PDB-8w1f: Crystal Structure of DPS-like protein PA4880 from Pseudomonas aer...

ID or keywords:

Entry

Database: PDB / ID: 8w1f

Title

Crystal Structure of DPS-like protein PA4880 from Pseudomonas aeruginosa (dodecamer, Mg bound)

Components

DPS-LIKE PROTEIN

Keywords

METAL BINDING PROTEIN / PA4880 / DPS protein / metal binding / DNA cleavage / dodecamer

Function / homology

Function and homology information

ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P. / Rivera, M.

Funding support

United States, 1items

Citation

Journal: Front Mol Biosci / Year: 2024
Title: Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity.
Authors: Rajapaksha, N. / Yao, H. / Cook, A. / Seibold, S. / Liu, L. / Battaile, K.P. / Fontenot, L. / Donnarumma, F. / Lovell, S. / Rivera, M.

History

Deposition	Feb 15, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 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

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Full document	8w1f_full_validation.pdf.gz	35.3 MB	Display
Data in XML	8w1f_validation.xml.gz	66.2 KB	Display
Data in CIF	8w1f_validation.cif.gz	89.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w1/8w1f ftp://data.pdbj.org/pub/pdb/validation_reports/w1/8w1f	HTTPS FTP

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Related structure data

Related structure data	8w1dC 8w1eC 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
Related items in Molecule of the Month	#35 - Nov 2002 Ferritin and Transferrin similarity (6) #111 - Mar 2009 Hydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #244 - Apr 2020 Photosynthetic Supercomplexes similarity (1) #114 - Jun 2009 Vaults similarity (1) #57 - Sep 2004 Catalase similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #61 - Jan 2005 Phenylalanine Hydroxylase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#35 - Nov 2002
Ferritin and Transferrin
similarity (6)
#111 - Mar 2009
Hydrogenase
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#244 - Apr 2020
Photosynthetic Supercomplexes
similarity (1)
#114 - Jun 2009
Vaults
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (1)
#61 - Jan 2005
Phenylalanine Hydroxylase
similarity (1)

Deposited unit

A: DPS-LIKE PROTEIN

B: DPS-LIKE PROTEIN

C: DPS-LIKE PROTEIN

D: DPS-LIKE PROTEIN

E: DPS-LIKE PROTEIN

F: DPS-LIKE PROTEIN

G: DPS-LIKE PROTEIN

H: DPS-LIKE PROTEIN

I: DPS-LIKE PROTEIN

J: DPS-LIKE PROTEIN

K: DPS-LIKE PROTEIN

L: DPS-LIKE PROTEIN

hetero molecules

249 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, 12 mer

Unit cell

Length a, b, c (Å)	215.790, 215.790, 277.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	F-204- MG

#1: Protein	DPS-LIKE PROTEIN Mass: 20241.627 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4880 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUT3
#2: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	... ChemComp-FE2 / FE (II) ION Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 6.65 Å³/Da / Density % sol: 81.51 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Salt Rx G2: 1 M magnesium sulfate, 100 mM Bis-Tris pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2022
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 3→49.94 Å / Num. obs: 130805 / % possible obs: 100 % / Redundancy: 14.3 % / CC_1/2: 0.997 / R_merge(I) obs: 0.202 / R_pim(I) all: 0.055 / R_rim(I) all: 0.209 / Χ²: 1 / Net I/σ(I): 12.1 / Num. measured all: 1874799
Reflection shell	Resolution: 3→3.05 Å / % possible obs: 100 % / Redundancy: 15.1 % / R_merge(I) obs: 1.798 / Num. measured all: 96579 / Num. unique obs: 6414 / CC_1/2: 0.719 / R_pim(I) all: 0.476 / R_rim(I) all: 1.861 / Χ²: 0.99 / Net I/σ(I) obs: 1.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.21rc1_5156: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3→31.27 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2036	6576	5.04 %
R_work	0.1792	-	-
obs	0.1804	130536	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→31.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16144	0	281	23	16448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	16536
X-RAY DIFFRACTION	f_angle_d	0.87	22359
X-RAY DIFFRACTION	f_dihedral_angle_d	12.275	6179
X-RAY DIFFRACTION	f_chiral_restr	0.042	2465
X-RAY DIFFRACTION	f_plane_restr	0.01	2982

