PDB-8cj4: Crystal structure of ClpP from Staphylococcus epidermidis, tetrad...

ID or keywords:

Entry

Database: PDB / ID: 8cj4

Title

Crystal structure of ClpP from Staphylococcus epidermidis, tetradecamer

Components

ATP-dependent Clp protease proteolytic subunit

Keywords

HYDROLASE / Serine protease / apo protein / ClpP

Function / homology

Function and homology information

endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Staphylococcus epidermidis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Alves Franca, B. / Rohde, H. / Betzel, C.

Funding support

Germany, 3items

Organization	Grant number	Country
German Research Foundation (DFG)	390715994	Germany
German Federal Ministry for Education and Research	05K16GUA	Germany
German Federal Ministry for Education and Research	5K19GU4	Germany

Citation

Journal: Sci Rep / Year: 2024
Title: Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds.
Authors: Alves Franca, B. / Falke, S. / Rohde, H. / Betzel, C.

History

Deposition	Feb 12, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Feb 14, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	8cj4_validation.pdf.gz	549.6 KB	Display	wwPDB validaton report
Full document	8cj4_full_validation.pdf.gz	562.6 KB	Display
Data in XML	8cj4_validation.xml.gz	100 KB	Display
Data in CIF	8cj4_validation.cif.gz	143.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cj/8cj4 ftp://data.pdbj.org/pub/pdb/validation_reports/cj/8cj4	HTTPS FTP

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Related structure data

Related structure data	8qyfC 9fswC 9g6iC 9g72C C: citing same article (ref.)
Similar structure data	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: ATP-dependent Clp protease proteolytic subunit

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

H: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

J: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

hetero molecules

311 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, SEC-SAXS results indicate that the structure is a tetradecamer (approx. 300kDa)

Unit cell

Length a, b, c (Å)	95.423, 123.662, 126.787
Angle α, β, γ (deg.)	90.00, 91.21, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 22106.025 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus epidermidis (bacteria) Gene: clpP, E1M97_03460, E1M98_06460, E1N00_07180, E1N03_05195, E1N04_00635, E1N05_04945, E1N06_06240, E1N09_07235, E1N11_03825, E1N12_01760, E1N13_04220, FHG76_01330, FHQ17_10195, H3963_07430, I3V53_07130 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: A0A0N1MQL5, endopeptidase Clp
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1641 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.1 %
Crystal grow	Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M sodium acetate (pH 4.5), 35% v/v MPD and 40mM calcium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.9→44.96 Å / Num. obs: 227961 / % possible obs: 98.65 % / Redundancy: 7 % / B_iso Wilson estimate: 27.82 Å² / CC_1/2: 1 / R_rim(I) all: 0.09 / Net I/σ(I): 14.12
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 22466 / CC_1/2: 0.8 / R_rim(I) all: 0.94 / % possible all: 97.58

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
XDS		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→44.96 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2194	2392	1.05 %
R_work	0.1825	-	-
obs	0.1829	227921	98.66 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 31.38 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→44.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19366	0	112	1641	21119

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	0.949
X-RAY DIFFRACTION	f_dihedral_angle_d	7.376	2752
X-RAY DIFFRACTION	f_chiral_restr	0.059	3116
X-RAY DIFFRACTION	f_plane_restr	0.01	3492

