PDB-2yey: Crystal structure of the allosteric-defective chaperonin GroEL E4...

ID or keywords:

Entry

Database: PDB / ID: 2yey

Title

Crystal structure of the allosteric-defective chaperonin GroEL E434K mutant

Components

60 KDA CHAPERONIN

Keywords

CHAPERONE / CHAPERONIN / COOPERATIVITY / TWINNING / LOW-RESOLUTION REFINEMENT

Function / homology

Function and homology information

GroEL-GroES complex / chaperonin ATPase / virion assembly / ATP-dependent protein folding chaperone / response to radiation / protein refolding / response to heat / protein folding / magnesium ion binding / ATP hydrolysis activity ...
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.5 Å

Authors

Cabo-Bilbao, A. / Mechaly, A.E. / Agirre, J. / Spinelli, S. / Sot, B. / Muga, A. / Guerin, D.M.A.

Citation

Journal: J.Struct.Biol. / Year: 2006
Title: Crystal Structure of the Temperature-Sensitive and Allosteric-Defective Chaperonin Groele461K.
Authors: Cabo-Bilbao, A. / Spinelli, S. / Sot, B. / Agirre, J. / Mechaly, A.E. / Muga, A. / Guerin, D.M.A.

History

Deposition	Mar 31, 2011	Deposition site: PDBE / Processing site: PDBE
Supersession	May 18, 2011	ID: 3FBH
Revision 1.0	May 18, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2014	Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yey.cif.gz	2.6 MB	Display	PDBx/mmCIF format
PDB format	pdb2yey.ent.gz	2.2 MB	Display	PDB format
PDBx/mmJSON format	2yey.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ye/2yey ftp://data.pdbj.org/pub/pdb/validation_reports/ye/2yey	HTTPS FTP

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Related structure data

Related structure data	2eu1C 1xckS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5opw-d 2ynj-d 5w0s-d 4hel-d 4wsc-d 1oel-1 6kfv-d 1xck-d 2nwc-d 3e76-d 4wgl-d 4v43-2 3c9v-d 1ss8-1 4v43-1 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: 60 KDA CHAPERONIN

B: 60 KDA CHAPERONIN

C: 60 KDA CHAPERONIN

D: 60 KDA CHAPERONIN

E: 60 KDA CHAPERONIN

F: 60 KDA CHAPERONIN

G: 60 KDA CHAPERONIN

H: 60 KDA CHAPERONIN

I: 60 KDA CHAPERONIN

J: 60 KDA CHAPERONIN

K: 60 KDA CHAPERONIN

L: 60 KDA CHAPERONIN

M: 60 KDA CHAPERONIN

N: 60 KDA CHAPERONIN

773 kDa, 14 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)	171.908, 171.908, 454.592
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	60 KDA CHAPERONIN / GROEL PROTEIN / PROTEIN CPN60 Mass: 55220.172 Da / Num. of mol.: 14 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: POF39 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6F5
Sequence details	RESIDUE 1 IS AN INITIATOR METHIONINE AND IS REMOVED.

#1: Protein

60 KDA CHAPERONIN / GROEL PROTEIN / PROTEIN CPN60

Mass: 55220.172 Da / Num. of mol.: 14 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: POF39 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A6F5

Sequence details

RESIDUE 1 IS AN INITIATOR METHIONINE AND IS REMOVED.

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 5 Å³/Da / Density % sol: 75.5 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
Detector	Type: ADSC QUANTUM 210 / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection twin	Operator: h,-h-k,-l / Fraction: 0.5
Reflection	Resolution: 4.5→20 Å / Num. obs: 87597 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / R_merge(I) obs: 0.15 / Net I/σ(I): 6
Reflection shell	Resolution: 4.5→4.74 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XCK

1xck

Resolution: 4.5→19.992 Å / σ(F): 0.93 / Phase error: 22.75 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2397	4012	2.4 %
R_work	0.1669	-	-
obs	0.1653	87551	96.44 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 99 Å² / k_sol: 0.316 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-8.2812 Å²	0 Å²	0 Å²
2-	-	-8.2812 Å²	0 Å²
3-	-	-	16.5623 Å²

Refinement step

Cycle: LAST / Resolution: 4.5→19.992 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	53984	0	0	0	53984

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.029	57208
X-RAY DIFFRACTION	f_angle_d	2.298	73416
X-RAY DIFFRACTION	f_dihedral_angle_d	15.014	20524
X-RAY DIFFRACTION	f_chiral_restr	0.111	8932
X-RAY DIFFRACTION	f_plane_restr	0.013	9618

