PDB-5ldi: Crystal structure of E.coli LigT in apo form

ID or keywords:

Entry

Database: PDB / ID: 5ldi

Title

Crystal structure of E.coli LigT in apo form

Components

RNA 2',3'-cyclic phosphodiesterase

Keywords

HYDROLASE /

Enzyme / 2H phosphoesterase/ligase

Function / homology

Function and homology information

RNA 2',3'-cyclic 3'-phosphodiesterase / 2'-5'-RNA ligase activity /

2',3'-cyclic-nucleotide 3'-phosphodiesterase activity /

Biological species

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Myllykoski, M. / Kursula, P.

Citation

Journal: PLoS ONE / Year: 2017
Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Authors: Myllykoski, M. / Kursula, P.

History

Deposition	Jun 27, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ldi.cif.gz	425.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ldi.ent.gz	358 KB	Display	PDB format
PDBx/mmJSON format	5ldi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldi ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldi	HTTPS FTP

-
Related structure data

Related structure data	5ldjC 5ldkC 5ldmC 5ldoC 5ldpC 5ldqC 1iuhS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ldj-2 4d7u-1 2p1w-d 5u7c-1 4hng-d 4g6v-4 5u82-1 6gtq-2 5u7c-2 3qqm-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA 2',3'-cyclic phosphodiesterase

B: RNA 2',3'-cyclic phosphodiesterase

C: RNA 2',3'-cyclic phosphodiesterase

D: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

1

A: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

defined by author
20.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

defined by author
20.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

defined by author
20.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: RNA 2',3'-cyclic phosphodiesterase

defined by author
20 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.390, 88.320, 73.840
Angle α, β, γ (deg.)	90.00, 115.01, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	RNA 2',3'-cyclic phosphodiesterase / RNA 2' / 3'-CPDase Mass: 20045.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: thpR, ECBD_3472 / Plasmid: pTH 27 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NFI1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.34 Å³/Da / Density % sol: 47.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 14% (w/v) PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 43063 / % possible obs: 99.6 % / Redundancy: 3.81 % / B_iso Wilson estimate: 35.6 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.076 / Net I/σ(I): 11.93
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 3.83 % / R_merge(I) obs: 0.918 / Mean I/σ(I) obs: 1.3 / % possible all: 99.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBid:1iuh

1iuh

Resolution: 2.1→36.604 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.89

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2267	2153	5 %	Random selection
R_work	0.1774	-	-	-
obs	0.1799	43031	99.81 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 54.9 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→36.604 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5520	0	3	509	6032

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5726
X-RAY DIFFRACTION	f_angle_d	0.981	7790
X-RAY DIFFRACTION	f_dihedral_angle_d	12.279	2123
X-RAY DIFFRACTION	f_chiral_restr	0.037	832
X-RAY DIFFRACTION	f_plane_restr	0.004	1015

