PDB-3mb2: Kinetic and Structural Characterization of a Heterohexamer 4-Oxal...

ID or keywords:

Entry

Database: PDB / ID: 3mb2

Title

Kinetic and Structural Characterization of a Heterohexamer 4-Oxalocrotonate Tautomerase from Chloroflexus aurantiacus J-10-fl: Implications for Functional and Structural Diversity in the Tautomerase Superfamily

Components

4-oxalocrotonate tautomerase family enzyme - alpha subunit
4-oxalocrotonate tautomerase family enzyme - beta subunit

Keywords

ISOMERASE / TRANS-3-CHLOROACRYLIC ACID DEHALOGENASE / CAAD / DEHALOGENASE / HYDROLASE / 4-Oxalocrotonate tautomerase / 4-OT / heterohexamer

Function / homology

Function and homology information

: / isomerase activity
Similarity search - Function

Biological species

Chloroflexus aurantiacus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.41 Å

Authors

Burks, E.A. / Fleming, C.D. / Mesecar, A.D. / Whitman, C.P. / Pegan, S.D.

Citation

Journal: Biochemistry / Year: 2010
Title: Kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from Chloroflexus aurantiacus J-10-fl: implications for functional and structural diversity in the tautomerase superfamily
Authors: Burks, E.A. / Fleming, C.D. / Mesecar, A.D. / Whitman, C.P. / Pegan, S.D.

History

Deposition	Mar 24, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3mb2.cif.gz	155.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3mb2.ent.gz	125.9 KB	Display	PDB format
PDBx/mmJSON format	3mb2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3mb2_validation.pdf.gz	531 KB	Display	wwPDB validaton report
Full document	3mb2_full_validation.pdf.gz	555.2 KB	Display
Data in XML	3mb2_validation.xml.gz	32.3 KB	Display
Data in CIF	3mb2_validation.cif.gz	44.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mb/3mb2 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/3mb2	HTTPS FTP

-
Related structure data

Related structure data	1mwwS 1s0yS S: Starting model for refinement
Similar structure data	5rb5-2 1ufy-1 4lyr-d 5raz-2 5rb7-2 2orm-d 1d2q-2 1j7h-d 3wux-d 3s9j-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	#220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

B: 4-oxalocrotonate tautomerase family enzyme - beta subunit

C: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

D: 4-oxalocrotonate tautomerase family enzyme - beta subunit

E: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

F: 4-oxalocrotonate tautomerase family enzyme - beta subunit

G: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

H: 4-oxalocrotonate tautomerase family enzyme - beta subunit

I: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

J: 4-oxalocrotonate tautomerase family enzyme - beta subunit

K: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

L: 4-oxalocrotonate tautomerase family enzyme - beta subunit

hetero molecules

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

1

A: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

B: 4-oxalocrotonate tautomerase family enzyme - beta subunit

C: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

D: 4-oxalocrotonate tautomerase family enzyme - beta subunit

E: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

F: 4-oxalocrotonate tautomerase family enzyme - beta subunit

hetero molecules

defined by author&software
48 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

H: 4-oxalocrotonate tautomerase family enzyme - beta subunit

I: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

J: 4-oxalocrotonate tautomerase family enzyme - beta subunit

K: 4-oxalocrotonate tautomerase family enzyme - alpha subunit

L: 4-oxalocrotonate tautomerase family enzyme - beta subunit

hetero molecules

defined by author&software
47.9 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.062, 106.062, 109.961
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Details

Biological assembly is one of the two heterohexamers located in the asymmetric unit.

#1: Protein	4-oxalocrotonate tautomerase family enzyme - alpha subunit Mass: 7738.895 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: 4-oxalocrotonate tautomerase, Caur_1354 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3), / References: UniProt: A9W9U6, EC: 5.3.2.2
#2: Protein	4-oxalocrotonate tautomerase family enzyme - beta subunit Mass: 7971.898 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: 4-oxalocrotonate tautomerase, Caur_1358 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3), / References: UniProt: A9W9V0, EC: 5.3.2.2
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.79 Å³/Da / Density % sol: 67.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.25 M (NH4)2SO4 and 4% PEG 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.41→91.85 Å / Num. all: 49937 / Num. obs: 49737 / % possible obs: 99.6 % / Redundancy: 6 % / B_iso Wilson estimate: 32.143 Å² / R_merge(I) obs: 0.072 / Net I/σ(I): 27.6
Reflection shell	Resolution: 2.414→2.477 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.377 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3293 / % possible all: 88.69

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S0Y Alpha Subunit PDB ENTRY 1MWW Beta Subunit