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 (%)
4.5021-4.5788	0.2802	192	0.2362	8259	X-RAY DIFFRACTION	95
4.5788-4.661	0.279	198	0.2308	8412	X-RAY DIFFRACTION	95
4.661-4.7495	0.2892	199	0.2198	8232	X-RAY DIFFRACTION	95
4.7495-4.8451	0.3098	191	0.2146	8298	X-RAY DIFFRACTION	95
4.8451-4.9489	0.2618	210	0.2144	8343	X-RAY DIFFRACTION	95
4.9489-5.0622	0.2494	197	0.2069	8527	X-RAY DIFFRACTION	95
5.0622-5.1866	0.2759	207	0.2145	8202	X-RAY DIFFRACTION	95
5.1866-5.3243	0.2875	197	0.2101	8345	X-RAY DIFFRACTION	95
5.3243-5.4779	0.3093	192	0.2077	8318	X-RAY DIFFRACTION	95
5.4779-5.6508	0.2887	186	0.2086	8331	X-RAY DIFFRACTION	95
5.6508-5.8479	0.2867	176	0.1981	8393	X-RAY DIFFRACTION	95
5.8479-6.0757	0.3191	180	0.1962	8298	X-RAY DIFFRACTION	95
6.0757-6.3438	0.2779	191	0.1905	8309	X-RAY DIFFRACTION	94
6.3438-6.6665	0.2635	199	0.1737	8260	X-RAY DIFFRACTION	94
6.6665-7.0668	0.208	198	0.1514	8299	X-RAY DIFFRACTION	94
7.0668-7.5846	0.171	207	0.1343	8210	X-RAY DIFFRACTION	94
7.5846-8.2979	0.1927	177	0.1121	8269	X-RAY DIFFRACTION	94
8.2979-9.3882	0.1392	221	0.0859	8195	X-RAY DIFFRACTION	93
9.3882-11.4462	0.1782	187	0.0906	8241	X-RAY DIFFRACTION	93
11.4462-19.9919	0.3505	195	0.1708	8025	X-RAY DIFFRACTION	92

