PDB-4v0w: The crystal structure of mouse PP1G in complex with truncated hum...

ID or keywords:

Entry

Database: PDB / ID: 4v0w

Title

The crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-669)

Components

PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

Keywords

HYDROLASE/HYDROLASE REGULATOR / HYDROLASE-HYDROLASE REGULATOR COMPLEX

Function / homology

Function and homology information

Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids ...
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Chen, R. / Yan, Y. / Casado, A.C. / Ron, D. / Read, R.J.

Citation

Journal: Elife / Year: 2015
Title: G-actin provides substrate-specificity to eukaryotic initiation factor 2 alpha holophosphatases.
Authors: Chen, R. / Rato, C. / Yan, Y. / Crespillo-Casado, A. / Clarke, H.J. / Harding, H.P. / Marciniak, S.J. / Read, R.J. / Ron, D.

History

Deposition	Sep 18, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2019	Group: Data collection / Database references / Other Category: citation / pdbx_database_proc / pdbx_database_status Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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	4v0w.cif.gz	278.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4v0w.ent.gz	227.4 KB	Display	PDB format
PDBx/mmJSON format	4v0w.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4v0w_validation.pdf.gz	446.3 KB	Display	wwPDB validaton report
Full document	4v0w_full_validation.pdf.gz	447.8 KB	Display
Data in XML	4v0w_validation.xml.gz	29.4 KB	Display
Data in CIF	4v0w_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/4v0w ftp://data.pdbj.org/pub/pdb/validation_reports/v0/4v0w	HTTPS FTP

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Related structure data

Related structure data	4v0uC 4v0vC 4v0xC C: citing same article (ref.)
Similar structure data	4v0u-1 4v0u-3 4v0v-1 4v0u-4 5yqt-1 1ah0-d 4mhb-6 3amc-1 6czo-1 5j28-2 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	#176 - Aug 2014 Dynein similarity (6) #166 - Oct 2013 Proteasome similarity (1) #225 - Sep 2018 Phytase similarity (3)

Deposited unit

A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

1

A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

2

C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.010, 67.860, 156.750
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT Mass: 33921.035 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-300 Source method: isolated from a genetically manipulated source Details: TRUNCATED MOUSE PP1G INCLUDING RESIDUES OF 7- 300 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21 (bacteria) References: UniProt: P63087, protein-serine/threonine phosphatase
#2: Protein/peptide	PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B Mass: 5148.678 Da / Num. of mol.: 2 / Fragment: RESIDUES 631-669 Source method: isolated from a genetically manipulated source Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-669 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SWA1
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H₂O
Nonpolymer details	MN A301 AND O A302 ARE MODELLED AS ALTERNATE CONFORMERS MN C301 AND O C302 ARE MODELLED AS ...MN A301 AND O A302 ARE MODELLED AS ALTERNATE CONFORMERS MN C301 AND O C302 ARE MODELLED AS ALTERNATE CONFORMERS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.64 Å³/Da / Density % sol: 53.49 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 3 M NACL, 0.1 M HEPES, PH7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.55→33.94 Å / Num. obs: 96347 / % possible obs: 92.6 % / Observed criterion σ(I): 1.8 / Redundancy: 5.1 % / R_merge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.9_1692)	refinement
MOSFLM		data reduction
Aimless		data scaling
CCP4I		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: THE CRYSTAL STRUCTURE OF MOUSE PP1G IN COMPLEX WITH TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-660

Resolution: 1.55→33.936 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2029	4800	5 %
R_work	0.1727	-	-
obs	0.1743	96347	92.32 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.55→33.936 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5047	0	4	609	5660

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5204
X-RAY DIFFRACTION	f_angle_d	1.053	7029
X-RAY DIFFRACTION	f_dihedral_angle_d	12.443	1955
X-RAY DIFFRACTION	f_chiral_restr	0.042	753
X-RAY DIFFRACTION	f_plane_restr	0.004	915