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 (%)
3-3.03	0.305	216	0.2917	4098	X-RAY DIFFRACTION	100
3.03-3.07	0.3254	227	0.2946	4030	X-RAY DIFFRACTION	100
3.07-3.11	0.3332	219	0.293	4109	X-RAY DIFFRACTION	100
3.11-3.15	0.3237	215	0.3004	4097	X-RAY DIFFRACTION	100
3.15-3.19	0.3272	204	0.2964	4090	X-RAY DIFFRACTION	100
3.19-3.23	0.3022	197	0.2757	4093	X-RAY DIFFRACTION	100
3.23-3.28	0.2799	210	0.2449	4098	X-RAY DIFFRACTION	100
3.28-3.33	0.2535	192	0.2305	4120	X-RAY DIFFRACTION	100
3.33-3.38	0.2658	235	0.2306	4072	X-RAY DIFFRACTION	100
3.38-3.43	0.249	232	0.227	4049	X-RAY DIFFRACTION	100
3.43-3.49	0.2638	204	0.2294	4142	X-RAY DIFFRACTION	100
3.49-3.56	0.276	215	0.2177	4095	X-RAY DIFFRACTION	100
3.56-3.62	0.2005	205	0.1924	4114	X-RAY DIFFRACTION	100
3.62-3.7	0.2028	249	0.1807	4042	X-RAY DIFFRACTION	100
3.7-3.78	0.2289	203	0.1821	4143	X-RAY DIFFRACTION	100
3.78-3.87	0.2205	217	0.1719	4122	X-RAY DIFFRACTION	100
3.87-3.96	0.1887	204	0.168	4105	X-RAY DIFFRACTION	100
3.96-4.07	0.1865	233	0.1579	4138	X-RAY DIFFRACTION	100
4.07-4.19	0.1572	207	0.1394	4103	X-RAY DIFFRACTION	100
4.19-4.32	0.1562	233	0.1375	4119	X-RAY DIFFRACTION	100
4.32-4.48	0.1604	228	0.1329	4115	X-RAY DIFFRACTION	100
4.48-4.66	0.1689	215	0.1237	4130	X-RAY DIFFRACTION	100
4.66-4.87	0.1564	239	0.1341	4128	X-RAY DIFFRACTION	100
4.87-5.12	0.1824	226	0.1512	4155	X-RAY DIFFRACTION	100
5.12-5.44	0.1685	213	0.1591	4169	X-RAY DIFFRACTION	100
5.44-5.86	0.2052	223	0.1809	4191	X-RAY DIFFRACTION	100
5.86-6.45	0.2287	207	0.1911	4203	X-RAY DIFFRACTION	100
6.45-7.37	0.1691	230	0.161	4226	X-RAY DIFFRACTION	100
7.37-9.24	0.1627	258	0.1363	4242	X-RAY DIFFRACTION	100
9.24-31.27	0.2054	220	0.196	4422	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	0.1152	0.2314	0.0168	0.4638	0.0403	0.081	-0.0725	-0.5769	-0.3037	-0.6376	0.204	-0.6081	0.0035	0.4406	-0.3259	0.9142	-0.2132	0.4858	1.1061	0.1404	1.1193	45.6872	-58.083	-90.1228
2	0.4328	0.0096	0.351	0.0931	0.102	0.3715	0.6194	1.3419	-0.199	0.1236	0.0414	-0.3679	-0.4906	0.5035	0.0664	0.6306	-0.1658	0.061	0.7023	-0.0412	0.7251	38.2013	-48.5381	-85.741
3	1.6531	-0.4237	-0.6124	0.2247	0.3662	1.1169	-0.0811	0.068	-0.079	-0.0664	0.0079	0.0449	-0.3141	-0.0509	0.0001	0.6309	-0.0541	-0.0365	0.4529	0.0335	0.6029	14.2521	-39.4685	-72.7381
4	0.2648	-0.1351	0.0089	0.36	-0.3289	0.6471	-0.4156	0.7316	-0.5559	0.0711	0.0535	0.1716	0.1508	-0.1858	-0.0004	0.6483	-0.0217	-0.0137	0.5579	-0.0235	0.6732	8.3013	-44.7814	-79.9291