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	0.3455	-0.1599	-0.1202	0.0572	0.2847	0.8417	-0.0152	-0.0368	-0.097	-0.0616	-0.1391	0.1391	0.272	0.0089	0.0594	0.9744	-0.1431	0.0413	0.8018	-0.0421	1.0112	-17.432	-33.1811	-35.0454
2	0.7964	-0.0696	0.3841	0.4181	-0.3866	0.5052	-0.4535	-0.1636	-0.5613	-0.5233	0.1483	-0.231	-0.2343	0.0606	0.1439	1.2829	-0.0441	0.3592	0.8308	0.0583	1.5941	-21.9994	-62.1402	-22.2359
3	0.1955	0.2255	-0.0266	0.6661	-0.1958	0.1005	0.225	0.2104	-0.0258	0.0188	-0.0712	-0.2592	-0.2565	-0.0482	-0.0462	1.0572	-0.0237	0.4134	0.7585	-0.1167	1.3325	-18.5045	-63.0443	-51.3527
4	0.0996	0.0767	-0.1004	0.0143	0.0068	0.0081	0.307	0.0267	-0.4174	-0.1691	0.2593	0.0609	0.0875	-0.041	-0.0278	0.9921	0.1465	0.2349	0.8222	-0.2485	1.1916	-15.7202	-69.7859	-52.3384
5	0.434	0.313	-0.1614	0.039	0.089	0.0062	-0.1874	-0.1601	-0.5966	0.1794	-0.3303	0.3358	-0.0045	0.0748	0.3281	1.2144	0.061	0.0154	0.7505	-0.1766	1.3979	-12.7106	-54.1237	-28.1756
6	0.1401	0.0391	0.1258	0.6303	0.3213	0.2267	-0.1825	-0.136	0.0057	0.4876	-0.1817	0.0261	-0.3313	0.0058	0.1006	1.1247	-0.1911	0.0901	0.6782	0.0068	0.4529	-22.6027	-38.5063	-10.4247
7	0.0311	-0.1247	-0.0525	0.4661	0.2286	0.3703	-0.0869	0.1637	-0.3985	0.0979	-0.0975	0.2921	-0.1186	-0.0093	-0.0046	1.3475	0.0575	-0.0598	0.793	0.153	1.3343	-10.9359	-35.942	-35.4276
8	0.7635	0.0969	0.2106	0.0146	0.039	0.0872	-0.4384	0.0767	0.4805	0.1111	-0.0327	0.1523	-0.3056	-0.106	0.2841	0.6764	-0.1149	-0.0327	0.485	0.0502	1.3266	-44.4137	-27.0361	-37.432
9	0.2113	-0.2059	-0.033	0.2794	-0.0319	0.3594	-0.0174	0.0228	-0.0606	0.3236	-0.5066	-0.1197	0.4045	-0.1027	0.2103	1.1251	-0.1928	0.0368	0.706	-0.1152	1.2381	-56.263	-34.2071	-43.8393
10	0.7724	0.42	-0.3296	1.1092	-0.1393	0.1246	-0.0237	-0.1284	-0.5392	-0.6706	-0.0416	-0.9049	-0.1535	-0.1341	0.2109	1.2568	0.0097	-0.0288	0.8404	0.1424	1.2728	-49.8848	-34.7589	-22.5565
11	0.8886	0.0405	0.0496	0.014	-0.0629	0.6232	0.1992	0.0931	0.2239	0.0321	-0.0387	-0.0285	0.3034	-0.1286	-0.0976	1.0465	-0.1771	-0.0462	0.9366	-0.0522	1.0513	-57.2871	-63.4357	-47.946
12	0.1811	-0.1989	-0.0522	0.4248	0.2641	0.0628	-0.1474	-0.0012	0.1272	0.0698	0.1312	-0.2571	0.1102	-0.0372	0.0504	0.9805	-0.2318	0.0062	0.8593	-0.0802	0.7843	-63.2031	-54.9084	-32.0451
13	0.9803	0.2938	0.7731	2.537	-0.5124	3.5038	-0.0263	-0.2822	0.1585	-0.5075	-0.5368	-0.0363	0.2614	0.5128	0.207	1.2163	-0.0882	0.0867	1.1353	-0.1615	0.95	-57.2589	-29.6075	-21.8995
14	0.7755	-0.3534	0.0393	0.5488	0.4434	0.844	-0.2133	0.0608	-0.0712	0.031	-0.1951	0.555	0.1173	-0.1762	0.2291	0.7583	-0.2657	0.1541	0.8928	-0.1624	0.8905	-61.447	-34.7034	-26.7801
15	3.3512	-1.6024	1.6499	2.1563	-0.8283	2.0616	-0.4752	0.1838	0.5269	0.1609	-0.2812	-0.1825	0.1133	-0.2696	0.4985	0.886	-0.2851	0.0772	0.9796	-0.1782	0.7356	-63.5319	-17.7009	-53.0177
16	0.4505	0.0139	-0.229	0.4575	-0.0436	0.1416	0.2535	0.1757	-0.3639	-0.2785	-0.1988	0.0987	-0.0006	-0.2732	-0.0244	1.4741	-0.1783	-0.2375	1.1837	-0.142	1.0347	-70.2272	-16.7398	-73.0727