1s0y

1mww

Resolution: 2.41→91.85 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.928 / SU B: 14.171 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25018	2670	5.1 %	RANDOM
R_work	0.20324	-	-	-
obs	0.20556	49737	98.58 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 32.143 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.44 Å²	0.22 Å²	0 Å²
2-	-	0.44 Å²	-0 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.41→91.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5422	0	85	249	5756

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.026	0.022	5608
X-RAY DIFFRACTION	r_angle_refined_deg	2.226	2.002	7629
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.529	5	703
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.881	23	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.167	15	947
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.149	15	56
X-RAY DIFFRACTION	r_chiral_restr	0.164	0.2	904
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	4088
X-RAY DIFFRACTION	r_mcbond_it	0.928	1.5	3569
X-RAY DIFFRACTION	r_mcangle_it	1.721	2	5763
X-RAY DIFFRACTION	r_scbond_it	3.326	3	2039
X-RAY DIFFRACTION	r_scangle_it	5.1	4.5	1866

LS refinement shell

Resolution: 2.414→2.477 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.407	182	-
R_work	0.301	3293	-
obs	-	-	88.69 %

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	3.2476	1.4579	-1.1803	5.4276	-2.8497	6.2304	0.1988	0.1365	0.1366	-0.0206	-0.328	-0.0099	-0.2991	0.169	0.1292	0.0672	0.0272	0.0035	0.0475	-0.0094	0.0612	8.8685	15.9133	-5.5961
2	5.4161	2.7818	-1.314	5.1091	0.1966	2.0604	0.2277	-0.3505	0.1279	0.2306	-0.4206	0.3203	-0.0447	-0.0868	0.1929	0.0979	0.0296	0.0103	0.0734	-0.0351	0.0367	6.087	11.3389	-1.1528
3	5.9662	-3.9496	0.334	14.7972	-1.6556	5.9745	-0.2908	0.3129	0.7822	-0.9245	0.0248	-0.9396	-0.1637	0.5254	0.266	0.322	-0.0076	0.0123	0.3124	0.0424	0.2268	29.038	17.4508	-6.2004
4	4.275	0.1153	2.0378	7.2809	-0.1757	4.4581	0.1098	0.0657	-0.5489	0.1445	-0.0383	-0.4608	0.3928	0.3885	-0.0715	0.0474	0.0073	-0.0164	0.136	0.0512	0.1214	29.0833	3.6747	10.7911
5	5.1008	3.1654	2.2577	5.5846	3.5524	4.7426	0.3221	-0.1381	0.0448	0.5206	-0.2762	-0.2695	0.208	0.1949	-0.0459	0.0724	-0.0299	-0.0268	0.0819	0.0519	0.0722	26.685	10.8342	11.894
6	15.6136	20.3605	14.5009	19.0362	16.9889	11.9675	0.7735	0.0018	-1.4628	0.6764	0.0806	-1.5057	0.7476	0.0456	-0.8541	0.7498	0.3498	0.4333	0.3889	0.0317	0.6824	17.3988	-7.9941	-5.7068
7	3.7813	-2.2075	0.738	5.5524	0.3553	4.6203	0.1478	-0.0407	0.2399	-0.086	-0.1495	0.1573	-0.2909	0.0063	0.0017	0.0795	-0.0617	0.0149	0.0672	-0.0106	0.0415	8.4042	24.3307	15.8373
8	2.8123	0.6518	1.5517	1.8045	-0.5196	5.9813	0.0814	0.085	0.0072	0.0373	-0.3231	-0.1799	-0.1438	0.6164	0.2417	0.0216	-0.0215	0.0227	0.1054	0.0323	0.0905	10.3339	18.6627	16.4413