5	0.044	-0.0176	0.0135	0.0298	-0.0209	0.0151	0.0807	-0.0097	0.6037	-0.2021	0.1997	-0.3336	-0.9431	0.2927	0.0006	0.8813	-0.1634	-0.0084	1.0467	0.0605	0.7277	0.3581	-66.7522	-108.8801
6	0.015	-0.0169	0.0328	0.1803	0.0236	0.1213	-0.1297	0.7376	-0.5062	-0.7516	-0.5067	0.096	-0.5928	-0.0127	-0	0.7415	-0.0738	-0.0078	1.0066	-0.07	0.7819	13.2546	-68.4883	-105.7105
7	0.6589	-0.1243	1.04	0.9735	0.0205	1.8169	-0.1035	0.0078	0.0774	-0.0392	-0.0211	-0.1359	0.0264	0.0895	0	0.5179	-0.0707	0.0635	0.6054	-0.0318	0.5516	33.7198	-67.4543	-85.2545
8	0.4716	0.1098	-0.403	0.4178	-0.0707	0.3632	-0.1754	-0.5914	0.3406	-0.0634	-0.0097	0.1418	-0.4256	-0.4556	-0.0004	0.5876	-0.0643	0.0005	0.6329	-0.0407	0.6212	30.3187	-57.7278	-82.1771
9	0.0694	0.0112	-0.0533	0.1013	0.002	0.0545	-0.6363	-0.4684	-0.3493	0.4867	0.7254	-0.2235	0.7108	0.753	0.0013	0.9003	0.3649	-0.1065	1.0348	-0.0771	0.9965	51.5075	-83.0896	-45.0468
10	0.0346	0.0086	-0.0315	0.0018	-0.0091	0.0468	0.0219	0.7298	-0.5168	0.121	-0.2896	-1.1645	0.1069	-0.4286	0.0001	0.6469	0.0673	-0.0498	1.1538	-0.1954	0.9038	52.2814	-79.9104	-55.7181
11	0.2733	0.3863	-0.004	0.5409	-0.0044	0.0002	0.1754	-0.5881	0.1835	0.4726	-0.2376	-0.5316	-0.1302	0.6395	-0.0172	0.6759	0.2951	-0.1082	0.8732	0.0005	0.8275	48.2314	-89.2437	-58.4451
12	0.1447	0.1456	-0.3265	0.8177	-0.2784	0.6588	0.0767	0.3042	-0.1661	-0.294	-0.0833	0.0059	0.2122	0.1359	0.0002	0.6104	0.0408	0.0697	0.5585	-0.1005	0.6528	33.4127	-85.381	-81.1633
13	0.1641	0.0192	0.1829	0.6269	-0.5018	0.5816	-0.269	-1.2807	-0.2311	-0.0241	0.0323	0.0732	0.0449	-0.8651	0.0007	0.5671	0.0434	0.0595	0.6354	-0.0559	0.6924	26.4695	-84.2676	-76.8892
14	0.2244	-0.0265	0.0504	0.0016	-0.026	0.1802	-0.3992	0.4653	0.5347	0.0523	-0.6039	-0.6662	0.039	0.4535	-0.0016	0.4637	0.0743	0.0388	0.9071	-0.056	0.7387	43.8744	-79.4578	-77.7402
15	0.2767	0.3153	-0.2179	0.3457	-0.2483	0.1715	-0.3126	0.152	0.1942	-0.4755	0.1272	-0.1352	0.4556	-0.1083	0.0075	0.5241	0.1012	-0.0214	0.7089	-0.1705	0.7395	34.422	-87.9097	-89.4227
16	0.875	0.9749	-0.107	1.0513	-0.1068	0.083	0.0519	-0.248	0.3334	-0.1777	-0.2438	-0.1123	1.0489	-0.4238	0.0005	0.7229	0.083	0.0493	0.5745	-0.1426	0.6365	32.2881	-96.5268	-78.8717
17	0.8779	-0.0595	-0.7293	0.0252	0.0477	0.6003	-0.094	-0.7841	-0.2089	0.1248	0.0367	0.0263	0.3008	-0.9051	0.0002	0.6949	0.014	-0.0044	0.6546	-0.0371	0.6824	26.111	-94.6647	-74.9167
18	0.0108	0.0525	-0.0414	0.2197	-0.1787	0.1418	-0.2954	0.2886	-0.2302	-0.2996	0.2278	-0.3019	0.3567	0.426	0.0001	1.0848	0.135	0.1275	0.6989	-0.0214	0.8231	32.1894	-102.3979	-87.1261