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 (%)
2.0999-2.1488	0.2943	142	0.2752	2698	X-RAY DIFFRACTION	100
2.1488-2.2025	0.3095	143	0.2561	2712	X-RAY DIFFRACTION	100
2.2025-2.2621	0.2988	144	0.2501	2737	X-RAY DIFFRACTION	100
2.2621-2.3286	0.308	143	0.2383	2702	X-RAY DIFFRACTION	100
2.3286-2.4038	0.3068	143	0.2265	2718	X-RAY DIFFRACTION	100
2.4038-2.4896	0.2962	142	0.2176	2701	X-RAY DIFFRACTION	100
2.4896-2.5893	0.2623	143	0.2107	2714	X-RAY DIFFRACTION	100
2.5893-2.7071	0.3126	143	0.2025	2715	X-RAY DIFFRACTION	100
2.7071-2.8498	0.2479	144	0.1989	2740	X-RAY DIFFRACTION	100
2.8498-3.0283	0.2502	144	0.1816	2737	X-RAY DIFFRACTION	100
3.0283-3.2619	0.2456	143	0.1735	2707	X-RAY DIFFRACTION	100
3.2619-3.5899	0.2239	144	0.169	2732	X-RAY DIFFRACTION	100
3.5899-4.1088	0.1974	144	0.1468	2748	X-RAY DIFFRACTION	100
4.1088-5.1743	0.1705	144	0.1333	2737	X-RAY DIFFRACTION	100
5.1743-36.61	0.168	147	0.1628	2780	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	3.0354	-0.6295	0.9894	4.836	-1.7339	8.7695	0.1986	0.4009	0.4647	-0.4229	0.1654	0.4043	-0.6382	-0.4945	-0.3965	0.3492	0.0387	0.0008	0.3427	0.1375	0.4102	92.2328	-16.4554	-9.2695
2	5.1072	-2.0334	-5.6429	6.3363	2.3036	9.3451	-0.1952	-0.1404	-1.1902	0.2241	-0.0369	0.2633	0.6779	-0.318	0.2342	0.2165	-0.0239	0.0028	0.2489	0.0188	0.2714	84.4226	-29.2894	8.3381
3	6.5119	-0.9413	1.2784	5.4995	0.2316	5.0688	-0.0396	-0.1627	0.3989	-0.3553	0.0869	-0.0314	0.0541	-0.3839	0.1953	0.225	-0.0267	0.0073	0.4279	0.0147	0.3583	74.3619	-23.9099	3.4029
4	3.7537	2.7002	-5.0718	3.766	-3.443	6.704	0.0456	0.4633	0.1755	-0.5582	-0.0796	-0.2156	-0.1367	-0.4701	0.0233	0.352	0.0609	0.0134	0.3944	0.0716	0.413	89.8154	-14.9954	-5.6556
5	6.6121	1.2828	3.9209	4.5428	1.6186	3.7399	0.3996	0.8029	0.7659	-0.7933	-0.5835	-1.0364	-0.4575	0.5068	0.0127	0.5445	0.1364	0.2742	0.6161	0.2358	0.766	102.1995	-9.4076	-13.7081
6	2.8644	-0.7043	-0.1579	0.8786	0.0061	0.8698	-0.2445	-0.1589	0.6409	0.1978	0.183	-0.1458	-0.2271	-0.0781	0.0285	0.3291	0.0334	-0.0311	0.2036	0.0022	0.3681	89.7172	-14.0135	8.5856
7	4.9506	-0.2615	-1.4487	7.8	-5.5124	4.4009	-0.0392	0.0203	1.3474	0.0594	-0.0399	-0.5711	-1.1476	0.2219	-0.0428	0.4627	-0.0322	0.0385	0.2575	0.0488	0.6929	99.4872	-5.8109	-0.5225
8	4.6959	-3.073	-0.6136	3.265	0.7575	0.2219	-0.111	0.7279	1.3886	0.0265	-0.297	-0.3608	-0.1127	-1.5631	0.2019	0.5509	0.0135	-0.0086	0.6554	0.059	0.937	88.7322	-3.5741	-1.1673
9	4.6198	-2.1003	4.3368	9.16	0.4366	7.6486	-0.1861	0.8941	0.5438	0.0428	-0.3024	0.3738	0.1577	-0.0867	0.426	0.2986	-0.0215	0.0431	0.2436	-0.0187	0.2866	78.2799	-17.2656	3.5026
10	4.456	-0.6995	-0.4851	2.2992	-1.0623	4.0562	0.0656	0.3786	0.1884	-0.1102	-0.0795	-0.0072	0.0086	-0.3846	0.021	0.3255	-0.0026	0.0045	0.2377	-0.0073	0.3078	88.9213	-22.0302	3.0884
11	2.5698	-2.2223	-0.1418	5.5833	2.5863	6.6359	0.0059	0.2732	-0.4459	-0.0813	-0.1879	-0.1927	0.0519	-0.135	-0.0159	0.3471	0.0444	0.0721	0.3176	0.1393	0.3462	96.5565	-21.0978	-6.7078
12	8.5751	4.0911	-4.3155	6.3856	-0.9967	7.8305	0.1658	-0.2622	-0.5327	0.2668	-0.1755	0.2333	0.1766	-0.1156	-0.0578	0.2513	0.0192	0.0085	0.2858	0.0743	0.3225	66.7007	3.8057	6.9072
13	4.1375	2.7733	4.3238	6.6784	5.1223	7.6814	0.2342	-0.3618	-0.2612	-0.0799	-0.106	-0.6215	0.7649	0.8601	-0.4153	0.3126	0.033	0.0059	0.3846	-0.003	0.3914	88.3744	7.7007	7.8579
14	2.0311	5.9184	3.4916	4.9907	2.3926	1.2715	1.9597	-2.951	-2.1172	1.04	-0.6898	-0.8448	1.1888	0.8434	-1.0505	0.5477	-0.2302	-0.0955	1.3903	0.0876	0.6512	85.1047	5.0984	19.792
