PDB-3e3o: Glycogen phosphorylase R state-IMP complex

ID or keywords:

Entry

Database: PDB / ID: 3e3o

Title

Glycogen phosphorylase R state-IMP complex

Components

Glycogen phosphorylase, muscle form

Keywords

TRANSFERASE / GLYCOGENOLYSIS / INHIBITION / TYPE 2 DIABETES / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate

Function / homology

Function and homology information

maltodextrin phosphorylase activity / glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function

Biological species

Oryctolagus cuniculus (rabbit)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.6 Å

Authors

Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators.
Authors: Leonidas, D.D. / Zographos, S.E. / Tsitsanou, K.E. / Skamnaki, V.T. / Stravodimos, G. / Kyriakis, E.

History

Deposition	Aug 7, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Aug 18, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 15, 2021	Group: Data collection / Database references / Derived calculations Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3e3o.cif.gz	647.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3e3o.ent.gz	532.4 KB	Display	PDB format
PDBx/mmJSON format	3e3o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e3/3e3o ftp://data.pdbj.org/pub/pdb/validation_reports/e3/3e3o	HTTPS FTP

-
Related structure data

Related structure data	3e3lC 3e3nC 7p7dC 2abbS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3e3n-1 3e3n-3 1gpa-2 3e3n-4 3e3l-2 2qll-1 3e3n-2 3e3l-1 2aw3-d 2ecp-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#24 - Dec 2001 Glycogen Phosphorylase similarity (7)

Deposited unit

A: Glycogen phosphorylase, muscle form

B: Glycogen phosphorylase, muscle form

C: Glycogen phosphorylase, muscle form

D: Glycogen phosphorylase, muscle form

hetero molecules

392 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycogen phosphorylase, muscle form

B: Glycogen phosphorylase, muscle form

hetero molecules

defined by author&software
196 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glycogen phosphorylase, muscle form

D: Glycogen phosphorylase, muscle form

hetero molecules

defined by author&software
196 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.680, 188.448, 87.853
Angle α, β, γ (deg.)	90.00, 109.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glycogen phosphorylase, muscle form / Myophosphorylase / Glycogen phosphorylase b Mass: 97519.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-IMP / INOSINIC ACID Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.32 %
Crystal grow	Temperature: 289 K / Method: microdialysis / pH: 7.5 Details: 1.1-1.3M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, MICRODIALYSIS, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2006
Radiation	Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8063 Å / Relative weight: 1
Reflection	Resolution: 2.6→99 Å / Num. all: 111241 / Num. obs: 105631 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / B_iso Wilson estimate: 65.109 Å² / R_sym value: 0.061 / Net I/σ(I): 7.07
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.62 / Num. unique all: 5388 / R_sym value: 0.441 / % possible all: 96.4

-
Processing

Software

Name	Version	Classification
REFMAC	5.3.0037	refinement
MAR345		data collection
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: pdb entry 2abb

2abb

Resolution: 2.6→30 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.915 / SU B: 31.917 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26703	5573	5 %	RANDOM
R_work	0.20073	-	-	-
obs	0.20405	105631	99.28 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 44.071 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.19 Å²	0 Å²	-0.37 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	1.8 Å²

Refine analyze

Luzzati sigma a obs: 0.312 Å

Refinement step

Cycle: LAST / Resolution: 2.6→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26382	0	132	116	26630

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	27096
X-RAY DIFFRACTION	r_angle_refined_deg	1.359	1.96	36680
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.279	5	3220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.781	23.464	1374
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.193	15	4739
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.987	15	241
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	3958
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	20669
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	12352
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	18056
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	868
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.227	0.2	63
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.156	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	0.462	1.5	16482
X-RAY DIFFRACTION	r_mcangle_it	0.827	2	26009
X-RAY DIFFRACTION	r_scbond_it	1.089	3	12003
X-RAY DIFFRACTION	r_scangle_it	1.811	4.5	10671