19	0.0411	-0.0004	0.084	0.0256	-0.0061	0.17	-0.151	0.1525	-0.6833	-0.2749	0.6142	-0.2143	-0.3664	0.9483	0.0009	0.8797	0.1545	0.1004	0.6599	-0.1185	0.7618	28.3505	-107.1356	-75.5912
20	1.1804	0.5252	0.4332	0.7842	-0.1615	0.3447	-0.2244	-0.1433	-0.3488	0.0084	0.1037	0.4411	0.4293	-0.1463	0	0.7207	-0.0101	-0.0099	0.3867	0.0644	0.6239	7.668	-104.014	-58.1936
21	0.514	-0.1097	-0.3908	0.1037	-0.1472	0.8978	-0.0011	0.0493	-0.3299	0.0547	-0.0334	0.076	0.2112	0.1176	0.0003	0.7414	0.0073	0.0002	0.4676	-0.0496	0.6947	8.9177	-99.2086	-60.2161
22	0.0198	0.0157	0.0599	0.0259	0.0772	0.1598	0.0158	-0.4734	-0.5346	-0.0549	-0.0504	0.0448	0.3531	0.0917	0.0012	0.8252	0.0434	0.0984	0.4736	-0.0164	0.6112	3.5656	-109.5158	-53.5085
23	0.446	-0.0442	0.5677	0.1121	0.0742	0.8035	0.1611	-0.333	-0.4453	-0.0402	-0.0935	0.0458	-0.0514	0.2999	-0.0002	0.8962	0.0256	-0.03	0.5555	0.0231	0.7552	16.6214	-106.4012	-51.5081
24	0.4575	-0.2757	0.1698	0.591	-0.2227	0.2256	0.409	-0.3806	0.2795	-0.0262	0.1386	-0.0918	-0.6138	0.8254	0.0006	0.694	0.0085	0.0497	0.575	-0.0126	0.6896	17.7394	-98.9391	-50.9561
25	0.2731	0.1401	-0.0666	0.156	-0.0232	0.0568	-0.8308	-0.1643	-0.514	0.8269	-0.2199	0.5133	-0.4252	-0.3528	-0.007	1.0877	-0.0555	-0.0313	0.7639	-0.145	0.5998	32.5944	-33.3425	-45.1181
26	0.0318	0.0328	-0.0428	0.0313	-0.0344	0.0754	0.32	-0.1024	1.3063	0.6471	-0.3486	0.1674	-0.5536	0.9947	-0.0002	0.8349	-0.1207	-0.0681	0.7927	0.0427	0.7172	33.33	-44.53	-37.8046
27	0.1978	-0.2707	0.1944	0.383	-0.0895	0.7077	0.0242	-0.1658	-0.2041	0.5731	0.1028	-0.3974	0.2658	0.1798	0.0003	0.6418	0.0781	0.0219	0.5704	0.0308	0.5079	24.9286	-71.9095	-32.7651
28	0.1532	-0.2369	0.0118	0.5142	-0.0939	0.0034	-0.3771	0.2037	0.3292	-0.4647	0.3914	0.4848	0.0461	-0.057	0	0.6916	-0.0001	-0.0191	0.6325	-0.0342	0.5773	19.0163	-71.5896	-38.491
29	0.1421	0.0626	-0.0564	0.027	-0.0271	0.026	-0.1293	0.3492	0.2078	-0.3204	0.9012	-0.9566	0.029	0.2948	0.0369	0.6026	-0.0446	-0.0982	0.5441	-0.0716	0.6316	36.0033	-66.4889	-35.0227
30	0.2265	-0.1103	0.0818	0.1458	0.0793	0.177	-0.052	-0.2174	-0.0248	0.9701	0.2981	-0.0675	-0.1133	0.2327	0.0005	0.7597	-0.0716	0.0018	0.573	0.0133	0.5985	26.115	-77.6298	-26.2975
31	1.2319	0.1924	-0.0116	0.15	0.2305	0.415	-0.3149	0.1356	0.0509	0.7669	0.8349	0.3122	0.0166	-0.0424	-0.0002	0.6792	0.0193	0.0713	0.5595	0.0108	0.606	17.4622	-66.7854	-25.7728
32	0.2599	0.064	0.1734	0.2174	0.1327	0.727	-0.1502	0.012	0.6345	-0.3185	0.3673	1.0323	0.0023	-0.0847	-0	0.6904	0.0456	0.0515	0.6161	0.0095	0.6145	12.6831	-66.7091	-31.5983