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 (%)
1.55-1.5676	0.2767	175	0.2529	3236	X-RAY DIFFRACTION	99
1.5676-1.5861	0.2792	155	0.2497	3243	X-RAY DIFFRACTION	99
1.5861-1.6054	0.2516	152	0.2349	3241	X-RAY DIFFRACTION	99
1.6054-1.6257	0.2477	160	0.2259	3270	X-RAY DIFFRACTION	99
1.6257-1.6471	0.2464	192	0.2221	3246	X-RAY DIFFRACTION	99
1.6471-1.6697	0.2592	174	0.2099	3254	X-RAY DIFFRACTION	100
1.6697-1.6935	0.2288	191	0.2083	3177	X-RAY DIFFRACTION	99
1.6935-1.7188	0.2288	170	0.2008	3277	X-RAY DIFFRACTION	100
1.7188-1.7457	0.2227	153	0.1923	3283	X-RAY DIFFRACTION	100
1.7457-1.7743	0.2372	160	0.1862	3263	X-RAY DIFFRACTION	100
1.7743-1.8049	0.2486	156	0.1851	3284	X-RAY DIFFRACTION	100
1.8049-1.8377	0.2203	173	0.1798	3287	X-RAY DIFFRACTION	100
1.8377-1.8731	0.2391	186	0.184	3247	X-RAY DIFFRACTION	99
1.8731-1.9113	0.2365	108	0.2082	1962	X-RAY DIFFRACTION	60
1.9113-1.9528	0.2458	81	0.2055	1401	X-RAY DIFFRACTION	48
1.9528-1.9983	0.1813	135	0.1643	2420	X-RAY DIFFRACTION	100
1.9983-2.0482	0.1905	168	0.1672	3262	X-RAY DIFFRACTION	100
2.0482-2.1036	0.171	128	0.1613	2302	X-RAY DIFFRACTION	70
2.1036-2.1655	0.2004	171	0.158	3306	X-RAY DIFFRACTION	100
2.1655-2.2354	0.1912	163	0.1757	3265	X-RAY DIFFRACTION	99
2.2354-2.3152	0.2339	131	0.1982	2257	X-RAY DIFFRACTION	69
2.3152-2.4079	0.1786	186	0.1631	3294	X-RAY DIFFRACTION	100
2.4079-2.5175	0.2229	169	0.1633	3314	X-RAY DIFFRACTION	100
2.5175-2.6502	0.2042	167	0.1714	3315	X-RAY DIFFRACTION	100
2.6502-2.8161	0.2348	117	0.1814	2868	X-RAY DIFFRACTION	85
2.8161-3.0334	0.187	180	0.1721	3313	X-RAY DIFFRACTION	100
3.0334-3.3385	0.1946	180	0.1649	3346	X-RAY DIFFRACTION	99
3.3385-3.821	0.1788	160	0.1479	2843	X-RAY DIFFRACTION	85
3.821-4.8118	0.1663	161	0.1366	3218	X-RAY DIFFRACTION	94
4.8118-33.9436	0.1946	198	0.1741	3553	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	4.331	2.2608	-1.544	6.1386	-0.6183	4.1269	-0.199	0.4142	-0.1619	-0.4406	0.1309	0.0896	0.01	-0.0918	0.0506	0.1727	0.0184	-0.0862	0.2728	-0.0385	0.1786	4.0555	80.2407	-4.8006
2	1.6168	-0.3692	-0.0445	1.7324	0.2049	1.537	0.0566	0.0713	-0.0575	-0.1097	0.0128	0.1169	0.0514	-0.1334	-0.0481	0.0739	-0.0068	-0.0379	0.1305	0.028	0.1168	8.4564	88.3642	6.386
3	1.0408	-0.3731	0.142	1.5866	0.3309	1.4626	0.0267	0.055	-0.0985	-0.0342	0.0648	-0.0339	0.1348	0.1247	-0.0926	0.0586	-0.0124	-0.0204	0.1264	0.0041	0.1227	14.791	84.748	8.2188
4	2.282	0.1361	-0.681	2.1857	-0.1495	3.5812	-0.0136	-0.2386	0.1335	0.1945	0.1201	-0.2058	-0.0897	0.3604	-0.0712	0.0822	0.0061	-0.0418	0.1591	-0.0405	0.1399	20.1768	92.5057	23.8064
5	3.4569	-2.5727	-0.3249	4.7791	0.1974	3.846	-0.2159	-0.3036	0.0489	0.3237	0.2099	0.104	-0.0943	-0.0453	0.0163	0.093	0.0158	-0.0303	0.1776	-0.0318	0.1019	14.9279	93.4277	31.9345
6	2.6605	1.1049	0.2142	5.0377	1.8733	3.295	-0.1216	-0.3495	-0.0693	0.2322	0.0756	0.4021	0.0463	-0.4694	0.0984	0.0737	0.0226	0.0026	0.2354	0.0503	0.1844	3.1705	91.2238	24.761
7	3.3617	2.1904	-0.0959	3.3597	1.5283	2.8996	0.0837	-0.1054	-0.3884	-0.09	-0.1103	0.422	0.2483	-0.3951	0.0111	0.1245	-0.0212	-0.034	0.298	0.0621	0.3009	-3.0783	88.0098	17.6991
8	2.0034	4.1152	-1.1677	8.996	-3.5021	8.7965	-0.2618	0.0025	0.2862	0.3376	-0.0145	-0.0972	-0.3367	0.1414	0.3085	0.2305	0.1337	-0.0122	0.4223	0.0304	0.3913	-0.6517	105.6457	22.5402
9	5.9634	5.5427	3.0571	7.4328	1.4696	2.3908	-0.107	-0.9731	0.5174	0.0949	-0.5196	2.0538	-0.2529	-1.7129	0.5813	0.2575	0.0495	-0.0289	0.8065	0.0148	0.6115	-10.9979	95.9486	20.8287