LS refinement shell

Resolution: 2.597→2.664 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.346	414	-
R_work	0.27	7369	-
obs	-	-	94.5 %

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	0.9007	0.7011	-2.1091	0.5458	-1.6418	4.9389	0.1275	0.5962	-0.3502	-0.4008	-0.2017	-0.3626	0.581	-0.4136	0.0742	0.1533	0.0822	-0.1191	-0.1223	-0.3453	0.9729	56.6782	-28.3103	50.75
2	1.705	0.3248	-0.4804	1.9733	2.1724	4.74	-0.0088	0.0885	-0.6909	0.0899	-0.0124	-0.1625	0.0822	0.1243	0.0212	0.0789	0.0084	-0.0388	0.0455	-0.1048	0.4357	50.325	-13.4844	51.5494
3	1.4488	0.7836	-0.6162	0.8504	-0.2647	1.913	-0.0744	0.2713	-0.4226	0.0543	0.0221	-0.1088	-0.0667	-0.2164	0.0523	0.1036	0.0037	0.0036	0.1503	-0.2037	0.3368	46.7341	-8.8081	37.3986
4	4.2128	-3.7803	3.1438	4.0972	-3.4596	2.9245	-0.4265	-0.1286	0.4369	0.5045	0.0948	-0.6013	-0.2985	-0.1259	0.3317	0.1881	-0.0109	-0.0963	0.1681	-0.1269	0.2211	48.057	11.7618	40.8085
5	3.226	1	-0.5415	1.2655	-0.4567	1.3945	-0.096	0.1811	-0.4949	-0.0885	-0.1154	-0.227	0.0146	0.1887	0.2114	0.1571	0.0116	0.0022	0.1242	-0.1671	0.2898	66.8811	-5.1837	33.0949
6	6.7591	2.5105	-1.072	7.774	1.8755	3.4979	0.4015	-0.1587	0.1065	0.4405	-0.2246	-0.3645	-0.4583	0.4182	-0.1769	0.2321	-0.0258	-0.0263	0.096	-0.0864	0.0772	69.3385	11.214	35.8738
7	3.125	1.1251	-1.2824	1.342	-0.7429	1.7192	-0.2427	0.4164	-0.9448	-0.0889	-0.0914	-0.2353	0.1588	0.0071	0.3341	0.0945	-0.0362	0.0816	0.2268	-0.3021	0.3579	68.2561	-8.9619	22.0731
8	1.6193	0.7303	-0.1192	1.2499	0.2431	3.1424	-0.1729	1.0277	-0.2466	-0.1808	0.0184	-0.02	-0.3146	-0.1923	0.1545	0.0421	-0.0251	0.0465	0.5271	-0.3156	0.0946	65.219	2.1146	8.9271
9	4.0775	1.015	-2.6317	0.9531	-0.9463	2.9214	-0.2358	1.2319	-0.44	-0.307	0.2632	-0.0828	-0.0166	-0.3916	-0.0275	0.0154	-0.1336	0.0248	0.5561	-0.384	0.0851	45.8677	-4.9716	13.4151
10	4.2098	0.48	-0.5624	5.6438	1.672	3.1546	0.0595	0.0302	-0.4352	0.3931	0.1115	0.1585	0.0466	-0.1731	-0.171	0.0742	-0.0557	0.0055	0.2124	-0.0548	0.1648	23.7751	-7.4018	33.2811
11	2.3154	0.365	0.5076	1.709	-0.0029	1.1391	-0.0988	0.3779	0.232	0.0409	0.1515	0.0797	-0.0645	-0.0078	-0.0528	0.0726	-0.0331	0.0016	0.2588	-0.0419	0.1148	29.4396	12.2218	27.5764
