PDB-6o0t: Crystal structure of selenomethionine labelled tandem SAM domains...

ID or keywords:

Entry

Database: PDB / ID: 6o0t

Title

Crystal structure of selenomethionine labelled tandem SAM domains (L446M:L505M:L523M mutant) from human SARM1

Components

Sterile alpha and TIR motif-containing protein 1

Keywords

SIGNALING PROTEIN / Axon degeneration

Function / homology

Function and homology information

extrinsic component of synaptic membrane / negative regulation of MyD88-independent toll-like receptor signaling pathway / NADP+ nucleosidase activity / MyD88-independent TLR4 cascade / Toll Like Receptor 3 (TLR3) Cascade / NAD+ catabolic process / NAD+ nucleosidase activity / regulation of synapse pruning / modification of postsynaptic structure / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Tiancong, Q. / Gilley, J. / Lai, J. / Gu, W. ...

Funding support

Australia, 6items

Organization	Grant number	Country
National Health and Medical Research Council (NHMRC, Australia)	1107804	Australia
National Health and Medical Research Council (NHMRC, Australia)	1160570	Australia
National Health and Medical Research Council (NHMRC, Australia)	1071659	Australia
National Health and Medical Research Council (NHMRC, Australia)	1108859	Australia
Australian Research Council (ARC)	DP160102244	Australia
Australian Research Council (ARC)	DP190102526	Australia

Citation

Journal: Science / Year: 2019
Title: NAD+cleavage activity by animal and plant TIR domains in cell death pathways.
Authors: Horsefield, S. / Burdett, H. / Zhang, X. / Manik, M.K. / Shi, Y. / Chen, J. / Qi, T. / Gilley, J. / Lai, J.S. / Rank, M.X. / Casey, L.W. / Gu, W. / Ericsson, D.J. / Foley, G. / Hughes, R.O. ...

History

Deposition	Feb 17, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 4, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6o0t.cif.gz	472.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6o0t.ent.gz	396.7 KB	Display	PDB format
PDBx/mmJSON format	6o0t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o0/6o0t ftp://data.pdbj.org/pub/pdb/validation_reports/o0/6o0t	HTTPS FTP

-
Related structure data

Related structure data	6o0qC 6o0rC 6o0sC 6o0uC 6o0vC 6o0wC 6o1bC C: citing same article (ref.)
Similar structure data	6o0s-d 6zg1-d 6qwv-1 6qwv-2 6zg0-d 11191 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (9) #60 - Dec 2004 Ubiquitin similarity (3) #122 - Feb 2010 Enhanceosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (3)

Deposited unit

A: Sterile alpha and TIR motif-containing protein 1

B: Sterile alpha and TIR motif-containing protein 1

C: Sterile alpha and TIR motif-containing protein 1

D: Sterile alpha and TIR motif-containing protein 1

E: Sterile alpha and TIR motif-containing protein 1

F: Sterile alpha and TIR motif-containing protein 1

G: Sterile alpha and TIR motif-containing protein 1

H: Sterile alpha and TIR motif-containing protein 1

165 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	94.240, 154.080, 120.995
Angle α, β, γ (deg.)	90.00, 94.55, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	Sterile alpha and TIR motif-containing protein 1 / Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM ...Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM domain-containing protein 2 / Tir-1 homolog Mass: 20598.246 Da / Num. of mol.: 8 / Mutation: L446M, L505M, L523M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SARM1, KIAA0524, SAMD2, SARM / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SZW1
Has protein modification	Y

#1: Protein

Sterile alpha and TIR motif-containing protein 1 / Sterile alpha and Armadillo repeat protein / Sterile alpha motif domain-containing protein 2 / SAM ...