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 (%)
1.9-1.94	0.2882	138	0.2523	13038	X-RAY DIFFRACTION	97
1.94-1.98	0.2681	140	0.2422	13140	X-RAY DIFFRACTION	98
1.98-2.03	0.3056	139	0.2246	13106	X-RAY DIFFRACTION	98
2.03-2.08	0.2847	139	0.2096	13102	X-RAY DIFFRACTION	98
2.08-2.13	0.2414	140	0.1988	13181	X-RAY DIFFRACTION	98
2.13-2.2	0.2289	139	0.1915	13134	X-RAY DIFFRACTION	98
2.2-2.27	0.2363	141	0.1814	13222	X-RAY DIFFRACTION	98
2.27-2.35	0.2098	140	0.1797	13208	X-RAY DIFFRACTION	99
2.35-2.44	0.2111	140	0.1824	13250	X-RAY DIFFRACTION	99
2.44-2.55	0.2139	141	0.1815	13251	X-RAY DIFFRACTION	99
2.55-2.69	0.2366	141	0.1823	13313	X-RAY DIFFRACTION	99
2.69-2.86	0.1971	141	0.1855	13312	X-RAY DIFFRACTION	99
2.86-3.08	0.2184	142	0.1897	13372	X-RAY DIFFRACTION	99
3.08-3.39	0.2703	142	0.1915	13362	X-RAY DIFFRACTION	100
3.39-3.88	0.21	142	0.1722	13388	X-RAY DIFFRACTION	99
3.88-4.88	0.1796	144	0.1522	13512	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	0.0655	0.0207	0.0665	-0.0112	0.0079	0.0111	-0.0918	-0.5298	-0.5616	0.1701	0.021	0.0174	0.4009	0.2817	-0.0002	0.511	0.033	0.098	0.4042	0.0944	0.322	-35.9264	-50.4774	2.4293
2	0.3311	-0.4497	0.1198	0.513	0.0298	-0.0244	-0.006	0.0193	-0.1069	0.1117	-0.0302	-0.0062	0.2346	-0.0689	0.1389	0.4204	-0.0463	0.1825	0.3253	0.0542	0.3272	-46.3958	-46.828	-5.0534
3	0.4972	-0.5694	0.1069	0.5546	-0.061	0.7345	-0.2385	-0.0784	0.0006	0.0674	-0.1422	0.2239	0.2003	-0.1644	-1.206	0.2931	-0.0838	0.1961	0.3215	0.0359	0.2816	-52.3159	-37.4405	-8.1301
4	0.3174	-0.0585	0.1479	0.5431	-0.0412	0.1001	-0.0792	0.0794	0.0239	-0.0459	-0.0946	0.4144	0.1775	-0.398	-0.0686	0.1917	-0.0539	0.0748	0.3208	-0.0065	0.3892	-59.7999	-34.3358	-21.9719
5	0.9071	0.0668	0.1892	0.3605	0.2184	0.5091	-0.1601	-0.1392	0.2612	0.2439	-0.0135	0.3135	-0.062	-0.2677	-0.2983	0.2956	-0.0099	0.1634	0.3727	0.0062	0.3724	-57.4549	-26.8267	-4.4358
6	0.0146	-0.0364	-0.0042	0.002	-0.0226	-0.0376	-0.1458	0.0359	-0.5314	0.0548	0.0008	0.2993	0.294	0.1035	0.0002	0.4288	0.0174	0.0181	0.3128	0.0575	0.3838	-21.4202	-48.7295	6.0576
7	0.4154	-0.3152	0.0998	0.7201	0.1155	0.2864	-0.0636	-0.123	-0.1647	0.1837	0.047	0.1516	0.1318	-0.0648	-0.1582	0.3684	0.0329	0.103	0.303	0.0946	0.212	-32.6032	-35.3726	7.2436
8	0.0693	0.0762	0.2668	0.4715	0.2361	0.1044	-0.1199	0.0406	0.0836	0.1112	-0.0307	0.0553	0.0448	0.0674	-0	0.3082	0.0679	0.0526	0.3164	0.0668	0.2404	-29.1986	-22.3372	3.5689
9	0.0154	-0.2965	0.0819	0.1001	0.1361	0.233	-0.1648	-0.161	0.0228	0.1232	0.0426	0.2758	0.1011	-0.3289	-0.0274	0.2648	0.0188	0.1005	0.3359	0.0437	0.3176	-42.2641	-16.5251	-1.3438