12	2.1254	0.2311	0.2772	1.4357	0.2781	0.6204	-0.2277	0.8335	-0.0403	-0.1915	0.2648	0.1669	-0.0774	-0.0091	-0.0371	0.0428	-0.1436	-0.0155	0.4675	-0.1022	0.0166	31.0053	7.5938	17.1774
13	6.7782	-3.4549	-2.228	5.8246	2.1676	0.9945	-0.0782	-0.6235	-1.5056	0.5502	-0.242	0.3734	0.1207	-0.2204	0.3202	0.0879	-0.0967	-0.0286	0.0814	0.0682	0.4274	50.6274	-19.0001	63.6907
14	2.7232	-0.0001	0.5311	2.1178	0.9788	2.511	0.1028	0.1032	-0.7046	-0.0026	-0.0652	-0.1039	0.0041	0.2228	-0.0376	0.1582	-0.0244	-0.0337	0.0107	-0.0694	0.4321	63.8773	-16.419	54.8411
15	1.5847	0.2889	0.0916	1.8783	1.0258	1.4952	0.1279	-0.1101	-0.5611	0.0308	0.0168	-0.2747	0.1977	0.1139	-0.1447	0.154	0.004	-0.0451	0.0591	0.0615	0.2072	68.5227	-7.1753	68.8455
16	38.3928	4.4772	4.7727	0.5221	0.5566	0.5933	-0.3415	1.1027	0.3617	-0.385	0.0597	0.0497	0.3268	0.2976	0.2818	0.1662	0.0465	-0.0005	0.2875	0.0222	0.1063	85.0883	0.3502	53.2358
17	1.8242	0.4052	0.3797	2.863	-0.6652	1.3637	0.0136	0.0461	-0.0637	0.0981	0.0651	0.3488	-0.1981	-0.0588	-0.0787	0.2316	-0.0173	0.0381	0.1582	0.0137	0.0899	61.4649	9.4174	62.4305
18	2.8559	-3.4799	1.3995	9.0025	-4.5911	10.9997	0.1998	0.6848	0.4294	-0.8472	-0.5123	-0.2804	-0.1969	0.1185	0.3126	0.3543	-0.104	0.1144	0.1733	0.0235	-0.0023	67.619	16.3541	47.9021
19	1.6396	0.2113	0.5198	2.0073	0.1587	2.9133	-0.0121	-0.1767	0.0939	0.0695	0.0759	0.104	-0.2362	0.061	-0.0637	0.2584	-0.0066	0.05	0.1658	-0.0043	0.0598	66.6538	20.771	73.4404
20	1.5713	0.3766	0.5569	2.1612	0.9951	1.2006	0.0004	-0.3147	0.0166	0.064	0.0654	-0.2437	-0.1884	0.1181	-0.0659	0.2199	-0.0473	0.0618	0.2446	-0.0069	0.0529	79.5967	15.8393	81.8711
21	5.5593	-0.8509	-2.5214	4.7502	-0.4177	5.1857	0.0481	-0.2297	-1.1356	-0.2016	0.1523	-0.3068	0.4399	-0.0851	-0.2003	0.099	-0.068	-0.1418	-0.0811	0.1343	0.421	87.1421	-20.1819	77.8606
22	2.6584	0.6879	0.3058	1.1637	-0.9423	2.5694	0.0251	0.0631	-0.541	0.016	-0.1055	-0.4364	-0.1075	0.0496	0.0804	0.1129	0.0144	-0.0384	0.0408	0.006	0.2648	99.4562	-4.9587	69.349
23	2.1298	0.5839	-0.7283	2.3003	-1.0182	2.0003	0.0745	-0.2218	-0.1042	0.3528	-0.2818	-0.6499	-0.7615	0.3575	0.2073	0.2287	-0.0862	-0.2688	0.047	0.1291	0.2165	106.997	6.6314	74.5089
