507	0.1389	-0.03	0.0312	-0.0033	0.0078	-0.0253	-0.0096	0.033	-0.0116	0.0043	0.1066	-0.0522	-0.0082	0.1192	-0.0003	0.0535	40.3353	51.5527	13.7288
20	2.783	0.9239	0.6491	0.3202	0.3223	0.9982	-0.0037	0.0065	-0.2839	0.0546	-0.0357	-0.0567	0.2805	-0.0943	0.0308	0.6012	-0.1064	0.1032	0.4478	-0.0474	0.45	32.0062	35.1029	20.6627
21	0.1088	-0.0224	-0.0613	0.0125	0.0393	0.1238	-0.0859	0.0639	0.0549	-0.0069	-0.0189	0.0008	-0.0498	0.0247	-0.2348	0.132	-0.0812	-0.0768	0.0908	0.0663	0.0531	48.7756	69.3454	12.8781
22	0.0266	0.0168	0.0208	0.0095	0.0084	0.0102	-0.0588	0.0038	0.0587	0.0949	-0.0455	-0.0617	-0.1176	0.0551	-0.1948	0.315	-0.0932	-0.2057	0.0801	0.0895	0.0408	45.0318	88.0015	15.0658
23	0.1168	0.0093	-0.0405	0.031	-0.0037	0.0235	-0.054	0.0754	-0.0471	0.0213	-0.0512	0.0014	-0.054	-0.004	-0.0139	0.1083	-0.0333	-0.0134	0.1084	-0.0203	0.0727	39.9089	59.4883	9.1717
24	0.0712	-0.0236	-0.0612	0.1235	0.0966	0.1355	-0.0186	0.072	0.0158	0.0753	-0.0063	-0.0281	0.2177	0.0562	-0.0522	0.1276	0.0594	-0.0306	0.1276	0.0542	0.0479	63.4802	41.4118	26.1612
25	0.1514	-0.0587	-0.0322	0.0716	-0.0038	0.0521	-0.0249	-0.0474	0.0041	0.0286	0.004	-0.0188	-0.081	-0.0177	-0.0225	0.1862	0.0151	-0.0877	0.1402	0.0452	0.1064	57.5234	61.0237	42.7753
26	0.0789	-0.0095	-0.0207	0.1624	-0.149	0.2133	0.0497	0.0433	-0.0367	0.0385	0.051	0.0193	0.0291	0.0546	0.0872	0.3607	0.1253	-0.1125	0.2423	-0.047	0.1353	29.5649	86.2818	54.5128
27	0.4663	0.5318	0.056	0.6199	-0.0479	0.9783	0.1273	-0.0865	0.1362	-0.0949	0.0213	0.0814	-0.0993	0.2101	-0.139	0.3344	-0.0761	0.0193	0.2447	-0.0936	0.2373	30.7929	95.957	60.3929
28	0.182	-0.0668	-0.0191	0.7	0.1827	0.2402	0.0694	-0.0542	0.1165	0.0664	-0.005	0.1466	-0.1085	-0.0008	-0.0525	0.7161	-0.0589	0.1579	0.6534	-0.0071	0.7732	20.5347	93.6209	72.4743

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:51)
2	X-RAY DIFFRACTION	2	(chain A and resid 52:105)
3	X-RAY DIFFRACTION	3	(chain A and resid 106:181)
4	X-RAY DIFFRACTION	4	(chain A and resid 182:188)
5	X-RAY DIFFRACTION	5	(chain A and resid 189:213)
6	X-RAY DIFFRACTION	6	(chain A and resid 214:241)
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8	X-RAY DIFFRACTION	8	(chain A and resid 254:315)
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10	X-RAY DIFFRACTION	10	(chain A and resid 405:505)
11	X-RAY DIFFRACTION	11	(chain A and resid 506:525)
12	X-RAY DIFFRACTION	12	(chain A and resid 526:554)
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17	X-RAY DIFFRACTION	17	(chain B and resid 108:180)
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20	X-RAY DIFFRACTION	20	(chain B and resid 209:214)
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27	X-RAY DIFFRACTION	27	(chain B and resid 555:595)
28	X-RAY DIFFRACTION	28	(chain B and resid 596:604)

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