10	0.1636	0.1448	0.0409	0.3183	0.1961	0.1086	-0.1009	-0.1107	0.3717	0.302	0.0424	0.1222	-0.1107	0.0005	-0.0004	0.3851	0.0777	0.0631	0.3424	0.0506	0.2943	-28.3247	-12.379	7.4221
11	0.0601	-0.1188	0.061	0.2685	-0.1083	0.1263	-0.1278	-0.5937	-0.3107	0.4603	0.3196	0.1941	0.2366	0.0614	0.0726	0.5982	0.1777	0.0059	0.4268	0.0423	0.1925	-21.2651	-24.306	16.9541
12	0.0221	-0.1427	-0.0748	0.0743	0.1044	0.0292	0.1075	0.0881	-0.2149	0.0675	0.037	0.3718	0.8291	0.0957	0.0001	0.4074	0.0246	0.0025	0.3033	0.0302	0.303	-10.1279	-53.9785	0.5766
13	0.9339	-0.3005	-0.133	0.9716	-0.3192	0.2356	-0.0526	0.0071	-0.0704	0.0747	0.0813	0.0823	0.0227	0.0228	0.0001	0.2817	0.0308	-0.0265	0.2247	0.0393	0.1796	-8.408	-36.7141	5.0146
14	0.1079	-0.1905	0.1254	0.0361	-0.1309	-0.1808	-0.0042	-0.0828	0.1012	-0.0492	0.0332	-0.1275	-0.0202	-0.1224	-0	0.3208	0.0303	-0.0591	0.2391	0.0197	0.2383	-1.8926	-27.1151	-1.4659
15	0.2181	-0.0124	0.0225	0.4156	-0.0466	-0.0252	-0.1876	-0.1147	0.214	0.4424	0.1014	-0.0977	-0.0979	-0.1472	0.0025	0.3701	0.0318	-0.0177	0.2454	-0.004	0.1833	-10.0622	-15.2446	1.9107
16	0.254	-0.0313	-0.2426	0.2223	-0.0958	0.1771	0.0211	0.0704	0.2903	0.08	-0.1755	-0.3626	-0.2575	0.2133	-0.0002	0.3621	-0.0228	-0.1189	0.276	0.0323	0.3007	5.9303	-20.8555	0.2586
17	0.0412	-0.0903	0.0375	0.0353	0.0343	0.0674	-0.0937	0.0171	0.1903	0.1645	-0.0489	-0.2593	0.0978	0.4123	-0.098	0.3612	0.0356	-0.1006	0.2933	0.0316	0.231	9.4922	-36.2022	5.3779
18	0.3308	0.0493	-0.1254	1.3483	0.2371	0.3267	0.0153	0.0312	-0.0332	0.2021	0.0149	0.0307	0.0626	-0.0106	-0	0.2393	-0.0001	-0.0313	0.2234	0.0285	0.2263	2.1961	-52.676	-9.7422
19	0.2349	0.0992	-0.0823	0.3237	0.1703	-0.1173	0.0018	-0.0409	0.0158	-0.1386	0.1124	-0.238	-0.0934	0.0612	0.0015	0.2552	0.0037	-0.0477	0.2446	0.0055	0.26	9.8328	-44.7113	-20.1814
20	0.3287	-0.0189	0.0907	0.1013	0.1318	0.112	-0.1484	-0.0573	0.1021	0.6976	0.0748	-0.4829	-0.2161	0.1299	0	0.2737	-0.0307	-0.046	0.2714	0.0189	0.2639	12.7999	-31.2833	-14.4203
21	0.7569	0.3228	-0.1055	0.2438	0.3105	0.8631	-0.0086	0.0051	-0.0579	-0.1269	-0.003	-0.2436	-0.0131	0.2739	-0.0003	0.1799	-0.0098	-0.0252	0.3158	-0.0081	0.3648	18.0915	-47.829	-23.1304
22	0.1612	0.0625	0.0292	0.0076	0.0325	0.0075	-0.0794	-0.2156	-0.2099	0.7529	-0.0426	0.295	-0.1936	0.1198	-0.0002	0.4687	-0.042	0.0431	0.3032	0.0266	0.3322	-18.2778	-69.2194	-16.8869
23	0.1973	0.2471	-0.4641	0.6653	0.2086	0.7912	0.005	0.0108	-0.088	0.1295	0.0292	-0.0497	0.1372	0.0301	-0	0.2137	-0.0188	-0.0469	0.171	0.029	0.2201	-4.2036	-66.5214	-28.5544