17	0.2	0.5378	-0.1636	1.1361	-0.236	0.6118	-0.1365	0.3178	-0.0197	-0.0525	-0.0318	0.2275	0.0778	-0.6442	0.0771	0.6699	-0.2121	0.0151	1.0655	-0.3259	1.0909	-82.9594	-22.9312	-58.5946
18	0.5293	0.2112	0.2505	0.1348	0.252	0.7704	-0.4461	0.071	0.3234	-0.1491	-0.3065	-0.2041	-0.0583	0.1506	0.3423	1.4517	-0.1798	0.008	1.4082	0.0997	1.7114	-78.1379	-44.8445	-79.174
19	0.7409	0.034	-0.6667	0.5192	0.3405	1.3679	-0.5292	0.0877	-0.0772	-0.0665	-0.3269	-0.1446	0.5255	0.2006	0.6205	1.5048	-0.2181	0.2863	1.6216	0.4742	1.722	-65.84	-48.3876	-73.1993
20	0.9867	0.4092	-0.5514	0.5026	-0.0348	1.2122	-0.0082	-0.2291	-0.1552	0.4334	-0.3432	-0.2838	-0.1541	0.139	0.2926	1.6013	-0.1171	0.2919	1.0425	0.1801	1.0135	-75.3309	-61.3501	-70.9264
21	1.7764	-0.6889	-0.3614	1.2152	-0.1996	1.2018	0.1358	-0.1344	0.1925	-0.3606	-0.3434	-0.2364	0.2363	-0.363	0.0212	1.1791	-0.2224	0.1027	0.8524	-0.0287	0.7919	-84.0797	-54.6936	-76.6858
22	-0.2467	0.1688	0.2408	0.3421	-0.1056	1.0571	0.0343	-0.1657	0.3061	0.0095	-0.1924	0.3137	0.0729	-0.1632	0.1559	0.4985	-0.0938	0.0424	0.6651	-0.2891	0.7581	-87.5983	-24.0297	-62.8025
23	0.022	0.1328	-0.3296	0.3612	-0.0855	0.238	-0.0518	-0.0591	-0.1217	-0.1898	-0.1289	0.059	-0.1283	-0.3805	0.1234	0.8601	-0.0166	-0.0979	1.0403	-0.2036	0.7796	-65.2553	-9.3453	-98.9377
24	2.2882	0.3231	-0.0768	0.8653	-0.2408	0.1341	0.1684	-0.664	-0.5759	-0.4133	-0.2538	-0.3347	0.068	-0.0622	-0.0054	1.5533	-0.1625	0.189	1.5729	0.0325	1.4847	-64.4669	-39.2559	-103.4548
25	0.1175	0.2591	-0.4071	0.0424	0.1391	0.3958	-0.159	-0.0689	-0.2586	0.0386	-0.1419	0.2836	-0.0866	-0.2394	0.1041	0.2033	0.3939	0.1416	-0.2353	-1.2728	-1.2166	-73.5878	-6.8516	-103.6387
26	1.1968	0.5686	-0.8717	0.0917	-0.1564	0.6469	-0.1318	0.0492	-0.0804	-0.148	-0.0887	-0.0181	0.1498	-0.1612	0.1147	0.696	0.0686	0.1134	0.7335	-0.0592	0.8694	-29.7363	-0.1064	-108.0854
27	0.5887	-0.0745	0.3942	0.5122	-0.373	0.5671	0.3396	0.0621	0.0343	-0.0145	-0.0357	-0.0137	0.1364	0.2134	-0.0474	1.5562	-0.1614	0.1205	1.3039	-0.0625	1.4815	-31.6139	-28.9563	-115.1601
28	0.335	-0.0137	0.0929	0.1897	0.1946	0.3856	-0.15	0.0252	-0.3163	-0.3466	-0.0176	-0.3075	0.0837	-0.2474	0.0322	1.8069	-0.0889	-0.0184	1.3919	-0.0787	1.7512	-36.6392	-29.7133	-125.9262
29	0.5708	-0.4962	-0.1935	1.1828	0.3675	0.2943	0.1176	-0.1087	-0.2175	-0.1876	-0.1807	0.455	-0.3197	0.0515	-0.0039	1.3819	-0.0521	0.187	1.1554	-0.1052	1.3623	-26.7856	3.8771	-118.8208
30	0.8535	-0.0963	0.1439	0.4525	0.2091	0.134	0.1255	-0.0614	0.3357	-0.2413	0.0882	-0.067	0.332	-0.3674	-0.1702	1.0435	0.0002	0.1346	0.8572	0.0435	0.8507	-38.8956	1.4494	-105.8256
31	0.0671	0.0908	0.1273	0.2174	-0.0137	0.016	-0.0749	0.2467	-0.317	-0.323	-0.0874	-0.0883	0.4878	-0.0497	-0.0187	0.4805	-0.286	-0.1611	-0.8536	-0.9602	0.5386	-4.6859	-8.8176	-82.9936
32	0.7595	-0.2514	-0.3429	1.0032	-0.2263	0.7905	0.0251	-0.1957	0.2195	-0.2214	-0.0469	-0.058	0.2137	0.2731	-0.0267	0.8012	0.0694	0.0423	0.9115	-0.0979	0.7935	11.6762	-9.0556	-96.5569
33	0.4858	0.0333	-0.1532	0.3959	0.2386	0.889	-0.2991	-0.1671	0.3186	0.4171	0.1008	-0.1525	-0.2638	-0.4351	0.0036	0.3416	-0.1491	1.4651	1.5104	0.1427	-1.6596	-3.7337	-36.718	-102.4047