33	0.079	0.0244	-0.0048	0.1218	0.1066	0.0979	0.4769	-0.7808	1.0263	0.459	-0.0374	0.3032	-0.8954	0.549	0.0007	0.8639	0.1486	0.0948	0.7673	-0.0528	0.8832	-13.0982	-39.4204	-37.8715
34	0.1523	-0.0733	-0.0074	0.0454	-0.0277	0.0873	0.4148	-0.4927	-0.1069	0.5134	0.1453	0.5879	-0.6754	0.1698	-0.001	0.8086	0.1588	0.111	0.649	-0.1497	0.7814	-0.1149	-37.0244	-38.2638
35	0.336	0.2445	-0.0002	0.747	-0.8248	1.1159	0.0791	-0.0176	0.0219	-0.0931	-0.0838	-0.0134	-0.6306	0.2889	0	0.6167	-0.0805	-0.0444	0.4583	-0.0417	0.5613	20.7829	-40.0378	-55.4989
36	0.3366	-0.1877	-0.1467	0.2906	-0.3074	0.6112	-0.526	-0.0509	-0.9369	0.5723	0.0594	0.374	0.0778	0.0595	0.0001	0.723	-0.0057	-0.0291	0.4637	-0.0393	0.6754	19.9964	-48.2649	-55.5311
37	0.1245	-0.003	0.0266	0.0539	0.0479	0.0414	-0.4618	0.2918	0.0271	-0.3658	0.0331	0.2592	-0.6789	-0.9388	0	0.9753	0.1129	0.0109	0.5712	0.004	0.7708	10.6423	-32.9143	-57.0038
38	0.1655	-0.2123	0.0507	0.2361	-0.0692	0.0994	-0.0262	-0.7054	-0.301	-0.1653	0.0762	0.0255	-0.3706	0.6065	0.0002	0.7818	0.02	-0.0012	0.4896	-0.1235	0.7295	27.7257	-35.1083	-57.3009
39	0.6423	-0.3196	0.6079	0.5405	-0.3119	0.5563	0.1008	-0.2974	-0.6806	-0.1834	-0.3221	0.2059	-0.8074	0.2933	0.0001	0.6302	-0.0463	-0.0336	0.4706	-0.0245	0.5223	25.3961	-41.227	-45.1218
40	0.3856	0.2799	0.1742	0.6894	-0.0069	0.3539	-0.7867	-0.3736	-0.8076	0.2528	0.2404	0.2441	0.105	0.2707	-0	0.6284	-0.0509	0.0256	0.6165	0.0319	0.5764	24.1372	-48.6819	-45.8259
41	0.039	-0.0266	0.0515	0.1387	-0.0593	0.0877	-0.4705	0.3054	-0.3347	-0.679	0.333	0.1848	-0.7345	-0.4874	-0.0006	1.0453	0.0357	-0.1332	0.8112	0.1316	0.9404	4.4004	-29.7129	-82.219
42	0.4514	-0.3273	-0.3578	0.2403	0.2597	0.2832	-0.2544	-0.0047	1.1598	-0.0787	0.6649	-0.017	0.0865	0.0502	0.0375	1.0731	-0.0355	-0.1115	0.6689	0.1019	0.7148	4.6231	-38.9426	-90.6895
43	1.1142	0.1955	-0.2197	0.2025	0.1878	0.3158	-0.2776	0.4186	-0.0337	-0.762	0.303	0.5611	0.252	-0.3003	0.0001	0.5448	-0.0907	-0.0886	0.7049	0.0028	0.4789	-4.2048	-64.6981	-92.52
44	0.655	0.451	-0.3716	0.4696	-0.0945	0.2696	0.0983	0.1411	0.0935	0.7607	-0.2237	-0.5865	0.0508	-0.1625	0.0004	0.7121	-0.0216	-0.0352	0.663	0.0081	0.5954	1.047	-67.3101	-86.7578
45	0.0661	-0.0602	0.0694	0.0525	-0.0605	0.056	-0.4226	-0.0072	0.3836	0.4052	0.6686	0.4811	-0.6639	-0.6342	0.0002	0.7277	-0.0076	-0.0653	0.7201	0.1278	0.6879	-10.9928	-54.3267	-90.4301
46	0.3963	-0.1182	-0.1809	0.1287	0.0302	0.0774	-0.2569	0.4893	-0.2366	-0.8057	0.5817	-0.0749	-0.1972	0.1263	0.0011	0.7979	-0.0428	0.0238	0.5741	0.0595	0.6007	-8.1263	-69.1655	-98.8467