9	19.3007	-11.8643	10.5882	26.0661	-5.3084	5.6011	-0.9569	-0.9128	0.366	0.6636	0.7421	1.9202	-0.6039	-0.7406	0.2148	0.4129	0.2975	0.0086	0.8162	0.1763	0.6324	-4.6825	23.0382	-2.6377
10	2.1684	-2.3039	1.1882	3.8377	1.2749	6.1879	-0.1252	-0.0834	-0.1881	0.5951	-0.0254	0.099	0.4774	-0.1732	0.1507	0.2014	-0.0183	-0.0992	0.0635	0.0113	0.1508	7.3692	0.2819	3.7357
11	1.2244	0.1561	-1.7676	2.7727	-0.8059	4.9289	0.0905	-0.0833	-0.0537	-0.2829	-0.2395	-0.0829	0.2115	0.4267	0.1489	0.0726	0.0518	0.0013	0.0553	0.0038	0.0429	11.617	3.9689	-3.5006
12	10.8011	-1.4406	-10.2939	-0.1137	1.0273	20.8805	0.0719	-0.3373	-0.8423	-0.0003	0.12	0.1831	0.1714	-0.9735	-0.1919	0.1277	-0.0603	0.0448	0.2238	0.0681	0.362	-1.1538	4.5891	19.386
13	2.8701	-1.2438	-1.0898	6.1141	-0.8169	2.5646	0.0195	-0.1574	0.1821	-0.1072	-0.2213	-0.0441	-0.3267	0.3058	0.2018	0.0828	0.0286	-0.0406	0.2035	0.0429	0.0589	26.3319	20.0739	6.0912
14	1.3784	0.0614	-0.4717	2.9345	0.2018	2.5613	0.149	0.1477	-0.067	-0.3957	-0.209	-0.2941	-0.0262	0.2618	0.0599	0.1165	0.0092	-0.02	0.1238	0.071	0.1006	27.7864	16.1333	6.167
15	17.2267	7.5306	0.8584	3.2602	-4.333	24.2242	0.4326	-0.2937	0.8258	0.5986	-0.3759	0.2767	-1.7702	1.0295	-0.0567	0.5084	-0.2152	-0.0478	0.225	0.0374	0.5985	19.0352	31.4501	22.0017
16	9.115	-0.3055	-2.1108	3.1096	1.5058	2.0311	0.1068	-0.6917	-0.697	-0.0661	-0.1871	-0.3869	0.5234	0.2687	0.0803	0.3579	0.1086	0.0665	0.1383	0.0851	0.1173	11.8221	7.1552	22.1875
17	-0.0279	-0.4931	-0.6095	15.7344	-5.8546	6.567	-0.0468	-0.036	-0.0114	0.4708	0.2759	0.532	-0.0183	-0.0007	-0.2291	0.0597	-0.0359	0.0337	0.0591	-0.0079	0.0352	2.259	13.6017	23.3504
18	8.5002	-4.3751	-0.2063	4.1568	-0.5943	1.4254	0.103	-0.0494	-0.3229	0.0962	-0.095	0.1955	0.0823	0.1118	-0.008	0.1015	-0.0457	-0.0269	0.0362	0.0153	0.0195	9.3598	11.5489	16.8261
19	3.4569	-3.1241	1.3324	6.5165	-3.3441	5.0991	0.081	-0.0402	-0.085	0.1595	-0.214	-0.1114	0.2321	0.229	0.1329	0.0759	-0.0353	0.0145	0.0553	-0.0295	0.0791	9.6243	45.0355	7.8404
20	6.4198	-2.6516	0.9138	5.1462	-0.5555	1.6683	0.1694	0.3245	-0.1131	-0.0475	-0.3468	0.3891	0.0492	-0.03	0.1774	0.1034	-0.0493	0.0018	0.0609	-0.0345	0.056	5.7782	49.6562	3.991
21	0.3835	-0.0068	-1.7176	6.8815	-6.322	12.0904	-0.2563	-0.228	-0.1486	1.5234	-0.2381	-0.3938	-0.1427	0.9556	0.4944	0.5776	-0.017	-0.1101	0.3413	0.1041	0.3337	29.0828	43.7476	8.6824
22	4.0517	-1.7901	-2.1059	4.7709	-1.3548	4.1762	0.212	-0.0427	0.6047	-0.2489	-0.018	-0.2052	-0.4883	0.4455	-0.194	0.1465	-0.0851	-0.0008	0.1868	0.0143	0.1289	28.3038	58.3315	-7.9362
23	7.2715	-3.4371	-0.7602	7.2779	1.7219	4.6939	0.1364	0.1785	-0.087	-0.644	-0.0536	-0.6527	0.0794	0.2541	-0.0828	0.1011	0.0107	0.0824	0.0925	0.0598	0.1402	31.0808	45.8018	-12.9786
24	5.2655	-0.7624	-4.659	7.3605	2.2704	10.2538	-0.0583	-0.458	0.581	-0.008	-0.0282	-0.3269	-1.114	0.3106	0.0865	0.2526	-0.0103	-0.1034	0.0932	-0.0669	0.1748	17.2139	65.1442	2.637