15	2.4431	1.2893	0.5166	3.5374	-0.2011	3.924	-0.2068	-0.6394	-0.1965	0.3505	0.1446	-0.1801	0.2633	0.1774	0.1744	0.3103	0.0274	0.0409	0.2827	-0.0107	0.2809	68.0294	6.0276	9.2112
16	6.4725	3.3701	-3.7948	2.4511	-1.5691	2.6139	-0.2788	0.0819	-0.4416	-0.1593	0.6777	0.2395	0.1003	-1.2447	-0.2073	0.1947	-0.0198	-0.0307	0.4378	0.0408	0.4229	54.6062	5.6219	0.6806
17	3.3545	0.7119	-0.5669	1.5771	-0.5281	0.0812	0.0725	-0.6644	0.5677	0.2347	-0.1188	0.0012	-0.1865	-0.0603	0.0339	0.3284	0.0182	0.0511	0.3913	-0.1322	0.385	76.0464	17.9248	8.6889
18	8.9225	4.9018	0.8431	6.3461	1.8805	4.9794	0.4647	-0.238	1.317	0.2006	0.1889	0.4711	-1.1258	-0.4868	-0.3098	0.3225	0.0693	0.0581	0.3241	0.0136	0.4013	62.6884	18.2318	3.0649
19	3.9485	-0.2751	-1.335	4.6781	-1.0005	0.8045	0.0582	-1.32	0.4099	0.8242	0.1729	-0.065	-0.64	-0.5888	-0.1568	0.5277	-0.017	0.089	0.7209	-0.0425	0.3515	70.3644	12.8229	14.8667
20	3.9327	1.1551	-1.4082	2.4373	0.5545	1.3827	0.049	-0.544	-0.3608	0.2341	-0.1314	-0.1294	0.2098	0.0846	-0.0361	0.1967	0.0275	-0.0117	0.3032	0.0508	0.268	77.8566	8.4065	7.6658
21	5.5834	-1.6992	3.3763	6.5186	-1.6701	2.8215	-0.1227	-0.296	-0.2068	0.1326	-0.049	-0.58	0.0741	0.0696	-0.0196	0.1987	0.0355	0.0213	0.1907	-0.0577	0.2991	69.0469	3.1403	1.0997
22	5.3103	4.6782	-3.3137	4.5808	-2.653	4.838	-0.3171	-0.911	-0.6015	-0.4926	-0.2095	-0.6881	-0.1639	1.3685	0.2263	0.4329	-0.0891	0.0776	0.5555	-0.0138	0.354	72.7509	19.2018	37.3736
23	8.4205	0.7288	0.0533	4.2287	3.8802	4.7816	-0.3872	-0.679	-0.88	0.06	0.2499	-0.7052	1.2584	0.9415	-0.0368	0.522	0.0156	0.0179	0.3564	0.0948	0.3477	63.4829	0.9318	40.9718
24	3.4146	0.3045	2.3254	3.2664	4.3011	6.7072	-0.8574	0.0723	-0.9253	-0.1182	0.7897	-2.2748	0.8648	1.3549	-0.4295	0.8288	0.0846	0.2657	0.5465	-0.044	0.9214	70.3278	-1.8221	30.4936
25	2.3438	1.8201	1.3699	3.6727	1.3131	3.19	-0.4501	0.1669	0.0742	-0.6893	0.2933	-0.3031	-0.2871	0.4161	0.1303	0.515	-0.0314	-0.0135	0.4296	0.0451	0.2616	65.6155	18.9219	34.0849
26	1.7987	-0.5674	0.69	4.0999	-0.3761	1.6947	-0.0623	0.5695	0.4037	-1.3398	-0.4158	0.0193	-0.8891	0.1624	0.4222	0.7876	-0.0661	-0.0956	0.4908	0.0508	0.4568	63.8685	22.8483	31.1092
27	2.8696	1.8754	0.3238	1.2108	-0.6253	2.5384	-0.33	0.4717	-0.5053	-0.4068	0.2527	-0.403	0.3354	0.3355	0.0252	0.3821	-0.0316	0.1148	0.3369	-0.095	0.3688	66.1281	9.2624	36.2176
28	2.7472	-2.3292	-0.719	3.4966	3.0683	6.576	-0.92	-0.0183	-0.4189	0.5601	0.3609	0.0269	0.5675	0.4648	0.2213	0.4111	-0.0528	0.0649	0.3034	0.0377	0.3744	72.0722	19.6901	43.091
29	2.5386	-0.1381	0.7223	0.33	0.8864	3.6501	-0.669	1.1141	-0.4341	-0.7213	0.3638	0.1018	0.9925	0.6283	0.31	0.9352	-0.2674	-0.0104	0.7733	-0.1544	0.38	73.9214	-3.7723	-32.3288
30	8.4178	6.5336	-7.0499	5.0613	-5.2496	5.7003	-0.3863	-0.0809	-0.8903	-0.2523	0.0883	-1.337	0.873	1.0514	0.1297	0.4542	0.0283	0.0425	0.4132	-0.088	0.3869	78.0571	-5.7315	-10.1819
31	1.7779	1.6144	-0.8944	2.0331	-2.5917	5.8492	-0.432	0.0874	-0.3373	-1.698	0.2993	-0.7089	2.7473	-0.4155	0.1135	0.995	-0.0136	0.0028	0.4707	-0.0325	0.4324	72.6769	-10.7442	-17.0789
32	1.2177	0.5148	-0.111	3.7773	2.9239	2.6817	-0.4887	0.8329	0.2516	-1.8321	0.3624	0.7214	0.9066	-0.0525	0.5591	1.0768	-0.4268	-0.1054	1.3052	-0.0272	0.354	70.7378	1.621	-40.3249
33	3.3153	-1.185	0.5783	0.512	-0.6347	2.8513	0.044	0.1519	0.1434	-0.5103	0.1256	0.5887	0.5349	-0.4547	-0.2145	0.3761	-0.0698	-0.0828	0.3561	0.0024	0.3357	65.8825	1.4217	-17.0061