34	0.1329	0.3375	0.0037	0.3317	0.072	-0.0804	-0.1867	0.1605	0.218	0.101	0.0628	-0.064	0.4698	0.0675	-0.0724	1.0276	-0.058	0.339	0.7152	-0.0777	0.0921	12.2345	-20.979	-104.7365
35	0.1981	0.1592	0.0548	0.4478	0.2476	0.4089	0.2062	0.1361	-0.1688	-0.1216	-0.0302	-0.4247	0.1597	0.0304	-0.0812	0.7496	-0.044	0.0461	0.727	-0.0586	0.966	9.288	0.9192	-89.6301
36	0.8671	0.0511	0.0177	0.2458	-0.1635	0.8394	0.0487	0.0539	-0.2679	0.2935	-0.4052	0.0432	0.3215	-0.1579	0.1768	0.9595	-0.0658	0.012	0.6802	-0.0501	0.7432	-3.436	-22.6183	-55.312
37	0.2579	0.1154	-0.109	0.0895	-0.0845	0.3213	-0.0306	-0.2438	-0.2584	0.0384	-0.0545	-0.1136	-0.1146	-0.1967	0.0491	0.4844	0.1262	-0.103	0.2603	-0.0101	0.6301	12.6972	-35.0242	-57.8955
38	0.9066	0.2965	-0.1707	0.4229	0.2744	0.5239	-0.01	0.0659	-0.0379	0.2356	0.1469	-0.3733	0.2787	0.0477	-0.0348	0.6974	0.0403	0.0814	0.5771	-0.0279	0.7219	5.4357	-53.6988	-77.6014
39	0.6937	-0.7984	-0.2622	0.8928	0.1963	0.7928	-0.2899	0.0211	-0.2214	0.2194	0.0629	0.2563	0.2459	0.0624	0.1811	0.8869	0.1206	-0.001	0.8691	-0.0258	0.9093	19.752	-40.2652	-59.1421
40	0.7554	-0.1197	0.096	0.0527	0.2447	1.1642	0.3767	-0.0382	-0.2521	-0.1176	-0.3938	-0.2486	0.3136	-0.1197	-0.0524	0.6979	0.0401	-0.1609	0.3942	0.0935	0.7996	14.9692	-19.7137	-50.2954
41	0.5982	0.0701	-0.2977	0.4632	-0.3355	0.1928	0.0374	0.0734	-0.1434	0.3315	0.1404	-0.1087	-0.0613	-0.105	-0.091	0.768	-0.0076	0.0094	0.5503	-0.0489	0.351	-33.5624	-2.5331	-14.2589
42	0.7009	0.0697	0.5772	0.5244	-0.1293	0.9119	0.138	-0.018	1.1875	-0.5858	0.3918	0.3941	0.297	0.0627	-0.0883	0.4162	-0.123	-0.1432	0.9268	-0.1243	-0.2513	-29.7342	24.4391	4.2511
43	0.9626	0.5868	-0.0887	0.3674	0.1326	0.4646	-0.3723	-0.5518	-0.346	-0.5054	0.24	-0.1161	-0.1326	0.0398	0.0636	0.6645	0.0221	-0.0043	0.6263	0.0397	0.3601	-28.0005	-1.0122	5.5267
44	0.3305	0.0539	0.1292	0.1194	0.1042	1.1037	0.1296	-0.3376	0.2994	0.5818	-0.2531	0.0862	0.3847	0.6072	0.1029	1.2627	0.0072	-0.037	1.0695	0.0326	0.6503	-39.0021	-1.7702	-9.9008
45	0.2935	0.3411	0.3023	0.5231	0.4709	0.9006	0.0931	-0.0383	0.0102	-0.1522	-0.0855	-0.3098	0.0279	0.0258	-0.0048	0.6344	0.0114	-0.018	0.4946	0.049	0.6881	3.1725	9.6723	-25.1114
46	0.2549	-0.166	-0.1009	0.4736	0.0023	0.179	-0.1678	-0.2663	-0.0172	-0.1395	0.0615	0.2189	-0.1264	0.1589	-0.018	0.9945	-0.0185	-0.2149	1.0526	-0.1017	1.1695	3.1806	27.7029	-12.1522
47	0.0052	0.0583	-0.0234	0.4298	0.2551	0.2832	0.1563	0.0168	-0.0216	0.1296	-0.098	-0.4231	0.1169	0.0226	-0.0132	0.7516	-0.0759	-0.2506	0.6171	-0.0497	0.8596	9.3648	1.7926	-25.84
48	0.5921	-0.1756	-0.2268	0.0909	-0.1845	0.5001	0.1502	0.0349	0.5642	0.0756	-0.2013	-0.0255	-0.0953	0.0471	-0.0051	0.5247	-0.0404	-0.019	0.3416	0.0098	0.6246	-1.4174	22.9415	-58.6246
49	2.2861	0.9277	-0.3828	0.6272	-0.2266	0.6294	-0.1705	-0.6926	-0.8044	0.3859	-0.3416	-0.4332	-0.1207	0.0779	0.2557	0.8857	0.0077	-0.0716	0.9626	0.0786	1.2614	16.0598	14.845	-55.8578
50	1.0453	0.2752	0.4622	1.0313	-0.196	0.4265	0.1364	-0.3611	0.3414	-0.363	-0.0461	-0.0638	0.1522	-0.0833	0.0277	0.8607	-0.2167	0.0381	0.7268	-0.0741	0.9302	6.2131	50.4205	-46.2034