10	3.0791	-2.3145	-1.2854	1.7593	1.1854	3.7152	0.0308	-0.397	-0.2463	0.1686	-0.3015	0.438	0.4583	-0.7731	0.2549	0.399	-0.2151	-0.1571	0.7696	0.1557	0.9835	-11.1343	82.7685	14.6758
11	0.9391	0.051	0.5873	2.383	-0.8716	0.7802	-0.0428	-0.4352	-0.0806	0.5242	0.0812	0.3464	0.3403	-0.4207	-0.4575	0.9207	-0.0666	0.1499	0.3084	0.1279	0.0844	29.057	59.004	46.2266
12	2.1989	-0.2491	-0.1832	2.0931	-0.1118	2.1981	0.077	-0.0526	-0.0064	0.2833	0.0059	0.0255	-0.0883	0.0493	-0.0699	0.1868	-0.0321	-0.0168	0.0876	0.0234	0.0815	35.8682	60.5084	33.0187
13	2.3022	-0.4286	0.2712	1.8965	-0.8722	2.5699	0.074	-0.0973	0.0126	0.2422	0.0777	0.1933	-0.2455	-0.2398	-0.1382	0.1907	-0.0033	0.0222	0.0765	0.0095	0.0942	29.1745	66.3159	32.797
14	5.2592	-2.3546	-2.9189	3.4478	1.4337	4.1411	0.1738	-0.1015	0.3019	0.125	0.0494	-0.1471	-0.4591	0.1067	-0.214	0.1771	-0.017	-0.0186	0.084	0.026	0.09	37.3925	68.983	28.1592
15	2.1415	0.6164	-0.598	3.4985	1.2336	3.8292	0.191	0.1009	0.2646	0.0482	-0.0476	-0.2134	-0.7263	0.2819	-0.1281	0.2793	-0.0561	0.0278	0.1601	0.0485	0.1949	41.8412	74.4769	17.927
16	4.4676	-1.0376	-1.2951	3.0388	-0.1689	3.7795	0.1216	0.2013	-0.0593	-0.3667	-0.0964	0.0235	-0.0875	0.0363	-0.0291	0.1755	-0.0103	0.0147	0.0786	0.0231	0.0963	37.841	65.6405	8.0825
17	4.3433	-0.0657	-2.1445	3.1004	-0.3457	4.4836	-0.0031	0.1069	-0.2309	-0.2849	-0.0893	-0.0229	0.3274	0.0657	0.0839	0.1611	0.014	-0.0313	0.0869	0.0037	0.1021	38.1736	54.6581	15.0785
18	1.8238	1.9935	-1.5897	3.8122	0.0248	3.4266	0.0295	0.0185	-0.1697	-0.0477	-0.0759	0.3156	0.2331	-0.1412	0.0139	0.1771	-0.011	-0.0316	0.0912	0.0027	0.1763	34.6103	48.5121	22.6064
19	4.8409	4.3804	-4.6783	5.0237	-3.296	5.6174	-0.4251	0.3837	-0.8154	-0.3626	-0.0687	-0.409	0.7009	-0.0724	0.3504	0.2586	0.0243	-0.0141	0.1703	-0.0181	0.3002	40.6064	43.6583	21.2238
20	1.8078	-0.3107	0.9455	2.8235	-2.8469	6.6874	-0.0977	0.7206	-0.8936	0.7891	1.0153	2.4033	0.5864	-1.9653	-0.8742	0.7756	-0.3254	0.1951	1.3404	-0.0277	0.8103	17.6965	50.3954	29.0975

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 31 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 32 THROUGH 99 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 100 THROUGH 172 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 173 THROUGH 215 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 216 THROUGH 239 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 240 THROUGH 271 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 272 THROUGH 300 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 639 THROUGH 643 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 644 THROUGH 648 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 649 THROUGH 653 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 6 THROUGH 31 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 32 THROUGH 99 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 100 THROUGH 145 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 146 THROUGH 172 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 173 THROUGH 199 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 200 THROUGH 238 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 239 THROUGH 271 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 272 THROUGH 300 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 639 THROUGH 653 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 654 THROUGH 660 )

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Feb 9, 2022. New format data for meta-information of EMDB entries

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