24	0.1397	-0.0866	0.0036	0.0559	-0.0008	0.0696	0.0207	0.0402	0.0731	0.1573	0.0661	0.0737	0.1304	-0.0239	0	0.3018	-0.0445	0.0205	0.264	-0.0233	0.3438	1.7979	-44.4798	-39.6619
25	0.2483	-0.143	-0.1544	0.1511	-0.0513	0.3696	-0.0796	-0.0535	-0.1408	-0.1692	0.1369	-0.4876	-0.0037	0.2008	0.0001	0.1957	-0.0066	0.0003	0.2779	-0.0232	0.286	9.1108	-52.8495	-38.396
26	0.1365	0.1049	-0.0088	0.0791	-0.076	0.3428	-0.1257	0.2897	0.0143	-0.4279	0.1238	0.0079	0.1989	0.0606	-0	0.2953	-0.0279	0.0344	0.257	-0.0254	0.3101	0.649	-64.2088	-47.7786
27	0.0103	-0.0081	-0.0062	0.1016	0.1424	0.208	0.1456	0.0004	-0.9222	0.0173	0.038	-0.2402	0.5523	0.2641	0.0157	0.3284	-0.0412	-0.0624	0.1985	0.035	0.3582	-7.4995	-76.6673	-39.8332
28	0.2881	-0.0166	-0.2284	0.0615	0.1812	0.1091	0.0769	-0.2812	0.0991	-0.0703	-0.0432	0.2844	0.0654	-0.0064	0.0003	0.3207	-0.0948	0.0435	0.3344	0.0419	0.3133	-30.9229	-66.4853	-20.9486
29	0.6355	-0.1521	0.2136	0.1665	0.0825	0.5184	-0.0181	-0.0904	-0.1079	0.1751	0.0716	0.208	0.0481	-0.0322	-0	0.2826	-0.0498	0.0234	0.2189	0.042	0.2341	-25.2282	-71.0505	-28.4755
30	0.5454	0.0859	-0.2705	0.2948	-0.042	0.3191	0.0768	0.0222	-0.1234	0.1534	-0.0179	0.0592	0.0357	-0.003	-0	0.2459	-0.0645	-0.0016	0.2307	0.0129	0.2573	-28.4677	-67.6802	-39.8681
31	0.0926	-0.0114	-0.1307	0.0824	0.0025	0.0561	0.0252	0.0543	-0.194	-0.1046	-0.0657	-0.0956	0.0866	0.0256	-0.0001	0.2434	-0.019	-0.0466	0.2546	-0.0026	0.2663	-18.4561	-63.5609	-51.67
32	0.4997	0.083	0.2818	0.4725	0.4599	0.4206	0.0348	0.1899	-0.1152	-0.1039	0.0518	0.2438	0.1735	-0.1848	0.0018	0.2247	-0.0656	-0.0149	0.2456	0.0022	0.3266	-37.0586	-68.4879	-48.8425
33	0.6626	-0.1285	-0.1126	0.3909	0.3977	0.3471	-0.0645	-0.0616	0.0991	0.2233	0.0881	0.3208	-0.0074	0.1833	-0.0211	0.2864	-0.0555	0.1187	0.311	0.0754	0.3879	-40.8342	-60.4848	-16.3816
34	0.7838	-0.1812	0.0594	0.412	-0.4117	0.6721	-0.0007	-0.0404	-0.2337	0.1549	-0.1311	0.3973	0.0736	-0.1525	-0.3323	0.249	-0.1026	0.1164	0.2749	0.0289	0.4064	-51.5649	-58.6489	-24.1768
35	0.2516	0.1737	0.1271	0.2492	-0.1063	0.4587	0.1153	-0.0416	0.0335	-0.0254	-0.0927	0.2317	0.0263	-0.0917	0.0001	0.2212	-0.0194	-0.0117	0.276	-0.0174	0.3661	-47.3492	-53.0885	-44.3508
36	0.4841	-0.3606	-0.2003	0.7616	0.8978	1.0874	0.3318	0.2427	-0.1839	-0.7322	-0.5404	1.0248	-0.4826	-0.6042	-0.2395	-0.1568	-0.2299	0.1657	0.2986	0.0201	0.5657	-61.6874	-50.4797	-30.6332