47	0.5705	-0.2829	-0.5655	0.299	0.1648	0.6047	-0.4786	0.566	-0.1182	-0.2797	0.8334	-0.4057	-0.121	-0.1102	-0.0002	0.6485	-0.1167	-0.0532	0.7221	-0.0421	0.6427	4.8439	-64.2355	-99.5553
48	0.5793	0.2601	0.0759	0.2894	-0.3248	0.7318	-0.1013	0.0839	0.0392	0.5136	0.2762	-0.9573	0.0647	-0.0552	0.0001	0.6124	-0.1113	-0.0767	0.649	-0.0154	0.5849	8.9999	-66.4504	-93.6931
49	0.5239	-0.4568	0.2954	0.448	-0.2414	0.1301	-0.0985	-0.399	0.0786	0.7515	0.2081	-0.15	0.0176	-0.48	0	0.8393	0.0146	-0.0012	0.611	0.1285	0.7488	18.8466	-109.9017	-43.5884
50	0.5056	0.5105	-0.1632	1.1778	0.0486	1.0214	-0.0656	0.0002	0.0145	0.0266	0.1707	-0.1449	0.115	0.22	-0	0.5917	0.1005	-0.0202	0.6032	0.0326	0.6043	35.6853	-81.166	-44.6171
51	0.1943	0.0202	0.0957	0.3109	-0.4125	0.5574	-0.4815	0.5348	0.0233	-0.8762	0.6333	0.2227	0.5105	0.0387	-0.0002	0.6467	0.0308	-0.0302	0.6259	-0.0264	0.648	37.5103	-83.0548	-54.9483
52	0.0254	0.0018	-0.0025	0.0528	-0.0346	0.1076	0.3935	0.078	0.6505	0.1869	-0.2548	-0.2047	0.009	0.0292	-0.0014	0.9257	0.0986	0.0959	0.7081	-0.0815	0.6555	19.7678	-71.2025	-16.5863
53	0.2974	-0.0417	-0.1295	0.1636	-0.0388	0.0722	-0.2488	-0.8822	-0.3326	0.9089	-0.3376	0.0442	-0.1946	0.4769	-0.0006	0.7956	0.1513	0.0855	0.7889	-0.0099	0.6395	8.1202	-66.0879	-19.6747
54	0.6961	0.1354	0.105	0.4623	0.0254	0.5451	0.0666	-0.0026	0.1016	0.0397	-0.1074	0.1197	0.0484	0.0812	-0	0.6106	0.0511	0.1074	0.6	-0.0592	0.6189	-8.1848	-57.7396	-42.786
55	0.8547	0.5436	-0.0951	0.8103	-0.0539	0.4673	0.0566	-0.1897	0.2996	0.1708	-0.1937	0.0472	0.005	-0.1258	0.0002	0.6769	0.0988	0.0807	0.6086	-0.0314	0.6028	-10.203	-52.2916	-36.8829
56	0.8564	0.3377	-0.446	0.5081	-0.0019	0.3064	-0.1107	0.4461	0.419	0.1369	-0.3388	-0.2386	-0.1866	0.7117	-0.0002	0.5987	0.1144	0.0293	0.6092	-0.0054	0.6712	-1.3528	-48.6385	-43.387
57	0.3115	-0.1262	0.1444	0.0823	-0.0409	0.044	-0.235	0.6279	-0.2626	-0.2905	0.4652	0.477	0.7223	-0.0666	-0.0003	0.778	-0.1583	-0.0933	0.7006	-0.0706	0.7922	-18.0174	-100.6101	-80.754
58	0.7822	0.3722	0.0584	1.3759	-0.3165	0.4567	-0.0927	0.1644	0.0812	-0.042	0.1599	-0.0581	-0.0259	-0.2327	-0.0001	0.5051	-0.0465	-0.0456	0.7375	-0.0232	0.5821	-14.5727	-68.0789	-81.3687
59	0.0625	-0.2023	-0.3303	0.8442	1.0678	1.3639	-0.1338	0.102	0.0089	0.2658	0.1934	-0.0417	0.004	-0.4019	-0.0001	0.4492	0.0021	-0.0814	0.7411	-0.0352	0.7069	-24.1834	-65.2024	-79.1962
60	0.7113	-0.0788	-0.379	0.2564	-0.1507	0.3355	0.0395	-0.1662	-0.0755	1.0206	-0.0494	0.1388	0.2541	-0.2076	0.0002	0.5863	-0.0097	-0.061	0.7005	0.0139	0.6697	-20.6378	-67.4854	-70.1524