51	0.1725	-0.2471	0.2291	0.6092	-0.4173	0.3946	-0.4944	-0.0986	0.1345	0.224	0.0216	-0.5123	0.2416	-0.0385	0.2511	1.2169	-0.189	0.134	0.9318	-0.1051	1.4292	17.5411	53.9296	-43.9796
52	0.0502	-0.0972	0.0796	1.0328	-0.2794	0.0203	0.0509	-0.3747	-0.218	-0.1478	0.2865	-0.0903	0.1235	-0.0127	-0.1673	0.947	-0.0325	-0.1535	0.8582	-0.0028	1.0769	17.2314	33.4047	-63.8421
53	1.1062	0.0789	-0.2831	0.814	0.3491	0.3715	-0.2467	-0.0192	-0.195	-0.2763	0.0609	-0.4651	-0.2753	0.1765	0.1004	0.8259	-0.0619	-0.0531	0.5789	0.0102	0.7267	15.3056	20.1851	-65.2753
54	0.3327	-0.113	0.0331	0.1087	-0.0352	0.167	-0.1025	0.0557	0.3264	-0.4025	-0.0648	0.3347	-0.4061	-0.0003	0.0803	0.6618	-0.0128	-0.0974	0.3641	-0.0979	0.634	-24.9149	31.0665	-77.6192
55	0.3046	-0.2636	-0.2143	0.2261	-0.0513	0.4727	-0.0446	0.1508	-0.029	-0.1097	0.3273	-0.3433	-0.2208	-0.0496	-0.1547	0.9356	-0.134	0.0179	0.4506	-0.0769	0.6134	-14.281	32.387	-81.5142
56	0.1965	-0.0832	-0.2157	1.0831	0.2584	-0.0903	0.3406	0.1746	0.3701	-0.7196	-0.9658	-0.0662	0.3019	0.1561	0.1076	-0.1673	-1.0423	-0.0932	-1.227	0.0086	1.0193	-18.1494	60.6525	-72.3943
57	0.0764	-0.0052	0.2214	0.0692	-0.0157	0.4054	-0.081	0.5892	0.8086	-0.0388	0.2004	-0.2048	0.5085	0.4047	0.034	0.4047	-0.3812	-0.0373	0.3622	0.363	0.9549	-13.5345	60.1641	-85.616
58	1.3418	-0.6971	0.1968	0.4367	0.0412	0.7374	0.0604	0.2451	0.3058	-0.1208	-0.3591	-0.4255	-0.2355	0.0411	0.2091	1.3094	0.0665	-0.0218	0.8696	0.1077	1.1329	-18.551	34.6259	-101.354
59	0.2273	-0.3219	-0.108	1.0206	0.2348	0.1044	0.3967	-0.0212	0.1147	-0.6342	-0.2981	0.0321	-0.2503	-0.1205	-0.0175	0.4286	0.0202	0.0661	0.4117	0.1793	-0.1483	-11.0687	35.4168	-80.7838
60	0.8076	-0.3359	-0.0365	0.2442	0.1028	0.7793	-0.1011	0.1794	0.2174	-0.0118	-0.257	0.2134	-0.2336	-0.1385	0.2217	0.436	0.0617	-0.1132	0.5783	-0.1347	0.578	-52.531	31.7118	-74.1113
61	1.0137	-0.4812	-0.9415	0.8764	0.4162	0.895	0.2026	0.4894	0.0696	-0.1741	-0.3196	-0.3086	0.1935	-0.2149	0.0302	0.9181	0.1513	-0.2529	1.012	-0.1837	1.1847	-50.4548	34.4774	-93.2421
62	0.266	-0.0087	-0.1576	0.6126	-0.2366	0.2802	0.1284	0.1256	-0.121	0.2934	-0.3111	-0.4748	-0.2035	-0.1943	0.0548	1.305	0.337	-0.2988	1.0288	-0.1871	1.6494	-67.9582	56.8504	-74.5285
63	2.5607	-0.3076	0.0894	1.4308	-0.7249	1.5098	-0.0699	-0.2412	0.0827	0.1034	-0.4603	-0.2641	-0.0416	0.136	0.2096	1.3423	0.2463	-0.3368	1.2135	-0.0766	1.2984	-46.0846	66.2646	-56.6001
64	1.0677	0.2183	-1.3779	0.7075	-0.3521	1.9959	0.1209	-0.25	0.5556	-0.094	0.3724	0.2946	-0.1016	0.0249	-0.4263	1.3732	0.051	-0.0222	1.2297	0.2302	1.7707	-45.72	58.8879	-61.5097
65	1.5688	-0.9126	0.2176	0.8348	-0.5665	0.615	0.1275	-0.141	0.7257	0.238	-0.1984	-0.5823	-0.2635	0.006	0.006	1.8059	0.1689	0.1197	1.1461	-0.099	1.4275	-45.1472	73.7656	-66.9796
66	0.1103	0.3224	-0.181	0.8795	-0.4562	0.207	0.4493	0.0135	-0.1923	0.3721	-0.2226	0.318	0.0019	-0.2189	-0.1903	1.3277	0.4351	-0.4664	0.7088	-0.2158	1.2251	-57.3438	71.3855	-69.7275
67	2.4003	1.5929	-1.1946	1.8888	-1.0567	1.2809	0.5079	0.4661	-0.6345	0.1801	0.0496	-0.2696	0.1395	-0.0187	-0.1846	1.3618	0.4862	-0.2555	1.2769	-0.5244	1.5831	-58.3664	70.0026	-80.9374