37	0.0696	-0.0981	-0.0815	0.07	0.0395	0.0142	0.0151	0.4456	0.2327	-0.3972	0.0902	0.0896	-0.0476	-0.2229	-0.0004	0.467	-0.058	0.0222	0.3034	0.017	0.3246	-4.5959	0.513	-53.0831
38	0.2965	-0.1222	0.1272	0.0611	0.0202	0.2236	0.0566	-0.0015	-0.0991	-0.0967	-0.0672	0.1288	-0.1755	-0.1496	0.0037	0.3412	-0.0616	0.0745	0.2748	0.0048	0.2276	1.2832	-11.67	-55.248
39	0.3174	-0.1466	0.1699	0.2775	0.1105	0.2162	-0.0032	0.0942	0.0114	-0.1059	0.0989	-0.1107	-0.1171	0.0554	0.0068	0.2844	-0.0716	0.0841	0.2449	0.0038	0.2314	9.6152	-12.6487	-51.6433
40	0.3966	-0.1402	0.2579	0.258	0.0089	0.0991	-0.1013	0.1112	-0.0244	0.0702	0.1158	-0.1768	-0.0723	0.0071	0	0.2639	-0.0619	0.063	0.2379	0.0248	0.2728	14.949	-9.1216	-42.6989
41	0.1756	-0.0938	0.0339	0.0555	-0.0565	0.0341	0.0975	0.0552	-0.0235	0.1294	0.0213	0.2338	-0.0722	-0.0315	0.0002	0.3317	-0.0462	0.0162	0.2864	-0.0396	0.3311	4.7442	-34.8049	-41.1798
42	0.2319	-0.1802	0.1952	0.2168	-0.0854	0.0041	-0.0301	0.1173	-0.2572	-0.1675	0.0727	-0.5879	0.1342	0.1086	0.0535	0.2218	-0.0373	0.0662	0.2906	-0.0171	0.3003	13.3826	-32.2284	-47.7337
43	0.2611	-0.3048	-0.0233	0.2309	0.0533	0.291	-0.0365	-0.0258	-0.1891	0.3675	0.0043	-0.3806	-0.0292	0.2116	-0.0003	0.2434	-0.0657	0.0051	0.2836	-0.0029	0.3718	19.965	-20.1891	-37.577
44	0.0599	0.0188	-0.006	0.0171	0.0016	0.0119	0.0193	-0.1933	0.3717	-0.3906	0.0716	-0.5255	-0.4045	0.5129	-0.0003	0.3301	-0.0969	0.0702	0.2441	-0.0286	0.3876	18.3261	-4.2267	-42.1847
45	0.025	0.0051	0.0345	0.0508	0.1029	0.0698	0.123	-0.1787	0.1387	-0.1873	-0.1485	0.2947	-0.6568	-0.2388	0.0001	0.4301	-0.0566	0.0889	0.2986	-0.014	0.2973	-6.682	-8.8863	-63.4074
46	0.9485	-0.0203	0.3478	1.174	-0.1322	0.3825	0.0819	0.032	-0.0169	-0.0867	0.0174	-0.043	-0.1241	0.0308	0.1755	0.2899	-0.0219	0.083	0.2082	-0.001	0.1649	-4.4381	-25.9528	-67.7312
47	0.0346	-0.0621	-0.1366	0.0629	0.125	0.0186	0.1129	-0.1836	-0.0285	-0.0152	0.0076	0.0044	-0.054	0.0336	0.0001	0.2555	-0.0484	-0.0057	0.308	-0.0083	0.2944	-13.0219	-45.7726	-54.1771
48	0.2325	-0.2082	-0.2037	0.4732	0.2089	0.0024	-0.0589	0.2135	-0.1769	-0.3269	0.0818	-0.075	0.1126	-0.1392	-0	0.2829	-0.0198	0.0107	0.2474	-0.017	0.2185	-10.11	-46.4701	-64.928
49	0.1659	0.0143	0.0437	0.1283	-0.0883	0.0919	0.0417	-0.0078	-0.4415	-0.1285	-0.0247	-0.0315	0.3042	0.1694	-0.0008	0.2983	-0.0145	0.057	0.2621	-0.0253	0.3487	3.2711	-46.6586	-63.2157
50	0.2136	0.031	0.2941	0.3391	0.107	0.41	0.0035	0.0922	-0.0075	-0.009	-0.0424	-0.3136	-0.0205	0.1646	-0.0022	0.2957	-0.0276	0.1272	0.2567	-0.0219	0.2839	10.5674	-32.0745	-64.66