Mass: 20598.246 Da / Num. of mol.: 8 / Mutation: L446M, L505M, L523M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: SARM1, KIAA0524, SAMD2, SARM / Production host:

Escherichia coli (E. coli) / References: UniProt: Q6SZW1

Has protein modification

Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 17% PEG 8000, 20% ethylene glycol, 0.2 M sodium formate, 0.2 M ammonium acetate, 0.2 M trisodium citrate, 0.2 M sodium potassium L-tartrate, 10 mM DTT and 0.1 M Tris pH 7.9

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.8→47.49 Å / Num. obs: 41934 / % possible obs: 99 % / Redundancy: 3.1 % / B_iso Wilson estimate: 49.1 Å² / CC_1/2: 0.988 / R_merge(I) obs: 0.152 / R_pim(I) all: 0.099 / R_rim(I) all: 0.182 / Net I/σ(I): 6.8
Reflection shell	Resolution: 2.8→2.91 Å / Redundancy: 3.1 % / R_merge(I) obs: 1.185 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4410 / CC_1/2: 0.431 / R_pim(I) all: 0.76 / R_rim(I) all: 1.412 / % possible all: 96.9

-
Processing

Software

Name	Version	Classification
PHENIX	(DEV_3357: ???)	refinement
MOSFLM		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→43.19 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.47

	R_factor	Num. reflection	% reflection
R_free	0.238	1997	4.77 %
R_work	0.2	-	-
obs	0.202	41899	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.8→43.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9100	0	0	0	9100

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9260
X-RAY DIFFRACTION	f_angle_d	0.507	12448
X-RAY DIFFRACTION	f_dihedral_angle_d	15.597	3500
X-RAY DIFFRACTION	f_chiral_restr	0.037	1334
X-RAY DIFFRACTION	f_plane_restr	0.003	1614

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.8-2.8701	0.3432	130	0.3242	2872	X-RAY DIFFRACTION	100
2.8701-2.9476	0.3569	152	0.3041	2868	X-RAY DIFFRACTION	99
2.9476-3.0344	0.31	140	0.3045	2823	X-RAY DIFFRACTION	99
3.0344-3.1323	0.3488	142	0.2929	2858	X-RAY DIFFRACTION	99
3.1323-3.2442	0.2911	143	0.274	2854	X-RAY DIFFRACTION	99
3.2442-3.374	0.2853	154	0.2366	2838	X-RAY DIFFRACTION	99
3.374-3.5275	0.244	136	0.2207	2851	X-RAY DIFFRACTION	99
3.5275-3.7134	0.3008	142	0.203	2857	X-RAY DIFFRACTION	99
3.7134-3.9459	0.216	140	0.1815	2879	X-RAY DIFFRACTION	99
3.9459-4.2503	0.2007	145	0.163	2842	X-RAY DIFFRACTION	99
4.2503-4.6776	0.1792	146	0.1548	2851	X-RAY DIFFRACTION	99
4.6776-5.3534	0.2148	136	0.1539	2841	X-RAY DIFFRACTION	99
5.3534-6.7406	0.195	149	0.1895	2833	X-RAY DIFFRACTION	98
6.7406-43.1944	0.1866	142	0.164	2835	X-RAY DIFFRACTION	97