24	2.7314	-0.8173	-0.4187	0.8228	-0.171	1.4032	0.0786	-0.5559	-0.5398	0.3222	-0.0438	-0.2589	0.1336	0.0676	-0.0348	0.2229	-0.0445	-0.1265	0.1087	0.1532	0.2674	86.9648	-7.2049	84.0467
25	0.9774	-2.2286	-4.741	11.7273	14.7637	25.3489	-0.5704	0.8369	0.7085	-0.5028	0.2577	0.0343	-0.9239	1.2626	0.3126	-0.0478	-0.1876	-0.0972	0.4669	0.3396	0.3527	103.3929	63.4476	18.223
26	1.5396	-0.6177	0.2135	2.2975	0.0174	0.1709	-0.0133	0.1686	0.4724	0.2377	0.0546	0.0804	-0.1752	0.0858	-0.0414	0.1447	-0.0802	0.0184	0.1276	0.0794	0.1733	101.5658	53.6752	34.0425
27	2.4109	-1.0881	5.1253	0.4911	-2.3131	10.8957	0.1605	-0.3263	0.3425	0.5249	-0.0231	0.2254	-0.1636	-1.158	-0.1375	0.2527	-0.0568	0.1274	0.3065	0	0.1017	90.2152	44.2949	50.076
28	1.5494	0.9999	0.2916	3.7783	-0.3515	0.6678	-0.0356	0.1617	0.1138	-0.297	-0.0358	0.138	0.0536	0.0075	0.0714	0.1529	-0.0343	0.0389	0.288	0.0503	0.066	97.8803	33.661	26.5555
29	19.9437	8.6377	4.8791	9.8387	3.0368	5.7568	0.0409	0.8976	0.3969	0.032	-0.3139	1.2303	0.3953	-0.3646	0.273	0.0792	-0.0163	0.1126	0.3042	-0.0268	0.1116	81.6197	28.8579	33.1727
30	2.1644	0.1021	0.2379	2.8638	0.1055	1.141	-0.066	0.1032	-0.0753	0.0027	0.0917	-0.2063	0.1478	0.1115	-0.0257	0.1163	-0.005	0.0078	0.2584	-0.0304	0.0938	107.6206	22.6342	30.3917
31	1.6142	-0.4135	-0.2664	4.1029	0.4402	1.0049	-0.0015	0.0034	-0.2277	0.4322	0.0239	-0.5216	0.1748	0.2807	-0.0224	0.1423	0.0039	-0.093	0.2683	0.0361	0.0982	117.883	24.6569	43.3806
32	2.0748	-0.2874	-1.2464	3.4422	1.1951	3.8778	0.0709	0.0236	0.7333	0.486	-0.1295	0.0739	-0.7812	0.1841	0.0586	0.3673	-0.2785	-0.1229	0.0041	-0.0004	0.1486	116.1964	60.9757	54.6754
33	2.1746	0.4417	-0.0598	1.3703	-0.4874	2.3353	0.2946	-0.2687	0.1051	0.6809	-0.2672	-0.0118	-0.3239	0.0992	-0.0274	0.4333	-0.2231	-0.0774	0.0947	-0.0323	0.0152	107.6934	45.455	65.0469
34	1.7842	2.7409	-1.8424	4.5877	-1.9824	3.8097	0.285	-0.1833	-0.0252	1.0033	-0.291	-0.7597	0.0816	0.4748	0.006	0.4848	-0.285	-0.4503	0.2008	0.1141	-0.0163	117.067	32.3753	73.3835
35	3.3447	0.6853	-0.2779	3.4725	-1.3277	1.3313	0.5598	-0.7742	-0.1079	0.8644	-0.43	-0.1534	-0.0836	0.1352	-0.1298	0.6066	-0.3082	-0.1856	0.1783	-0.0399	-0.1635	107.7064	38.8905	74.1449
36	2.434	0.9965	-0.6515	2.8661	1.9362	2.8255	0.2782	0.0218	0.3532	0.2321	-0.0992	-0.5258	-0.2603	0.3598	-0.179	0.1532	-0.1212	-0.077	0.2511	0.0465	0.2313	122.6636	48.0827	41.9754