51	0.1456	0.0775	-0.026	-0.0228	-0.0214	-0.0121	0.0593	-0.1371	0.3289	-0.1731	0.1213	0.122	-0.4752	-0.1722	0.0001	0.3643	-0.0038	0.0548	0.3161	0.0169	0.2927	-19.1193	-13.4347	-69.1874
52	0.9714	0.2137	-0.2775	0.8493	0.0904	0.4364	0.0211	0.0232	0.0418	-0.1272	-0.0322	0.1009	-0.1315	-0.0095	0	0.2903	0.0091	-0.0344	0.2593	0.0276	0.1874	-29.3399	-27.7428	-71.3335
53	0.4423	0.2449	0.219	0.2893	-0.0222	0.313	-0.0243	0.0511	-0.0576	-0.136	-0.0236	0.1684	0.0656	-0.0504	-0	0.2267	0.0049	-0.0448	0.243	-0.0045	0.3144	-41.1179	-42.6519	-60.1951
54	0.2975	0.0248	0.3367	0.5609	0.1485	0.1885	0.0359	0.0783	-0.1801	-0.1654	-0.0382	0.0224	0.0149	0.0763	-0	0.3027	0.0078	-0.0156	0.2876	-0.0053	0.2282	-26.2662	-44.851	-73.5096
55	0.0594	-0.0386	-0.1049	0.04	-0.019	0.0658	0.153	0.0272	0.7869	0.0061	-0.2529	-0.2038	-0.406	0.3454	0.0002	0.4111	-0.0467	0.0062	0.3796	0.0322	0.3609	-32.262	-9.0636	-66.077
56	0.6523	0.1141	-0.2452	0.8371	0.2446	0.5311	0.033	0.0167	0.0376	-0.1353	-0.1026	0.0944	-0.0659	0.0493	-0	0.2108	0.0367	-0.0591	0.2588	0.0121	0.2606	-48.0105	-16.0009	-59.2662
57	0.0247	0.0133	-0.1068	0.1152	-0.3282	0.3774	0.0583	-0.0011	0.0242	-0.0332	-0.0599	0.22	0.1253	-0.1303	0	0.2187	0.0056	-0.037	0.3046	-0.0128	0.3705	-56.8956	-24.7565	-41.0957
58	0.5557	0.0358	-0.2199	0.247	0.1259	0.2685	-0.0442	0.1168	-0.2116	-0.0719	-0.0984	0.2917	0.2695	-0.179	-0.0022	0.2476	0.006	-0.0585	0.319	-0.0174	0.3351	-56.4203	-31.3272	-60.2711
59	0.0361	0.0509	0.0428	0.0477	0.1078	0.1009	0.0098	0.1229	0.0261	-0.2289	0.1022	-0.1976	-0.2327	0.4362	0.0003	0.2795	-0.0358	-0.0741	0.4427	0.0522	0.3215	-37.1632	-0.7206	-55.4639
60	0.3998	0.1652	-0.2255	-0.0006	-0.0292	0.2105	-0.0115	0.0573	-0.0749	-0.1131	-0.1039	-0.091	0.0126	0.1208	-0.0001	0.1987	0.0035	-0.0696	0.27	0.0526	0.322	-38.8715	2.1407	-42.6152
61	0.2543	0.0037	0.0666	-0.0268	-0.0296	-0.024	-0.0135	0.1669	0.003	0.1144	-0.0871	-0.0575	-0.1954	0.053	-0.0003	0.2245	0.0248	-0.0652	0.2675	0.0426	0.2895	-46.5435	2.411	-44.5988
62	0.1272	-0.0779	0.1659	-0.0593	-0.397	0.7102	-0.0248	-0.0154	0.0334	0.0269	-0.0707	-0.0143	-0.0306	0.0129	0	0.1804	0.003	-0.0509	0.2459	0.0086	0.2929	-48.8965	-2.5664	-35.6518
63	0.2295	-0.008	-0.0895	0.1443	-0.0441	0.0904	-0.1833	-0.1324	0.1406	0.1659	-0.0596	0.0543	-0.2302	-0.1062	0	0.2576	0.011	-0.0139	0.2759	0.008	0.3142	-47.5004	-3.3823	-19.7161
64	0.0298	0.022	0.0298	0.03	0.0192	0.0258	0.0646	-0.6056	-0.2175	0.3353	0.1393	0.2167	0.1097	-0.6008	0.0001	0.2427	0.0115	0.0074	0.4283	-0.0201	0.3754	-60.3996	-5.707	-24.1762