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	2.8169	-2.487	-1.4484	4.6812	5.7826	9.1284	0.7376	0.4373	-0.8673	-0.1834	-0.7034	1.7866	0.7457	-2.6519	0.2855	0.3101	0.0576	0.0377	0.2934	0.0799	0.6177	19.8848	46.638	41.912
2	2.9003	1.63	-2.5275	8.3277	-2.0188	2.7866	-0.3931	-0.8327	0.158	0.9214	-0.0465	0.3667	0.1907	-0.4532	0.0659	0.2916	-0.0427	0.0131	0.5352	0.1169	0.3682	25.2551	46.6865	50.0077
3	7.1024	-1.8165	-0.7799	5.9716	0.6645	5.4135	0.6031	-2.1151	-1.7271	0.832	-0.9749	-1.3623	0.6831	-0.0001	-0.1577	0.3316	-0.0591	-0.3331	0.6327	0.069	-0.7033	29.6909	52.3835	54.5105
4	2.5411	1.5386	-1.3902	5.0381	-0.6007	8.5738	-0.0365	-0.488	0.4282	0.323	-0.1289	0.1675	-1.5895	0.1612	0.321	0.2488	-0.042	-0.0634	0.328	-0.0245	0.4361	24.6652	56.9688	44.1385
5	5.8546	-5.5382	-0.0034	5.4856	0.274	5.7448	-0.662	-0.6684	0.0905	0.651	0.7505	-0.3843	-0.3558	-0.008	0.0445	0.4938	-0.0052	-0.1919	0.5711	-0.0418	0.7921	35.0742	61.1014	48.7628
6	6.2304	3.6381	6.0077	2.5567	3.9264	7.3235	0.2333	-0.4033	-0.2036	-0.2484	-0.5786	-0.1081	0.9823	0.7561	-0.1384	0.0548	-0.1365	-0.2921	0.2329	-0.1937	0.6066	36.588	50.3118	42.4255
7	6.3797	-3.0387	2.3742	3.8619	-4.2412	5.4222	0.1637	1.1877	-0.5412	0.1414	0.0686	-0.1126	-0.95	0.2045	0.1583	0.2135	-0.1162	-0.1826	0.3862	-0.1654	0.6415	20.348	46.7411	30.8008
8	2.0217	-7.3852	1.0207	6.2912	-0.8435	8.7635	1.041	0.339	-0.893	-1.0607	-0.3684	-0.1143	0.7481	-0.3182	-0.2022	0.4334	-0.0503	0.0623	0.6306	-0.1267	0.2992	29.1898	46.6789	23.3043
9	6.123	3.8891	-3.5472	4.4983	0.1875	8.882	0.3492	0.0716	-0.3533	-0.5888	-0.4844	-0.7164	-0.8717	0.9099	0.0486	0.2917	-0.0744	-0.0977	0.2437	0.0166	0.3776	29.1186	51.3245	29.8916
10	7.4754	-3.9535	-2.2707	5.3267	-2.8794	8.4515	-1.0701	1.0552	-0.4824	-0.4678	0.504	0.9285	-1.0305	-0.91	0.5781	0.6021	-0.3256	-0.7384	0.3796	-0.0444	0.6258	21.2899	55.8965	22.0843
11	4.9341	6.009	5.3436	7.3795	6.5452	5.8828	0.1006	0.766	-0.2513	-0.1358	0.6398	-2.3519	-0.0755	0.8835	-0.6088	0.6333	-0.0508	-0.0349	0.6081	0.0532	0.825	29.8523	62.2835	22.2538
12	5.8048	-6.6465	-1.7573	9.1062	-0.0156	3.2968	0.0457	0.0687	0.1352	1.1671	-0.0888	0.003	-0.0893	-0.3611	0.1383	0.332	0.0503	-0.1264	0.4118	-0.0119	0.3343	33.3705	59.5376	30.1545
13	2.9628	0.107	4.2233	6.3689	3.6287	2.089	-0.5508	0.6114	0.3854	-1.195	-0.6259	0.2327	-0.7162	-0.0965	0.9295	0.2555	-0.0966	0.1414	0.6786	-0.1335	0.6171	34.6562	54.447	18.6368
14	2.9536	-1.628	3.073	5.179	0.2372	4.5846	0.6427	-0.8352	0.3429	1.8861	0.1068	2.1785	-0.4357	-3.2081	-0.2896	-0.1573	-0.319	0.1299	0.7447	0.3656	1.4774	4.4979	71.9312	46.4021