68	0.2736	0.0156	0.2323	1.0759	0.2595	0.3002	-0.1635	0.227	0.2276	-0.0287	0.0186	0.3726	-0.2478	-0.0189	0.2087	1.1618	0.2318	-0.0849	1.1059	-0.1607	1.0939	-65.8809	44.8963	-85.6419
69	0.3057	-0.0359	0.131	0.3482	-0.1309	0.4009	0.1266	0.0232	-0.1853	0.0501	-0.0875	-0.4404	-0.4541	-0.225	0.0635	0.751	0.1861	-0.2137	0.786	-0.1297	0.8439	-60.7709	33.3321	-90.2251
70	0.0868	-0.1967	-0.2783	0.606	0.1941	0.3678	0.1413	0.0212	0.1611	-0.142	-0.0837	0.0863	-0.2971	0.018	0.0005	0.9235	0.0065	-0.1165	0.9232	-0.2003	1.0607	-78.2282	23.2846	-51.7875
71	0.756	0.0761	-0.565	0.0477	0.0668	1.6246	0.5585	-0.119	-0.3899	0.4211	-0.2827	-0.2116	-1.1741	0.0106	-0.0187	1.6712	0.0433	-0.3148	1.2637	-0.1096	1.5396	-71.1603	50.8986	-38.7338
72	-0.1907	-0.0896	0.086	0.7778	0.0429	0.33	-0.8207	0.2543	0.5522	-0.0405	0.2853	0.1459	0.1816	-0.2614	0.1112	0.45	0.3814	-0.3242	0.7076	-0.4286	1.0809	-87.3772	28.3872	-51.7712
73	0.4937	-0.3916	0.2018	0.7036	-0.1982	0.2919	0.2303	-0.095	0.2218	-0.0924	0.0013	-0.0518	0.3148	0.0122	-0.0571	0.8996	-0.0031	-0.0802	0.8626	-0.2311	0.9296	-58.5772	6.5198	-26.607
74	0.961	-0.3245	0.0456	0.1929	0.2753	0.8845	-0.3817	-0.1198	-0.1257	-0.1302	0.2283	-0.0059	-0.3946	0.0729	0.0858	1.2766	0.1167	-0.1392	1.1722	-0.1316	1.1741	-69.0382	24.9495	-8.2628
75	0.7675	-0.1122	0.2499	0.5215	0.0093	0.4617	0.2396	-0.1838	0.2561	0.1345	-0.082	0.0191	0.0188	-0.3019	0.0026	0.78	-0.0418	0.1053	0.8722	-0.1908	0.7486	-73.6437	-4.1673	-19.4453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 2:133)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 134:179)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 180:296)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 297:338)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 339:458)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 459:493)
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESSEQ 494:525)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 2:30)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 31:88)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 89:133)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 134:352)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 353:433)
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESSEQ 434:458)
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESSEQ 459:525)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 2:27)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 28:64)
17	X-RAY DIFFRACTION	17	CHAIN C AND (RESSEQ 65:156)
18	X-RAY DIFFRACTION	18	CHAIN C AND (RESSEQ 157:246)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 247:281)
20	X-RAY DIFFRACTION	20	CHAIN C AND (RESSEQ 282:312)
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESSEQ 313:354)
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESSEQ 355:525)
23	X-RAY DIFFRACTION	23	CHAIN D AND (RESSEQ 2:216)
24	X-RAY DIFFRACTION	24	CHAIN D AND (RESSEQ 217:338)
25	X-RAY DIFFRACTION	25	CHAIN D AND (RESSEQ 339:525)