65	0.2388	0.0028	-0.1006	0.1387	0.1868	0.349	0.0098	-0.1603	0.0838	0.0383	-0.0872	0.3976	0.1032	-0.2448	-0.0601	0.1716	0.0003	-0.0245	0.3098	-0.0246	0.3851	-59.8816	-11.0284	-34.0357
66	0.0879	0.0326	-0.0887	0.0384	-0.0054	0.042	-0.0045	-0.0485	0.1848	-0.1711	0.1362	0.415	-0.5373	-0.4371	0.0014	0.2255	0.034	-0.1023	0.292	0.01	0.343	-60.4285	-2.8259	-45.5494
67	0.1513	0.078	0.0688	0.0445	0.059	0.0134	0.0681	0.2961	-0.2875	-0.5184	-0.324	-0.0528	-0.3672	0.3005	-0.0025	0.293	0.0341	-0.0921	0.3625	0.0404	0.3147	-29.2054	7.2717	-46.9352
68	1.1021	-0.0324	0.2527	0.195	-0.0337	0.8963	-0.0382	0.0075	0.0776	-0.1136	0.0075	0.1083	-0.0671	0.0138	-0.0024	0.3033	-0.0267	-0.0913	0.187	0.0362	0.2353	-25.5535	9.7889	-29.7826
69	0.1851	-0.0418	0.3663	0.245	0.0013	0.2295	-0.1087	-0.1177	-0.0147	0.0731	0.0713	-0.0527	-0.03	0.0019	0	0.2863	0.0018	-0.0291	0.2275	0.0145	0.2046	-16.9916	-0.3609	-12.1183
70	0.2225	0.1631	-0.1417	-0.0073	0.0513	0.3211	-0.0933	-0.3655	0.016	0.1679	0.0713	0.2058	-0.2062	-0.2696	0.0002	0.3311	0.0341	-0.0437	0.3187	0.0153	0.3062	-33.0903	6.6112	-11.5578
71	0.0609	-0.0362	-0.0036	0.0179	0.0248	0.0458	-0.2825	0.056	0.6401	-0.0414	0.0496	0.3064	-0.2869	0.0366	0.0002	0.3772	-0.006	-0.1119	0.2568	0.0154	0.3662	-39.2069	15.1056	-24.6617
72	0.1245	-0.0758	0.1037	0.0308	-0.0685	0.0074	0.0658	0.3866	-0.241	-0.4576	-0.0335	0.1999	0.3514	0.2912	-0	0.414	-0.0206	-0.1077	0.257	0.0057	0.2664	-14.6085	7.8421	-45.7397
73	0.3023	-0.5844	0.2532	0.4912	-0.0183	0.8529	0.0591	0.0507	0.0951	-0.153	0.0145	-0.0161	-0.0646	0.0262	-0.0001	0.3028	-0.0485	0.0001	0.2004	0.0233	0.2012	-0.9606	3.3212	-36.4458
74	0.1941	-0.0321	0.2521	0.2983	0.0161	0.3319	-0.1511	-0.083	-0.144	-0.0544	0.141	-0.2113	-0.1197	-0.0321	0.0025	0.2725	-0.0269	-0.0438	0.2367	0.0356	0.2241	-3.5144	8.6618	-24.465
75	0.0536	-0.0058	0.1048	0.0225	-0.0291	0.1291	-0.0815	-0.0293	0.0889	-0.0466	0.0582	0.096	0.0369	-0.1536	-0.0001	0.3068	-0.0398	0.0242	0.242	0.0167	0.3056	2.5424	-18.186	-23.0471
76	0.5653	-0.1377	0.0099	0.1195	0.0946	0.1511	-0.0311	0.0047	0.131	-0.2295	0.0502	-0.2929	-0.0549	0.0363	-0.0001	0.2501	-0.0307	0.0003	0.2565	-0.0073	0.245	10.3992	-10.3671	-24.0248
77	0.1956	0.09	-0.0852	0.0689	-0.0356	0.0266	-0.1124	-0.2753	-0.0741	0.2457	0.1938	-0.0957	-0.0817	0.0156	0.0001	0.2991	-0.0123	-0.0486	0.2715	-0.0077	0.2597	2.2823	1.5316	-15.0077
78	0.0857	0.1141	-0.0387	0.1115	-0.0061	0.053	0.0303	-0.2267	0.3969	-0.161	-0.0016	0.177	-0.5437	0.0058	0.0002	0.4138	-0.0066	-0.0196	0.2302	-0.0238	0.2945	-4.4372	14.5553	-23.1672