15	1.6808	-0.3783	0.9396	5.3046	-2.1571	5.3832	0.2711	-0.7136	0.2569	0.918	0.1925	0.9324	-0.707	0.0114	-0.2102	0.4518	-0.0537	0.0489	0.4101	-0.0414	0.4469	12.9002	75.6075	49.291
16	3.2777	-3.1787	0.4478	3.3497	-1.3437	9.398	0.4934	0.2568	-0.2811	0.2518	-0.2614	0.6539	0.678	0.1183	0.112	0.5565	0.065	-0.1543	0.5074	-0.1013	0.779	22.8664	74.5157	48.6438
17	6.0918	-6.3364	4.4778	8.0426	-5.4827	7.0097	-0.0224	0.2332	-0.4355	-0.2255	0.3034	0.6194	0.2099	-0.2288	-0.2916	0.2607	-0.0584	-0.1255	0.3153	0.0831	0.5668	16.5199	65.6943	42.1268
18	9.807	3.5201	-2.0453	1.9128	0.0364	8.2182	0.5884	0.1875	0.8963	0.3499	0.2201	0.6243	0.0026	-1.3679	-0.1916	0.1304	-0.1676	-0.4667	0.5554	-0.1728	1.1763	2.6406	74.7112	29.9495
19	4.6441	-0.7025	-3.4193	5.0669	3.6574	4.8403	-0.2075	0.4415	-0.1675	-0.5062	0.1671	1.0962	-0.0002	0.0894	0.171	0.4464	-0.0192	-0.262	0.4686	0.0854	0.5327	10.678	72.5662	25.7068
20	5.4418	-1.721	5.4651	8.5247	-1.821	5.6043	1.2057	0.5966	-1.5432	-0.4166	-0.2066	-1.0411	0.8616	0.1353	-0.7571	0.6429	0.0089	-0.1257	0.652	-0.059	0.866	20.6659	78.6251	22.1004
21	8.075	2.3192	-2.7056	7.9298	2.2159	5.8181	-0.0649	0.7556	0.0883	-0.8776	-0.2453	-0.0981	-0.4314	-0.4449	0.2528	0.5843	0.1662	-0.1648	0.3768	0.0131	0.558	19.2007	70.9162	21.814
22	5.4681	-2.4146	5.4635	5.4089	-3.3944	8.9055	0.049	-1.7977	1.8154	0.2059	0.4905	1.1418	-0.1998	-1.5799	-0.0973	0.3055	0.0596	0.2092	0.3259	-0.157	1.0122	9.5259	101.0559	47.7365
23	8.1521	0.7647	1.4083	2.1295	-1.197	8.2177	0.6237	-1.133	0.7157	0.4022	0.0522	0.0397	0.3391	-0.1945	-0.7838	0.3721	-0.0453	0.0449	0.3858	-0.024	0.5269	18.4079	102.3544	47.2632
24	8.4364	4.1	2.5821	3.3372	-1.8709	9.0968	0.6674	-1.233	0.0899	-0.0839	-0.7138	0.1203	1.0695	-0.063	0.0664	0.567	-0.0362	-0.1008	0.4894	-0.0063	0.7919	23.2887	92.3423	48.7852
25	1.0671	-2.4636	2.744	6.0647	-5.8479	8.6512	-0.0883	-0.0313	0.2501	-0.032	0.1588	0.8457	0.7434	-0.9978	-0.4367	0.2233	0.036	-0.1337	0.3488	0.2527	0.9801	12.8931	90.5403	41.8534
26	5.9576	6.4623	-6.0327	8.1065	-4.1695	2.1069	0.1587	0.1021	-0.4828	-0.6769	-0.5275	1.5589	-0.952	-0.9496	0.0349	0.5407	0.035	-0.2895	0.5231	0.0444	1.3898	9.5492	106.541	29.0108
27	6.5442	4.1567	4.0363	5.9257	4.4856	3.7837	-0.3545	0.3434	0.7422	-0.5667	-0.3475	1.1412	0.1426	0.4064	0.551	0.4636	-0.0123	-0.1175	0.4699	0.1784	0.7181	12.6422	97.6857	26.5427
28	5.6308	4.3445	-4.1363	5.9393	-1.2773	4.2623	0.0786	-0.065	0.0829	-0.3666	-0.0872	0.0671	0.1562	-0.1335	-0.0302	0.4677	0.0529	-0.248	0.4616	0.0485	0.6218	23.2703	98.4846	23.5112