61	0.1429	-0.0223	-0.1285	0.0317	-0.0007	0.1152	0.316	0.261	-0.5701	0.3077	-0.7346	0.1632	0.5606	-1.4176	0.0017	0.927	-0.1731	0.1639	0.9632	-0.0545	0.7918	-25.7036	-85.9662	-37.4291
62	0.0357	-0.0213	-0.0275	0.0451	-0.0383	0.1019	-0.2121	0.9089	-0.4348	0.25	0.3746	0.7383	-0.8572	-0.4081	0.0011	0.7719	-0.1723	0.1278	0.9237	-0.0239	0.7352	-24.7854	-92.389	-48.9727
63	0.4577	-0.2262	0.1623	0.5699	0.0274	0.0624	-0.0406	0.309	-0.6379	-0.1188	-0.0917	-0.0221	0.1057	-0.1422	-0.0004	0.6579	-0.1611	-0.0259	0.483	-0.035	0.6875	-5.4585	-100.5377	-66.3115
64	0.3532	-0.2626	-0.2284	0.1991	0.082	0.1849	0.3602	-0.039	0.6418	-0.1242	0.3932	0.2446	-0.3188	-0.2207	0.0001	0.5993	-0.1388	0.0083	0.6149	0.0082	0.6093	-3.011	-92.7851	-67.7653
65	0.3744	-0.0595	-0.0078	0.4133	-0.2031	0.1258	-0.05	-0.0027	-0.5263	0.0774	-0.0417	0.0738	0.0893	0.1405	0.0001	0.6911	-0.2081	0.088	0.7052	0.0362	0.6686	-5.8548	-106.1515	-63.8052
66	0.4452	0.2109	0.3027	0.1812	-0.1227	0.8173	0.3103	0.211	-0.3567	-0.2768	-0.1331	0.0777	-0.4304	-0.4296	-0.0002	0.7223	-0.1289	-0.0225	0.6973	-0.0192	0.678	-14.7206	-97.9734	-72.4486
67	0.4793	0.0332	0.3738	0.3241	0.0615	0.3345	0.6922	0.2243	0.5063	-0.1247	0.1478	0.0103	-0.6826	-0.5779	0.0006	0.6787	-0.1303	0.0178	0.646	-0.0185	0.6502	-11.2679	-91.2493	-74.3112
68	0.2013	-0.076	0.034	0.0506	0.0119	0.0249	-0.0584	-0.3309	0.3607	0.4668	0.5533	0.2201	-0.2514	-0.5401	0.0003	0.6556	0.078	-0.0268	1.1359	0.1432	0.9024	-32.4315	-59.686	-76.7246
69	0.0128	0.0402	-0.0178	0.2366	-0.0521	0.0205	0.3207	0.1322	0.793	-0.5021	-0.77	0.3876	-0.0925	-0.5403	-0.0031	0.4769	0.0718	-0.0203	1.1234	0.0259	0.8372	-32.8228	-67.0599	-66.3862
70	0.6567	0.3049	-0.4719	0.6914	0.3731	0.8939	0.2866	-0.1734	-0.3511	0.1914	-0.1339	0.1391	0.4758	-0.3655	0.0004	0.5606	-0.047	0.1361	0.6447	-0.0218	0.6821	-18.0291	-70.9089	-43.8185
71	0.354	0.26	0.3509	0.2113	0.1908	0.4342	0.4864	0.8885	-0.4273	-0.2141	-0.4759	0.4035	0.4306	0.5764	0.0003	0.4395	-0.0042	0.124	0.6075	0.007	0.6674	-11.5132	-73.5711	-48.1062
72	0.1913	0.1732	0.2173	0.6335	0.395	0.3128	-0.0842	-0.1038	0.0911	0.0527	-0.1797	-0.0378	0.1326	-0.6036	0.0001	0.3288	0.0546	0.0389	0.7157	0.0273	0.7473	-21.9368	-67.199	-40.8807
73	0.3383	-0.2755	0.0196	0.9435	0.046	-0.0026	0.2751	0.1359	0.0901	-0.0086	-0.2939	0.2103	0.8498	0.1029	0	0.6637	-0.0968	0.1134	0.7511	0.0226	0.7142	-22.725	-81.1576	-45.9006
74	0.1748	0.1063	0.1163	0.0863	0.0925	0.1654	0.2054	0.59	-0.2496	-0.2149	-0.1701	0.154	0.5496	0.4329	-0.0003	0.6923	0.0058	0.0755	0.7923	0.0117	0.6906	-16.4996	-82.7734	-49.8814