37	3.7312	-2.1503	-3.0461	2.7128	8.0629	29.485	-0.2337	0.2833	0.9779	-0.1181	-0.0501	0.267	-1.1649	-1.2375	0.2838	0.142	-0.2244	-0.0686	-0.1992	0.266	0.7481	90.0672	72.3679	22.7203
38	2.826	0.0531	-0.4519	0.0797	0.2787	1.1203	-0.1403	0.4066	0.7569	-0.0257	0.1057	0.0978	-0.0976	0.17	0.0346	0.0991	-0.0708	-0.024	0.1077	0.3285	0.4149	81.7749	59.281	18.8691
39	1.1522	0.5061	0.1423	0.6349	0.4763	1.215	-0.002	0.583	0.2895	-0.1147	0.0547	0.1167	0.1674	0.235	-0.0528	0.1031	-0.0387	-0.0246	0.2331	0.2702	0.2807	75.5573	48.9659	13.5883
40	2.7009	1.223	-0.9551	2.1813	-2.0609	3.6204	0.1441	-0.1211	0.5488	0.3279	0.0444	0.1153	-0.2655	0.0671	-0.1885	0.1751	-0.0037	-0.0003	0.0052	0.096	0.3768	69.854	52.2426	35.4928
41	3.0099	-1.2795	-2.3622	7.4859	-2.5254	3.6926	-0.2667	-0.0474	-0.1521	0.1714	-0.1493	-0.11	0.5911	0.4232	0.4159	0.2259	0.0196	0.1018	0.0459	0.0899	0.2154	70.7947	36.8201	35.1228
42	1.6719	0.2614	0.6016	2.1903	-0.6258	0.8791	-0.0315	0.0041	0.688	0.2795	-0.0017	0.0243	-0.1031	-0.0336	0.0332	0.1134	-0.0059	0.032	-0.0028	0.1181	0.486	57.8232	57.5083	37.2223
43	1.759	0.1971	-0.1314	0.8974	-0.4128	1.4369	-0.0238	0.3001	0.4788	-0.0091	0.0024	0.173	0.1046	-0.2257	0.0215	0.083	-0.0351	-0.006	0.0747	0.1784	0.4222	47.7451	50.6402	25.233
44	2.4524	-0.1362	-0.3477	3.5026	1.7967	2.125	-0.4499	0.5249	0.2388	-0.4415	0.3774	0.1476	-0.1079	0.559	0.0725	0.1506	-0.038	0.0705	0.4595	0.5182	0.2307	67.7089	57.8072	-7.2134
45	2.4972	-0.0982	0.4151	3.5216	-0.0631	3.3203	0.0409	1.0716	0.0743	-0.5719	-0.0107	-0.1854	0.3726	-0.0038	-0.0302	0.1646	-0.078	0.0233	0.5744	0.2145	-0.1327	60.5187	34.2637	-5.9525
46	0.1128	0.3462	0.1789	2.3983	-1.0506	2.201	-0.1907	1.1136	1.1647	-0.1544	0.1379	-0.1013	0.2208	-0.1533	0.0528	0.0333	-0.0569	0.0146	0.4911	0.488	0.2666	58.1038	49.5223	2.06
47	1.2869	-0.4162	0.1979	3.7735	-1.1949	1.8586	-0.0038	1.1983	0.1808	-0.3992	0.2616	0.3576	0.3992	-0.5134	-0.2578	-0.0257	-0.2197	-0.1404	0.7366	0.2636	-0.046	44.1051	35.31	-3.9931
48	1.9097	0.4147	0.222	1.2588	0.3896	1.6543	-0.0096	0.9558	0.563	-0.2379	0.0574	-0.0361	0.1439	-0.1524	-0.0478	-0.0017	-0.038	-0.0454	0.4853	0.4578	0.1796	55.0138	48.9023	1.0131