29	8.0299	-0.2227	4.3718	3.548	-1.7158	3.8526	-0.5925	1.1078	0.8685	-0.8884	-0.659	-0.4785	-0.7316	1.0657	0.9703	0.7704	-0.0221	-0.1582	0.4526	-0.055	0.8684	17.9603	91.9703	18.2342
30	6.3324	-0.7094	-1.5862	6.0881	-2.1931	6.2303	0.0885	-0.4463	0.6874	0.2762	0.1328	0.2626	-0.01	-0.0122	-0.1969	0.2623	-0.0716	-0.0008	0.3495	-0.1008	0.5282	36.0537	115.172	48.2003
31	5.0061	4.1298	-4.0944	5.5474	-4.8561	4.8248	0.996	0.9416	0.5925	-0.1141	-0.2841	0.8484	-0.1098	0.291	-0.3754	0.244	-0.1073	0.1406	-0.1626	0.0528	0.6174	27.7974	110.9346	42.187
32	5.8362	-2.7077	0.6409	2.9237	0.2717	5.169	0.2475	0.4763	0.7948	-0.0728	-0.0035	0.2769	-0.3049	0.1349	-0.1781	0.423	0.0501	0.0052	0.3383	0.1823	0.7064	35.6707	118.8467	27.1149
33	2.7753	2.4621	-2.3804	3.0527	-3.4084	3.6807	0.0143	0.9925	-0.3159	-0.3157	1.233	1.8388	0.8539	-0.6646	-0.9353	0.4793	0.0526	-0.0992	0.6868	0.0614	0.952	41.6103	106.8323	22.1244
34	4.2966	-0.8498	2.8905	8.2005	-0.6305	7.142	-0.0364	0.856	-0.0734	-0.2906	0.1207	0.1683	-0.2735	0.2282	0.2227	0.2362	-0.0438	-0.0303	0.5712	0.0752	0.6615	33.9176	108.1509	21.8093
35	7.0328	-1.8041	0.646	1.2959	1.3962	7.56	1.0161	-0.2265	0.0669	-0.5556	-1.2186	-1.1785	-1.212	2.6775	0.4105	0.1293	0.0188	0.0476	0.3088	0.1019	0.5657	69.4307	117.9109	41.744
36	3.2684	-3.4666	-1.4539	5.2976	1.4163	2.2836	-0.0704	-0.1216	1.1997	0.4321	0.7667	-1.7973	-0.5866	0.9339	-0.6552	0.3773	-0.0611	-0.0196	0.3413	-0.0302	0.6314	64.0481	118.056	49.9698
37	7.6354	-1.5624	1.1044	4.5411	-2.5652	7.6817	-0.0743	-1.3948	0.1153	1.0583	-0.2539	0.3521	-0.0146	-0.3766	0.0601	0.4373	-0.0704	0.0926	0.4317	-0.0469	0.1789	59.3641	112.2886	54.572
38	2.0455	2.821	-0.1215	6.6334	-2.0429	8.8425	-0.035	-0.2278	-0.8413	0.3644	0.0712	0.2551	1.4248	-0.3212	-0.1844	0.3176	-0.0099	-0.0091	0.3699	-0.0277	0.5498	64.6383	107.694	44.2438
39	3.5586	-3.3337	-1.7839	3.3225	1.2885	4.7965	-0.1056	0.0496	0.0774	0.1066	0.6119	-0.3039	0.0909	-0.1186	-0.1932	0.4173	-0.004	-0.026	0.5666	0.0824	0.807	54.1946	103.65	48.9395
40	5.2706	3.8687	-4.184	3.0399	-3.9335	6.3565	-0.0777	0.4391	0.3511	0.1725	0.2136	0.0017	-0.0771	-0.2835	-0.0618	0.1807	-0.024	0.0053	0.2284	0.0532	0.5313	59.169	115.6833	37.8587
41	6.5349	-6.5522	-4.6287	8.9332	8.013	8.1735	0.6065	1.7147	1.6619	-1.1231	-0.2314	-0.2037	-1.9144	-0.0387	-0.0826	0.3792	-0.1377	0.0069	0.5965	0.2312	0.3903	60.3047	117.8479	23.1473
42	5.6022	-4.5617	1.2764	9.6306	0.3033	2.4603	0.6001	0.3008	-0.4513	-0.7656	-0.6371	0.5722	0.2296	-0.4524	0.172	0.3381	-0.0074	0.0028	0.3591	0.0674	0.4758	60.346	113.2219	29.8642