34	3.3872	-0.3252	1.6166	6.6175	2.0552	8.0692	-0.2141	2.1044	1.3688	-1.2658	-0.101	2.3073	0.0908	-2.4415	0.045	0.6266	-0.1099	-0.2975	1.1222	0.3695	0.7283	64.6867	8.4986	-31.1517
35	5.1632	-0.0987	-2.4116	3.8867	0.9988	2.0771	0.6067	0.7459	0.039	-2.0546	-0.073	1.6288	2.1456	-1.9353	-0.1828	0.8428	-0.2367	-0.1275	0.6455	0.0177	0.5852	62.8538	-3.3145	-22.7553
36	5.1596	-0.639	0.9931	6.0895	4.3431	3.7358	0.0154	-0.6678	-1.2844	-0.1655	-0.4775	-0.3576	1.1684	-0.2493	0.2232	0.6767	-0.0773	0.0358	0.498	-0.0511	0.3798	67.4203	-6.4252	-7.2603
37	3.3041	1.2626	-0.1103	1.5279	0.4375	0.4782	-0.6456	0.4784	-0.7309	-0.3631	0.5058	0.0229	1.2442	0.2972	-0.0251	0.8224	-0.046	0.0401	0.4271	-0.0687	0.4161	76.8263	-2.4158	-26.9447
38	7.7465	1.8038	-0.4539	3.4696	-1.3106	4.2968	-0.346	0.7366	-0.4323	-0.6232	0.0077	-0.2771	1.041	-0.3234	-0.0673	0.6305	-0.0992	0.0603	0.4462	-0.0622	0.3354	78.2539	0.3041	-30.1765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 28 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 29 through 38 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 39 through 53 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 54 through 66 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 67 through 96 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 97 through 113 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 114 through 124 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 125 through 134 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 135 through 162 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 163 through 176 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 14 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 15 through 28 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 29 through 38 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 39 through 53 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 54 through 66 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 67 through 96 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 97 through 111 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 112 through 134 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 135 through 162 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 163 through 176 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 4 through 14 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 15 through 28 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 29 through 38 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 39 through 96 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 97 through 130 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 131 through 162 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 163 through 176 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 2 through 14 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 15 through 28 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 29 through 46 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 47 through 66 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 67 through 96 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 97 through 113 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 114 through 130 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 131 through 145 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 146 through 162 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 163 through 176 )

-
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