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	7 - 25	7 - 25
2	X-RAY DIFFRACTION	2	A	A	26 - 76	26 - 76
3	X-RAY DIFFRACTION	3	A	A	77 - 161	77 - 161
4	X-RAY DIFFRACTION	4	A	A	162 - 187	162 - 187
5	X-RAY DIFFRACTION	5	A	A	188 - 246	188 - 246
6	X-RAY DIFFRACTION	6	A	A	247 - 294	247 - 294
7	X-RAY DIFFRACTION	7	A	A	295 - 360	295 - 360
8	X-RAY DIFFRACTION	8	A	A	361 - 452	361 - 452
9	X-RAY DIFFRACTION	9	A	A	453 - 497	453 - 497
10	X-RAY DIFFRACTION	10	A	A	498 - 560	498 - 560
11	X-RAY DIFFRACTION	11	A	A	561 - 691	561 - 691
12	X-RAY DIFFRACTION	12	A	A	692 - 837	692 - 837
13	X-RAY DIFFRACTION	13	B	B	7 - 33	7 - 33
14	X-RAY DIFFRACTION	14	B	B	34 - 67	34 - 67
15	X-RAY DIFFRACTION	15	B	B	68 - 161	68 - 161
16	X-RAY DIFFRACTION	16	B	B	162 - 184	162 - 184
17	X-RAY DIFFRACTION	17	B	B	185 - 246	185 - 246
18	X-RAY DIFFRACTION	18	B	B	247 - 281	247 - 281
19	X-RAY DIFFRACTION	19	B	B	287 - 418	287 - 418
20	X-RAY DIFFRACTION	20	B	B	419 - 498	419 - 498
21	X-RAY DIFFRACTION	21	B	B	499 - 559	499 - 559
22	X-RAY DIFFRACTION	22	B	B	560 - 694	560 - 694
23	X-RAY DIFFRACTION	23	B	B	695 - 773	695 - 773
24	X-RAY DIFFRACTION	24	B	B	774 - 837	774 - 837
25	X-RAY DIFFRACTION	25	C	C	9 - 28	9 - 28
26	X-RAY DIFFRACTION	26	C	C	29 - 163	29 - 163
27	X-RAY DIFFRACTION	27	C	C	164 - 188	164 - 188
28	X-RAY DIFFRACTION	28	C	C	189 - 248	189 - 248
29	X-RAY DIFFRACTION	29	C	C	249 - 280	249 - 280
30	X-RAY DIFFRACTION	30	C	C	289 - 412	289 - 412
31	X-RAY DIFFRACTION	31	C	C	413 - 499	413 - 499
32	X-RAY DIFFRACTION	32	C	C	500 - 559	500 - 559
33	X-RAY DIFFRACTION	33	C	C	560 - 702	560 - 702
34	X-RAY DIFFRACTION	34	C	C	703 - 743	703 - 743
35	X-RAY DIFFRACTION	35	C	C	744 - 795	744 - 795
36	X-RAY DIFFRACTION	36	C	C	796 - 837	796 - 837
37	X-RAY DIFFRACTION	37	D	D	8 - 28	8 - 28
38	X-RAY DIFFRACTION	38	D	D	29 - 104	29 - 104
39	X-RAY DIFFRACTION	39	D	D	105 - 188	105 - 188
40	X-RAY DIFFRACTION	40	D	D	189 - 243	189 - 243
41	X-RAY DIFFRACTION	41	D	D	244 - 294	244 - 294
42	X-RAY DIFFRACTION	42	D	D	295 - 376	295 - 376
43	X-RAY DIFFRACTION	43	D	D	377 - 505	377 - 505
44	X-RAY DIFFRACTION	44	D	D	506 - 559	506 - 559
45	X-RAY DIFFRACTION	45	D	D	560 - 646	560 - 646
46	X-RAY DIFFRACTION	46	D	D	647 - 701	647 - 701
47	X-RAY DIFFRACTION	47	D	D	702 - 751	702 - 751
48	X-RAY DIFFRACTION	48	D	D	752 - 837	752 - 837

-
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