43	7.5913	-5.0764	1.2561	3.475	-0.3783	5.9164	-0.6154	0.987	0.4167	-0.4094	0.9194	-1.0696	-0.0995	0.5029	-0.4158	0.5602	-0.1338	0.121	0.5519	-0.0707	0.5788	68.2366	108.5585	22.2325
44	6.6052	5.103	-3.4621	5.4046	-0.8766	4.1739	0.3086	0.9535	0.61	-0.3068	0.4948	2.2026	-0.0739	-0.7549	-0.7843	0.4887	0.0231	-0.0455	0.6385	-0.0288	0.7676	59.6476	102.1631	22.3119
45	4.4333	-4.1665	-1.5035	4.2697	0.156	7.6195	0.3374	0.0635	-0.6179	1.5921	0.2366	0.3472	0.8078	0.3143	-0.5796	0.4506	0.0417	-0.0922	0.422	-0.015	0.6061	56.0089	105.0028	30.2596
46	8.3343	-0.9094	-4.2818	9.7108	-5.2639	7.0006	-0.7988	0.7697	-1.0936	-1.5586	-1.946	-0.8506	0.1258	0.851	1.3522	0.2804	-0.1614	-0.2843	0.6168	0.0914	1.0586	54.9536	109.9719	18.5546
47	3.5562	-0.1992	2.4072	1.2423	2.3708	6.7504	1.3129	1.3367	-0.1839	-0.5358	1.4767	-1.6263	0.2256	1.2825	0.9645	-1.8299	-0.4974	0.1248	0.7452	-0.4473	1.3781	87.5748	89.8818	41.7188
48	6.9578	-5.0866	-4.4489	6.1791	0.2584	6.6407	0.567	-1.2395	-0.5507	0.9079	0.4962	-2.3863	-0.7077	2.2698	-0.5117	0.3182	-0.1101	-0.1983	0.9464	-0.0737	0.8686	83.5586	93.901	50.0509
49	5.453	-2.7378	0.576	2.4082	-1.5575	7.2018	-0.5647	-1.5722	0.04	0.7803	0.8799	-0.5382	0.0627	0.4936	-0.4228	0.4635	0.0164	0.0271	0.8522	-0.0039	0.4514	76.3532	92.781	54.5759
50	3.18	3.9136	-1.7987	4.9307	-3.6929	8.8701	0.5372	-0.7074	0.039	0.5865	0.1486	-0.6304	0.1991	-0.525	-0.861	0.3881	-0.0205	-0.0934	0.3187	-0.0749	0.7881	76.8361	85.9596	44.2192
51	2.7647	-2.7463	-3.2979	3.18	4.1855	8.0105	0.3771	0.1364	0.0897	0.5502	0.0567	-0.2104	0.1298	-0.6729	-0.2161	0.5855	0.0532	0.0416	0.5488	0.0313	0.8557	66.4894	90.1343	48.8903
52	7.5009	-7.2303	-5.233	8.0729	6.0128	8.8482	0.1877	-0.0435	0.3796	-0.4551	0.0389	-0.7488	-0.6327	0.473	-0.3545	0.2663	-0.0836	0.0034	0.292	0.0258	0.6003	72.8305	98.9437	42.3685
53	4.8858	-0.1606	6.527	0.3835	-0.318	8.8545	1.073	0.575	-0.9132	0.2561	0.218	-0.188	-0.3914	2.0237	-0.8005	0.4939	-0.1179	0.2577	0.662	0.0775	1.0256	86.7958	89.9174	30.201
54	3.4478	2.0142	1.7087	3.4596	-1.284	3.201	0.0418	0.3615	1.4229	-0.9109	0.2309	-0.7734	-0.9116	0.4444	-0.4195	0.5145	0.0171	0.2587	0.4724	0.0582	0.7765	80.4336	96.2726	23.0205
55	3.8281	2.2602	1.3813	3.639	-3.4919	8.0911	-0.058	-0.3112	-0.1627	-0.5916	0.0101	-0.3613	-0.2323	-0.1871	-0.0735	0.3527	0.0343	0.0366	0.3481	-0.0598	0.3543	77.3976	93.0187	29.7932
56	8.4603	4.4021	6.9715	4.1703	2.8162	6.1376	1.6717	1.4596	-0.4859	0.4825	-0.2155	-0.8003	1.4057	0.1771	-1.07	0.5235	0.0608	0.1814	0.7433	-0.1334	0.5762	79.2546	84.2049	21.8037
57	3.2219	1.9592	-3.4226	8.9443	-1.8652	3.6277	0.775	0.3692	2.4663	-0.0987	-0.0294	0.8798	-0.6666	-0.0264	-0.2755	0.5665	-0.0504	0.0522	0.6173	0.0543	0.8309	68.8714	85.8736	22.2538
58	2.8577	1.6091	2.6634	2.7098	4.2577	6.7941	1.3414	-0.9805	0.4126	0.4483	-0.3445	0.8414	0.8739	0.1268	-0.5727	0.6118	0.1485	0.0189	0.3162	0.0273	0.523	68.5138	90.3114	30.2561
59	4.9357	1.6768	-4.5574	7.9333	0.4038	4.6988	-0.5463	0.9255	-0.5277	-1.4765	0.2544	-0.2537	0.5523	-0.228	0.4892	0.524	0.0763	0.0254	0.4055	-0.0244	0.5961	70.9753	94.8002	18.6583
60	5.7609	1.2532	-0.6235	6.518	1.107	7.6272	0.2088	-0.8566	-0.9509	0.4867	-0.2039	-1.1951	0.2931	0.4788	0.0507	0.265	0.022	-0.1058	0.3611	0.0731	0.6031	76.1256	62.8779	47.7929
61	3.8466	3.6326	1.2993	3.4883	1.1625	2.4231	1.1178	-1.2074	1.2542	-0.607	-1.255	-0.1276	-0.8144	0.1212	-0.1209	0.5013	0.0166	0.0356	0.4574	-0.0833	0.8038	66.0647	72.1563	48.9358
62	1.8213	-3.4079	-2.6717	6.1398	5.3179	7.4545	-0.2464	0.2809	0.0375	0.1931	0.1626	-0.0975	0.1109	0.6231	0.2478	0.2888	-0.064	0.0601	0.391	-0.1479	0.7654	76.4244	74.0322	42.1695
63	2.0268	1.7064	-0.1052	4.4715	-1.5589	7.0781	-0.0318	0.1106	-0.2875	-0.8395	-0.2008	-1.3418	0.1497	0.1764	0.285	0.4579	0.0649	0.169	0.4773	-0.085	0.8173	76.604	63.078	26.7128
64	9.662	-7.2791	-7.4867	5.5373	5.6188	5.8949	0.6094	-0.4055	0.844	-0.9759	-0.3058	-0.806	-1.0138	-0.4518	-0.4607	0.5094	-0.0299	0.1079	0.6257	-0.0241	0.8186	63.8442	67.4991	22.0507
65	2.7927	3.3916	1.853	6.1584	-0.3969	9.1783	-0.0866	0.4304	0.3429	-0.9767	0.0659	-0.692	0.0721	0.4295	-0.0323	0.5225	-0.0006	0.1067	0.333	0.0331	0.5906	70.2498	72.1269	21.8163
66	8.58	0.7808	1.5588	8.0516	1.4372	6.2353	0.112	-0.42	-0.5481	0.1322	0.1605	-0.3577	0.0914	0.0216	-0.1441	0.1781	-0.0217	-0.0555	0.257	0.0239	0.4111	53.2227	49.306	48.2869
67	5.1603	5.6605	4.7525	8.2701	6.1396	4.6851	0.2306	0.1448	-0.2959	0.1328	0.2237	-0.5381	-0.0163	0.1502	-0.4538	0.2717	0.0633	-0.0098	0.3058	-0.0639	0.4468	61.4925	53.6322	42.2802
68	4.2803	-1.1347	-0.8776	3.2743	-1.2096	5.8025	0.1341	0.5462	-0.8783	-0.2892	0.061	-0.0324	0.5388	-0.0535	-0.2911	0.3397	0.0401	-0.0525	0.3339	-0.2262	0.578	53.7433	45.7534	27.2105
69	7.7031	3.4482	3.4564	4.4116	4.2227	4.4314	-0.0299	0.2405	0.7783	-0.6948	0.7786	-0.8388	-0.6233	1.0787	-0.5538	0.4438	0.0556	0.0269	0.4655	-0.0598	0.7274	47.9465	57.6823	22.1992
70	2.6514	-2.0977	-2.265	7.2792	0.4916	2.6674	-0.2058	0.2849	0.1246	-0.1662	0.1269	-0.1283	0.4283	-0.4334	-0.0914	0.2733	-0.0523	0.0199	0.4885	-0.0643	0.3975	55.5791	56.4316	21.9285

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 406 through 447 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 448 through 459 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 460 through 486 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 487 through 507 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 508 through 525 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 526 through 545 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 406 through 423 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 424 through 447 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 448 through 459 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 460 through 486 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 487 through 507 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 508 through 517 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 518 through 525 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 526 through 545 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 407 through 423 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 424 through 435 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 436 through 447 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 448 through 459 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 460 through 475 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 476 through 486 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 487 through 495 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 496 through 507 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 508 through 517 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 518 through 525 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 526 through 545 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 407 through 413 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 414 through 423 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 424 through 435 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 436 through 447 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 448 through 459 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 460 through 475 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 476 through 507 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 508 through 517 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 518 through 525 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 526 through 531 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 532 through 545 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 406 through 413 )
38	X-RAY DIFFRACTION	38	chain 'E' and (resid 414 through 423 )
39	X-RAY DIFFRACTION	39	chain 'E' and (resid 424 through 447 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 448 through 459 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 460 through 486 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 487 through 495 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 496 through 517 )
44	X-RAY DIFFRACTION	44	chain 'E' and (resid 518 through 525 )
45	X-RAY DIFFRACTION	45	chain 'E' and (resid 526 through 545 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 406 through 413 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 414 through 423 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 424 through 447 )
49	X-RAY DIFFRACTION	49	chain 'F' and (resid 448 through 459 )
50	X-RAY DIFFRACTION	50	chain 'F' and (resid 460 through 475 )
51	X-RAY DIFFRACTION	51	chain 'F' and (resid 476 through 486 )
52	X-RAY DIFFRACTION	52	chain 'F' and (resid 487 through 495 )
53	X-RAY DIFFRACTION	53	chain 'F' and (resid 496 through 507 )
54	X-RAY DIFFRACTION	54	chain 'F' and (resid 508 through 517 )
55	X-RAY DIFFRACTION	55	chain 'F' and (resid 518 through 525 )
56	X-RAY DIFFRACTION	56	chain 'F' and (resid 526 through 545 )
57	X-RAY DIFFRACTION	57	chain 'G' and (resid 406 through 423 )
58	X-RAY DIFFRACTION	58	chain 'G' and (resid 424 through 435 )
59	X-RAY DIFFRACTION	59	chain 'G' and (resid 436 through 447 )
60	X-RAY DIFFRACTION	60	chain 'G' and (resid 448 through 459 )
61	X-RAY DIFFRACTION	61	chain 'G' and (resid 460 through 475 )
62	X-RAY DIFFRACTION	62	chain 'G' and (resid 476 through 495 )
63	X-RAY DIFFRACTION	63	chain 'G' and (resid 496 through 517 )
64	X-RAY DIFFRACTION	64	chain 'G' and (resid 518 through 525 )
65	X-RAY DIFFRACTION	65	chain 'G' and (resid 526 through 545 )
66	X-RAY DIFFRACTION	66	chain 'H' and (resid 406 through 423 )
67	X-RAY DIFFRACTION	67	chain 'H' and (resid 424 through 459 )
68	X-RAY DIFFRACTION	68	chain 'H' and (resid 460 through 475 )
69	X-RAY DIFFRACTION	69	chain 'H' and (resid 476 through 525 )
70	X-RAY DIFFRACTION	70	chain 'H' and (resid 526 through 545 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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