26	X-RAY DIFFRACTION	26	CHAIN E AND (RESSEQ 2:179)
27	X-RAY DIFFRACTION	27	CHAIN E AND (RESSEQ 180:267)
28	X-RAY DIFFRACTION	28	CHAIN E AND (RESSEQ 268:354)
29	X-RAY DIFFRACTION	29	CHAIN E AND (RESSEQ 355:493)
30	X-RAY DIFFRACTION	30	CHAIN E AND (RESSEQ 494:525)
31	X-RAY DIFFRACTION	31	CHAIN F AND (RESSEQ 2:88)
32	X-RAY DIFFRACTION	32	CHAIN F AND (RESSEQ 89:179)
33	X-RAY DIFFRACTION	33	CHAIN F AND (RESSEQ 180:338)
34	X-RAY DIFFRACTION	34	CHAIN F AND (RESSEQ 339:433)
35	X-RAY DIFFRACTION	35	CHAIN F AND (RESSEQ 434:525)
36	X-RAY DIFFRACTION	36	CHAIN G AND (RESSEQ 2:64)
37	X-RAY DIFFRACTION	37	CHAIN G AND (RESSEQ 65:216)
38	X-RAY DIFFRACTION	38	CHAIN G AND (RESSEQ 217:352)
39	X-RAY DIFFRACTION	39	CHAIN G AND (RESSEQ 353:433)
40	X-RAY DIFFRACTION	40	CHAIN G AND (RESSEQ 434:525)
41	X-RAY DIFFRACTION	41	CHAIN H AND (RESSEQ 2:134)
42	X-RAY DIFFRACTION	42	CHAIN H AND (RESSEQ 135:338)
43	X-RAY DIFFRACTION	43	CHAIN H AND (RESSEQ 339:493)
44	X-RAY DIFFRACTION	44	CHAIN H AND (RESSEQ 494:525)
45	X-RAY DIFFRACTION	45	CHAIN I AND (RESSEQ 2:179)
46	X-RAY DIFFRACTION	46	CHAIN I AND (RESSEQ 180:458)
47	X-RAY DIFFRACTION	47	CHAIN I AND (RESSEQ 459:525)
48	X-RAY DIFFRACTION	48	CHAIN J AND (RESSEQ 2:88)
49	X-RAY DIFFRACTION	49	CHAIN J AND (RESSEQ 89:133)
50	X-RAY DIFFRACTION	50	CHAIN J AND (RESSEQ 134:316)
51	X-RAY DIFFRACTION	51	CHAIN J AND (RESSEQ 317:385)
52	X-RAY DIFFRACTION	52	CHAIN J AND (RESSEQ 386:433)
53	X-RAY DIFFRACTION	53	CHAIN J AND (RESSEQ 434:525)
54	X-RAY DIFFRACTION	54	CHAIN K AND (RESSEQ 2:64)
55	X-RAY DIFFRACTION	55	CHAIN K AND (RESSEQ 65:112)
56	X-RAY DIFFRACTION	56	CHAIN K AND (RESSEQ 113:338)
57	X-RAY DIFFRACTION	57	CHAIN K AND (RESSEQ 339:433)
58	X-RAY DIFFRACTION	58	CHAIN K AND (RESSEQ 434:493)
59	X-RAY DIFFRACTION	59	CHAIN K AND (RESSEQ 494:525)
60	X-RAY DIFFRACTION	60	CHAIN L AND (RESSEQ 2:88)
61	X-RAY DIFFRACTION	61	CHAIN L AND (RESSEQ 89:133)
62	X-RAY DIFFRACTION	62	CHAIN L AND (RESSEQ 134:216)
63	X-RAY DIFFRACTION	63	CHAIN L AND (RESSEQ 217:246)
64	X-RAY DIFFRACTION	64	CHAIN L AND (RESSEQ 247:282)
65	X-RAY DIFFRACTION	65	CHAIN L AND (RESSEQ 283:313)
66	X-RAY DIFFRACTION	66	CHAIN L AND (RESSEQ 314:352)
67	X-RAY DIFFRACTION	67	CHAIN L AND (RESSEQ 353:385)
68	X-RAY DIFFRACTION	68	CHAIN L AND (RESSEQ 386:433)
69	X-RAY DIFFRACTION	69	CHAIN L AND (RESSEQ 434:525)
70	X-RAY DIFFRACTION	70	CHAIN M AND (RESSEQ 2:179)
71	X-RAY DIFFRACTION	71	CHAIN M AND (RESSEQ 180:338)
72	X-RAY DIFFRACTION	72	CHAIN M AND (RESSEQ 339:525)
73	X-RAY DIFFRACTION	73	CHAIN N AND (RESSEQ 2:88)
74	X-RAY DIFFRACTION	74	CHAIN N AND (RESSEQ 89:408)
75	X-RAY DIFFRACTION	75	CHAIN N AND (RESSEQ 409:525)

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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About Yorodumi

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

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Mar 5, 2020. Novel coronavirus structure data

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Jul 12, 2017. Major update of PDB

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Yorodumi