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 147 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 148 through 177 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 8 through 17 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 18 through 32 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 33 through 147 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 148 through 177 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 10 through 17 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 18 through 22 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 23 through 32 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 33 through 63 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 64 through 93 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 94 through 104 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 105 through 118 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 119 through 147 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 148 through 177 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 8 through 22 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 23 through 32 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 33 through 63 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 64 through 104 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 105 through 118 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 119 through 147 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 148 through 177 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 8 through 17 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 18 through 32 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 33 through 63 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 64 through 93 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 94 through 104 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 105 through 118 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 119 through 147 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 148 through 177 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 8 through 22 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 23 through 32 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 33 through 63 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 64 through 93 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 94 through 104 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 105 through 118 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 119 through 147 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 148 through 177 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 9 through 22 )
42	X-RAY DIFFRACTION	42	chain 'G' and (resid 23 through 32 )
43	X-RAY DIFFRACTION	43	chain 'G' and (resid 33 through 63 )
44	X-RAY DIFFRACTION	44	chain 'G' and (resid 64 through 93 )
45	X-RAY DIFFRACTION	45	chain 'G' and (resid 94 through 104 )
46	X-RAY DIFFRACTION	46	chain 'G' and (resid 105 through 118 )
47	X-RAY DIFFRACTION	47	chain 'G' and (resid 119 through 147 )
48	X-RAY DIFFRACTION	48	chain 'G' and (resid 148 through 177 )
49	X-RAY DIFFRACTION	49	chain 'H' and (resid 9 through 32 )
50	X-RAY DIFFRACTION	50	chain 'H' and (resid 33 through 147 )
51	X-RAY DIFFRACTION	51	chain 'H' and (resid 148 through 177 )
52	X-RAY DIFFRACTION	52	chain 'I' and (resid 9 through 17 )
53	X-RAY DIFFRACTION	53	chain 'I' and (resid 18 through 32 )
54	X-RAY DIFFRACTION	54	chain 'I' and (resid 33 through 93 )
55	X-RAY DIFFRACTION	55	chain 'I' and (resid 94 through 147 )
56	X-RAY DIFFRACTION	56	chain 'I' and (resid 148 through 177 )
57	X-RAY DIFFRACTION	57	chain 'J' and (resid 9 through 32 )
58	X-RAY DIFFRACTION	58	chain 'J' and (resid 33 through 104 )
59	X-RAY DIFFRACTION	59	chain 'J' and (resid 105 through 147 )
60	X-RAY DIFFRACTION	60	chain 'J' and (resid 148 through 177 )
61	X-RAY DIFFRACTION	61	chain 'K' and (resid 8 through 22 )
62	X-RAY DIFFRACTION	62	chain 'K' and (resid 23 through 32 )
63	X-RAY DIFFRACTION	63	chain 'K' and (resid 33 through 63 )
64	X-RAY DIFFRACTION	64	chain 'K' and (resid 64 through 93 )
65	X-RAY DIFFRACTION	65	chain 'K' and (resid 94 through 118 )
66	X-RAY DIFFRACTION	66	chain 'K' and (resid 119 through 148 )
67	X-RAY DIFFRACTION	67	chain 'K' and (resid 149 through 177 )
68	X-RAY DIFFRACTION	68	chain 'L' and (resid 9 through 22 )
69	X-RAY DIFFRACTION	69	chain 'L' and (resid 23 through 32 )
70	X-RAY DIFFRACTION	70	chain 'L' and (resid 33 through 63 )
71	X-RAY DIFFRACTION	71	chain 'L' and (resid 64 through 93 )
72	X-RAY DIFFRACTION	72	chain 'L' and (resid 94 through 118 )
73	X-RAY DIFFRACTION	73	chain 'L' and (resid 119 through 147 )
74	X-RAY DIFFRACTION	74	chain 'L' and (resid 148 through 177 )

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-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