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 70 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 71 through 132 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 133 through 158 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 159 through 192 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 4 through 27 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 28 through 94 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 95 through 132 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 183 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 184 through 192 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 4 through 27 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 28 through 106 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 107 through 132 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 133 through 158 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 159 through 183 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 184 through 192 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 3 through 106 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 107 through 132 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 133 through 158 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 159 through 192 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 4 through 27 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 28 through 122 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 123 through 132 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 133 through 158 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 159 through 183 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 184 through 192 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 4 through 37 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 38 through 70 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 71 through 132 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 133 through 158 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 159 through 192 )
33	X-RAY DIFFRACTION	33	chain 'G' and (resid 4 through 54 )
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 55 through 122 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 123 through 158 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 159 through 192 )
37	X-RAY DIFFRACTION	37	chain 'H' and (resid 4 through 27 )
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 28 through 54 )
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 55 through 106 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 107 through 122 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 123 through 132 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 133 through 158 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 159 through 183 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 184 through 192 )
45	X-RAY DIFFRACTION	45	chain 'I' and (resid 4 through 27 )
46	X-RAY DIFFRACTION	46	chain 'I' and (resid 28 through 122 )
47	X-RAY DIFFRACTION	47	chain 'I' and (resid 123 through 132 )
48	X-RAY DIFFRACTION	48	chain 'I' and (resid 133 through 158 )
49	X-RAY DIFFRACTION	49	chain 'I' and (resid 159 through 172 )
50	X-RAY DIFFRACTION	50	chain 'I' and (resid 173 through 192 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 4 through 27 )
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 28 through 122 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 123 through 158 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 159 through 192 )
55	X-RAY DIFFRACTION	55	chain 'K' and (resid 4 through 27 )
56	X-RAY DIFFRACTION	56	chain 'K' and (resid 28 through 122 )
57	X-RAY DIFFRACTION	57	chain 'K' and (resid 123 through 158 )
58	X-RAY DIFFRACTION	58	chain 'K' and (resid 159 through 192 )
59	X-RAY DIFFRACTION	59	chain 'L' and (resid 4 through 27 )
60	X-RAY DIFFRACTION	60	chain 'L' and (resid 28 through 54 )
61	X-RAY DIFFRACTION	61	chain 'L' and (resid 55 through 70 )
62	X-RAY DIFFRACTION	62	chain 'L' and (resid 71 through 132 )
63	X-RAY DIFFRACTION	63	chain 'L' and (resid 133 through 158 )
64	X-RAY DIFFRACTION	64	chain 'L' and (resid 159 through 169 )
65	X-RAY DIFFRACTION	65	chain 'L' and (resid 170 through 183 )
66	X-RAY DIFFRACTION	66	chain 'L' and (resid 184 through 192 )
67	X-RAY DIFFRACTION	67	chain 'M' and (resid 4 through 27 )
68	X-RAY DIFFRACTION	68	chain 'M' and (resid 28 through 122 )
69	X-RAY DIFFRACTION	69	chain 'M' and (resid 123 through 158 )
70	X-RAY DIFFRACTION	70	chain 'M' and (resid 159 through 183 )
71	X-RAY DIFFRACTION	71	chain 'M' and (resid 184 through 192 )
72	X-RAY DIFFRACTION	72	chain 'N' and (resid 4 through 27 )
73	X-RAY DIFFRACTION	73	chain 'N' and (resid 28 through 106 )
74	X-RAY DIFFRACTION	74	chain 'N' and (resid 107 through 122 )
75	X-RAY DIFFRACTION	75	chain 'N' and (resid 123 through 132 )
76	X-RAY DIFFRACTION	76	chain 'N' and (resid 133 through 158 )
77	X-RAY DIFFRACTION	77	chain 'N' and (resid 159 through 183 )
78	X-RAY DIFFRACTION	78	chain 'N' and (resid 184 through 192 )

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-Aug 12, 2020. Covid-19 info

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi