PDB-2v1o: Crystal structure of N-terminal domain of acyl-CoA thioesterase 7

ID or keywords:

Entry

Database: PDB / ID: 2v1o

Title

Crystal structure of N-terminal domain of acyl-CoA thioesterase 7

Components

CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

Keywords

HYDROLASE / ACYL-COA THIOESTERASE 7 / SERINE ESTERASE / PROTEIN STRUCTURE / DOMAIN DUPLICATION / ACOT7 / MACROPHAGE / HOTDOG DOMAIN

Function / homology

Function and homology information

long-chain fatty acyl-CoA hydrolase activity / palmitoyl-CoA hydrolase / Mitochondrial Fatty Acid Beta-Oxidation / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid catabolic process / carboxylic ester hydrolase activity / mitochondrial matrix / neuron projection / neuronal cell body ...
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.78 Å

Authors

Forwood, J.K. / Thakur, A.S. / Guncar, G. / Marfori, M. / Mouradov, D. / Meng, W.N. / Robinson, J. / Huber, T. / Kellie, S. / Martin, J.L. ...

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural Basis for Recruitment of Tandem Hotdog Domains in Acyl-Coa Thioesterase 7 and its Role in Inflammation.
Authors: Forwood, J.K. / Thakur, A.S. / Guncar, G. / Marfori, M. / Mouradov, D. / Meng, W.N. / Robinson, J. / Huber, T. / Kellie, S. / Martin, J.L. / Hume, D.A. / Kobe, B.

History

Deposition	May 28, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2v1o.cif.gz	205.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2v1o.ent.gz	169.4 KB	Display	PDB format
PDBx/mmJSON format	2v1o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v1/2v1o ftp://data.pdbj.org/pub/pdb/validation_reports/v1/2v1o	HTTPS FTP

-
Related structure data

Related structure data	2q2bC C: citing same article (ref.)
Similar structure data	2iex-d 6oaw-d 1mx0-1 4zv3-d 6vfy-d 1x7h-1 5k0l-d 4dbz-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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

B: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

C: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

D: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

E: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

F: CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE

hetero molecules

106 kDa, 6 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)	55.741, 125.531, 81.780
Angle α, β, γ (deg.)	90.00, 95.39, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CYTOSOLIC ACYL COENZYME A THIOESTER HYDROLASE / LONG CHAIN ACYL-COA THIOESTER HYDROLASE / CTE-II / CTE-IIA / BRAIN ACYL-COA HYDROLASE / ACYL-COA ...LONG CHAIN ACYL-COA THIOESTER HYDROLASE / CTE-II / CTE-IIA / BRAIN ACYL-COA HYDROLASE / ACYL-COA THIOESTERASE 7 Mass: 16930.465 Da / Num. of mol.: 6 / Fragment: HOTDOG DOMAIN, RESIDUES 59-206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91V12
#2: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 730 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE SEQUENCE IN THE SEQRES RECORDS BELOW CORRESPONDS TO ISOFORM A OF THE PROTEIN SEQUENCE WHERE ...THE SEQUENCE IN THE SEQRES RECORDS BELOW CORRESPONDS TO ISOFORM A OF THE PROTEIN SEQUENCE WHERE RESIDUES 1-58 HAVE BEEN REPLACED WITH MSGPTTDTPAAIQIC. THE FTID FOR THIS ISOFORM IN THE UNIPROT SEQUENCE DATABASE IS VSP_000158

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52 %
Crystal grow	Details: 0.2 M SODIUM POTASSIUM TARTRATE, 15% PEG 2000 MONO METHYL ETHER

-
Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
Detector	Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.78→29.28 Å / Num. obs: 101344 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 5.87 % / R_merge(I) obs: 0.05 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.78→1.85 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.36 / Mean I/σ(I) obs: 3.7 / % possible all: 76.3

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
CrystalClear		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.78→29.29 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.936 / SU B: 4.761 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.244	5091	5 %	RANDOM
R_work	0.21	-	-	-
obs	0.212	96252	95.5 %	-

Displacement parameters

B_iso mean: 19.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.02 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.78→29.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6968	0	288	730	7986

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	7364
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.167	2.009	9982
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.531	5	884
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.661	24.151	318
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.439	15	1338
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.876	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1128
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5300
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	3560
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.287	0.2	5015
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	679
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.214	0.2	83
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.143	0.2	17
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.605	1.5	4597
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.859	2	7168
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.487	3	3088
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.253	4.5	2814
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.78→1.83 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.393	293
R_work	0.331	5112

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	3.836	-0.1523	-0.7987	1.6601	-0.8051	0.9857	-0.0289	0.1123	0.1275	-0.0212	-0.0639	-0.0889	-0.0669	-0.0785	0.0928	0.1119	0.0065	0.0063	0.0675	-0.0089	0.0632	-1.1859	18.2392	-48.3762
2	5.3858	-0.4134	-0.1643	1.242	0.4498	0.6893	-0.1208	0.0037	-0.0492	0.0368	0.0121	0.0778	0.0542	-0.0692	0.1087	0.1047	-0.0007	0.0297	0.0888	0.0059	0.0685	-24.2078	9.0572	-43.8801
3	5.5944	-0.1285	-0.8557	0.5313	0.4429	0.47	-0.0311	-0.1705	0.0208	0.0397	0.025	-0.0079	0.1526	0.0658	0.0061	0.1292	0.028	0.0101	0.088	0.0145	0.0514	-5.8225	17.4685	-35.0301
4	6.436	1.3418	-4.0604	0.576	-0.6589	3.2377	-0.0024	-0.2152	-0.198	0.0544	-0.0466	-0.0443	0.1096	0.1145	0.049	0.0938	0.0084	0.0113	0.0774	0.0166	0.0587	-10.7595	9.158	-38.7316
5	2.4399	-0.2542	-0.6297	0.4419	0.7028	1.1398	0.0552	-0.1223	0.0424	0.0125	-0.0087	0.0032	-0.0088	0.0093	-0.0465	0.0983	0.0282	0.0299	0.0372	0.04	0.0547	-14.0707	12.0783	-40.6482
6	6.2183	5.4948	2.5788	16.8925	1.8242	11.459	0.0771	-0.0342	-0.6942	0.5002	0.0306	-0.3499	0.5859	0.2335	-0.1077	0.0768	0.0037	0.0057	0.0539	0.0817	0.0668	-17.8899	0.0587	-26.6021
7	3.039	-3.6376	0.4408	12.577	0.4543	7.4339	-0.0889	-0.745	0.0677	0.8533	0.0029	-0.2794	-0.5739	-0.1455	0.086	0.1767	-0.0243	0.0142	0.1771	-0.0203	-0.0425	-18.8651	16.7497	-23.1676
8	2.9331	0.8278	1.0158	0.6434	-0.0994	2.1791	-0.1651	-0.0068	0.0291	0.0892	0.033	0.1234	-0.0007	0.1446	0.132	0.093	-0.0002	0.0177	0.0703	-0.022	0.0829	-0.8736	17.9294	-66.9661
9	5.9141	0.2663	0.3275	1.4413	-0.2261	1.5319	-0.1084	0.0749	0.0303	-0.0756	0.0225	0.1186	-0.1089	-0.0477	0.0859	0.0967	-0.0129	-0.0059	0.0872	-0.01	0.0775	-23.5572	17.725	-78.2654
10	2.7065	0.2788	0.9511	0.3029	-0.2036	0.6661	-0.1132	0.0896	-0.0242	-0.1259	0.1163	0.0045	0.0651	0.0559	-0.0032	0.1153	-0.0058	0.0389	0.0935	-0.0482	0.076	-4.8196	6.7063	-74.8566
11	4.6479	2.9045	2.9861	2.0821	1.7993	2.5922	-0.1725	0.3174	-0.0736	-0.1849	0.2133	-0.0347	-0.0446	0.1565	-0.0408	0.0727	-0.0195	0.0193	0.0839	-0.0301	0.0635	-10.9621	13.4852	-80.2524
12	1.9273	0.5023	0.1475	1.1483	0.3539	0.1478	-0.1245	0.1623	-0.077	-0.2059	0.1428	-0.1161	-0.0095	0.0736	-0.0183	0.0829	-0.0429	0.0218	0.1394	-0.0203	0.0396	-4.0298	15.4114	-77.9186
13	6.7006	-1.5804	-7.4853	2.9855	2.131	10.767	0.2197	0.3491	0.1746	-0.267	-0.0332	0.1583	-0.4314	-0.3909	-0.1864	0.0548	-0.0622	-0.0414	0.0659	-0.0242	-0.0116	-23.7669	10.4493	-84.2423
14	2.7313	0.9329	-2.3089	9.5753	-4.0812	10.411	-0.1188	0.3535	-0.4665	-0.2884	0.1431	-0.0249	0.5945	-0.0086	-0.0243	0.1089	-0.0344	-0.0125	0.074	-0.091	0.044	-16.4631	-2.0743	-85.0134
15	4.6865	-6.8839	5.9854	13.9981	-7.9284	9.1525	-0.0829	-0.1022	0.126	0.3794	0.0173	-0.2769	-0.5235	0.3799	0.0657	0.0726	-0.0181	0.0356	0.0925	-0.0117	0.0616	-14.7978	14.0775	-56.2174
16	9.1745	-3.5723	3.2322	2.0227	-1.6315	1.527	-0.1936	-0.0368	0.0499	0.0721	0.1376	-0.0074	-0.0669	-0.0485	0.0561	0.1042	0.0022	0.0229	0.0688	-0.0164	0.07	-5.9724	7.7739	-61.2745
17	3.8816	0.1015	0.3441	0.2711	0.0475	0.344	-0.0157	-0.0224	-0.1085	0.0148	0.0122	-0.0212	0.0814	0.0206	0.0035	0.0962	0.0122	0.0192	0.0636	-0.0085	0.0868	-1.5833	2.7693	-65.3743
18	4.6079	-2.8103	-1.9867	2.4508	1.0832	1.2073	-0.1063	-0.1437	-0.2325	0.0499	0.0648	0.0386	0.0682	0.0878	0.0415	0.0817	0.0166	0.0173	0.0713	-0.0294	0.0806	-3.8896	-0.4507	-61.2975
19	2.293	0.0083	-0.8764	0.1358	0.3748	1.3866	-0.0208	0.0736	-0.218	0.0349	-0.0282	-0.0224	0.0393	-0.0926	0.049	0.1016	0.0194	0.037	0.0483	-0.0051	0.0983	-7.8752	2.582	-60.7379
20	9.4385	8.7264	-2.188	12.0757	-2.5535	1.7747	0.1008	-0.0843	-0.3062	0.2359	0.0605	0.1355	0.0434	0.1557	-0.1614	0.0541	0.0812	0.0307	0.0131	-0.0078	0.1271	7.4675	-7.5778	-62.6835
21	4.0694	1.0141	-3.1767	10.3622	-8.1185	10.4823	0.1752	0.2846	-0.6007	-0.8487	-0.1399	0.2758	0.636	0.1967	-0.0352	0.0982	0.0555	-0.0104	0.0386	-0.141	0.1476	2.5085	-9.1286	-75.1043
22	3.226	-0.0229	1.5783	1.4259	0.917	1.7172	-0.0838	0.0164	0.0016	-0.0513	-0.0275	0.0322	0.0013	0.0186	0.1113	0.0994	0.009	0.0167	0.0828	0.0059	0.064	-14.8164	26.2957	-47.839
23	6.794	0.5812	-0.4624	2.2966	-0.4674	1.7965	-0.0763	-0.0168	0.0065	0.2172	0.0755	-0.1692	-0.1575	0.1022	0.0008	0.1036	0.0188	-0.0513	0.0461	-0.0178	0.1039	6.8733	35.1561	-39.3593
24	5.4506	0.1454	0.2423	0.873	0.078	0.0167	-0.1173	-0.0604	-0.0498	0.154	0.0433	-0.0411	-0.0453	-0.0507	0.074	0.1251	0.0234	0.0021	0.0882	-0.0296	0.0331	-6.2259	25.5985	-35.9325
25	5.4774	-0.0548	4.1937	0.6367	-0.0034	4.0348	-0.1317	-0.2453	0.2943	0.0707	0.0014	-0.0437	-0.0909	-0.1772	0.1303	0.0847	0.03	-0.0097	0.075	-0.0227	0.0617	-5.9614	33.074	-35.7518
26	2.938	-1.3013	1.0859	0.9657	-0.7531	0.9813	0.0247	-0.1161	0.1083	0.0102	-0.0007	-0.0556	-0.0303	-0.0464	-0.0239	0.0856	0.0398	-0.0136	0.0384	-0.0449	0.076	-4.9194	30.2731	-39.0562
27	6.8969	0.9692	-4.2035	5.7605	1.3869	7.619	0.3421	-0.5207	1.2666	0.4317	-0.1575	0.2034	-0.7341	0.0084	-0.1847	0.1398	0.0429	-0.1209	0.0737	-0.1575	0.1216	2.9215	38.2475	-24.6793
28	15.509	-14.2865	-8.3954	20.1394	6.5902	14.7945	-1.4036	-1.4866	-1.323	1.8846	0.4615	1.2401	1.7877	0.749	0.9421	0.2954	0.0753	0.1415	0.1871	0.1508	-0.0255	1.6412	22.7235	-21.2788
29	6.9114	-7.4345	-9.4725	11.2685	11.1965	13.3027	-0.1346	0.0189	0.0071	0.1758	-0.0629	0.0605	0.3759	-0.4853	0.1976	0.0935	0.0174	-0.0462	0.0492	0.0226	0.0917	-0.8365	31.9847	-53.6157
30	14.5339	-8.1269	-1.2232	5.2608	1.7833	1.7896	-0.1963	0.2337	0.0057	0.0467	0.1084	-0.093	-0.0753	0.0828	0.0879	0.1069	-0.042	-0.0113	0.047	0.0311	0.0963	-0.7993	35.7304	-61.1643
31	8.5058	0.3401	-0.0138	0.9936	-0.0262	2.5038	-0.1467	0.0118	0.2045	0.1305	0.0006	-0.0246	-0.0876	-0.2753	0.1461	0.1011	0.0621	-0.026	0.0884	-0.0239	0.0606	-23.717	44.095	-53.3141
32	13.5925	0.7481	3.2753	0.9342	-0.3045	1.0524	-0.1771	0.0339	0.8429	0.1071	-0.032	-0.0294	-0.1913	-0.0052	0.2091	0.1198	0.0127	-0.0484	0.0332	0.0043	0.1146	-5.1286	46.5707	-64.2362
33	4.1832	-3.4302	0.9764	3.2208	-0.5168	1.0243	-0.2432	-0.0904	0.4	0.0795	0.0629	-0.2145	-0.1593	-0.0727	0.1804	0.0861	0.0199	-0.0587	0.0156	0.0175	0.1305	-11.1534	48.0548	-55.9816
34	3.5287	-0.865	1.453	0.4641	-0.7433	2.1001	-0.1708	0.0651	0.2946	0.0853	-0.0498	-0.0936	-0.1725	0.0838	0.2206	0.0894	0.0122	-0.0532	0.0016	-0.0177	0.1063	-6.3171	44.5023	-55.4755
35	3.375	0.4967	-0.972	2.5149	-0.9098	2.5639	-0.1777	0.0226	0.4528	-0.0292	-0.002	0.0077	-0.4611	-0.1596	0.1797	0.1102	0.0694	-0.1251	-0.0519	0.0136	0.1354	-19.9063	57.0563	-62.0529
36	3.4651	0.6573	0.0396	1.9195	0.0408	3.7723	-0.1863	-0.0496	0.017	0.0979	0.0755	-0.0787	0.149	-0.2207	0.1107	0.1027	0.0017	0.0004	0.0555	0.0231	0.0598	-15.9449	30.5287	-65.0997
37	3.0446	-1.8635	-0.4235	2.3875	1.3427	2.5872	-0.2265	0.1889	0.0855	-0.1063	0.3133	-0.1162	-0.0952	0.2964	-0.0868	0.0703	-0.0857	0.0094	0.1117	0.0028	0.0643	5.1121	36.0939	-74.3471
38	14.2642	8.7571	-0.0312	9.3255	-3.533	5.3969	-0.1752	0.2103	0.1735	-0.3643	-0.0976	-0.1471	-0.0918	0.3332	0.2728	0.111	-0.0044	-0.0143	0.085	0.0516	0.0402	-15.1662	43.4415	-71.4893
39	6.0167	4.0284	-1.5818	3.7013	-1.4382	1.3211	-0.2585	0.5081	0.1752	-0.128	0.2267	0.0307	-0.1235	-0.0507	0.0317	0.1137	-0.082	-0.0193	0.0778	0.0539	0.0627	-5.7848	38.5604	-77.2196
40	2.9415	0.6619	0.1945	1.2769	0.7795	0.8722	-0.152	0.1036	0.2494	-0.1384	0.0992	0.0328	-0.1892	0.1248	0.0528	0.0956	-0.0743	-0.0307	0.0599	0.0724	0.0082	-2.5185	37.573	-73.8881
41	2.881	-4.7166	4.4293	8.1746	-6.2769	8.9055	0.0335	0.9993	0.5215	-1.3074	0.0599	-0.0075	0.3041	-0.4092	-0.0934	0.2565	-0.2398	-0.0546	0.5594	0.3082	0.3245	-0.0018	47.8851	-88.7133
42	12.9225	-7.5495	10.8998	12.7175	-3.269	18.7955	-1.6272	-0.1678	2.0045	1.1575	0.5728	-1.1147	-1.719	-0.8369	1.0543	0.2496	0.0103	-0.2127	-0.0619	0.0986	0.27	1.4203	56.276	-73.927

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 39
2	X-RAY DIFFRACTION	2	A	40 - 60
3	X-RAY DIFFRACTION	3	A	61 - 74
4	X-RAY DIFFRACTION	4	A	75 - 101
5	X-RAY DIFFRACTION	5	A	102 - 136
6	X-RAY DIFFRACTION	6	A	137 - 149
7	X-RAY DIFFRACTION	7	A	150 - 161
8	X-RAY DIFFRACTION	8	B	14 - 39
9	X-RAY DIFFRACTION	9	B	40 - 60
10	X-RAY DIFFRACTION	10	B	61 - 74
11	X-RAY DIFFRACTION	11	B	75 - 97
12	X-RAY DIFFRACTION	12	B	98 - 124
13	X-RAY DIFFRACTION	13	B	125 - 144
14	X-RAY DIFFRACTION	14	B	145 - 161
15	X-RAY DIFFRACTION	15	C	13 - 23
16	X-RAY DIFFRACTION	16	C	24 - 52
17	X-RAY DIFFRACTION	17	C	53 - 74
18	X-RAY DIFFRACTION	18	C	75 - 96
19	X-RAY DIFFRACTION	19	C	97 - 127
20	X-RAY DIFFRACTION	20	C	128 - 144
21	X-RAY DIFFRACTION	21	C	145 - 161
22	X-RAY DIFFRACTION	22	D	14 - 39
23	X-RAY DIFFRACTION	23	D	40 - 56
24	X-RAY DIFFRACTION	24	D	57 - 74
25	X-RAY DIFFRACTION	25	D	75 - 101
26	X-RAY DIFFRACTION	26	D	102 - 131
27	X-RAY DIFFRACTION	27	D	132 - 148
28	X-RAY DIFFRACTION	28	D	149 - 161
29	X-RAY DIFFRACTION	29	E	14 - 22
30	X-RAY DIFFRACTION	30	E	23 - 39
31	X-RAY DIFFRACTION	31	E	40 - 60
32	X-RAY DIFFRACTION	32	E	61 - 74
33	X-RAY DIFFRACTION	33	E	75 - 97
34	X-RAY DIFFRACTION	34	E	98 - 126
35	X-RAY DIFFRACTION	35	E	127 - 161
36	X-RAY DIFFRACTION	36	F	14 - 36
37	X-RAY DIFFRACTION	37	F	37 - 65
38	X-RAY DIFFRACTION	38	F	66 - 74
39	X-RAY DIFFRACTION	39	F	75 - 101
40	X-RAY DIFFRACTION	40	F	102 - 135
41	X-RAY DIFFRACTION	41	F	136 - 149
42	X-RAY DIFFRACTION	42	F	150 - 161

-
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://pdbjlc1.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