25	3.7758	2.2456	-1.3771	5.8126	-0.6755	5.7466	0.2072	0.1057	-0.3213	0.1379	-0.2392	0.1745	0.2622	-0.0005	0.0319	0.0734	0.0522	-0.0082	0.0673	-0.0175	0.0638	8.3236	36.9068	-13.5783
26	2.2958	-0.3565	-0.6748	1.2578	-0.27	5.4574	0.1361	-0.0303	-0.0027	-0.0277	-0.3157	-0.1442	-0.0788	0.4299	0.1796	0.0173	0.0039	-0.0257	0.1061	0.0261	0.0957	10.7045	42.4652	-14.58
27	13.8011	-2.3096	4.3081	31.4453	-2.055	4.7052	0.117	-0.5116	-0.9598	0.4517	-0.1136	1.0231	0.9588	-0.5836	-0.0034	0.2827	-0.1113	0.0868	0.1658	0.0314	0.2164	-2.4997	41.2104	5.2655
28	3.0132	3.1646	-0.6955	4.7809	0.9715	4.951	-0.0587	0.2025	0.323	-0.5599	-0.3578	0.2395	-0.4556	-0.0234	0.4165	0.1934	0.1378	0.0425	0.3323	0.141	0.1388	7.6736	60.3375	-1.3409
29	1.1883	0.4021	0.9508	2.0555	-0.4713	4.1758	0.0831	0.0333	0.0201	0.1842	-0.2745	-0.0866	-0.196	0.2965	0.1915	0.0434	-0.0391	0.009	0.0574	-0.0003	0.0609	10.9745	57.4381	4.8959
30	2.3286	-3.714	-1.8965	5.1227	3.58	11.3818	0.2817	0.1186	-0.2421	-0.3742	-0.2647	0.4695	-0.6263	-1.4737	-0.017	0.1445	0.0667	0.0422	0.2823	0.0141	0.4847	-3.3888	59.0883	-17.9752
31	4.3763	-0.882	0.5154	9.2884	0.7354	2.1557	-0.074	-0.0723	-0.281	0.1595	-0.0495	-0.3276	0.2497	0.2996	0.1235	0.0905	-0.0271	0.0233	0.1597	0.053	0.0587	28.1909	40.7123	-3.3402
32	2.5925	1.3312	0.5712	2.8805	0.695	3.7408	0.3189	-0.2843	0.1244	0.4153	-0.3251	-0.1893	0.0311	0.1626	0.0062	0.1114	-0.0121	0.0254	0.1175	0.0654	0.137	26.8272	46.1043	-3.8527
33	10.3786	-11.3224	-0.1915	11.4708	6.4837	30.021	0.3075	0.5398	-0.3729	-0.0692	-0.1667	0.1569	1.4587	1.2048	-0.1407	0.4937	-0.0138	0.1072	0.3606	-0.2074	0.6427	19.7768	28.9196	-19.7598
34	6.1664	0.2415	2.904	3.1098	0.964	1.8437	-0.2099	0.5993	0.5784	-0.0996	-0.0683	-0.3412	-0.4125	0.2168	0.2782	0.3097	0.03	-0.1109	0.0659	0.049	0.1285	11.6948	53.8543	-19.9218
35	3.4107	2.3731	-0.2963	6.0351	-1.201	4.4111	0.0578	-0.0203	0.1076	-0.057	0.0783	0.3771	-0.0134	-0.1059	-0.136	0.0337	0.0243	-0.0147	0.0215	-0.0019	0.0355	2.088	46.8135	-16.668
36	17.2529	-4.5767	4.6437	19.121	-3.2582	3.6586	0.1227	1.0275	-0.229	-0.7835	-0.3703	-0.5181	-0.5464	0.358	0.2475	0.2577	0.0143	-0.011	0.1221	0.0533	0.1114	24.7303	57.0145	-16.7565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 22
2	X-RAY DIFFRACTION	2	A	23 - 50
3	X-RAY DIFFRACTION	3	A	51 - 61
4	X-RAY DIFFRACTION	4	B	1 - 24
5	X-RAY DIFFRACTION	5	B	25 - 53
6	X-RAY DIFFRACTION	6	B	54 - 59
7	X-RAY DIFFRACTION	7	C	1 - 22
8	X-RAY DIFFRACTION	8	C	23 - 55
9	X-RAY DIFFRACTION	9	C	56 - 62
10	X-RAY DIFFRACTION	10	D	1 - 16
11	X-RAY DIFFRACTION	11	D	17 - 51
12	X-RAY DIFFRACTION	12	D	52 - 58
13	X-RAY DIFFRACTION	13	E	1 - 15
14	X-RAY DIFFRACTION	14	E	16 - 55
15	X-RAY DIFFRACTION	15	E	56 - 61
16	X-RAY DIFFRACTION	16	F	1 - 16
17	X-RAY DIFFRACTION	17	F	17 - 30
18	X-RAY DIFFRACTION	18	F	31 - 54
19	X-RAY DIFFRACTION	19	G	1 - 20
20	X-RAY DIFFRACTION	20	G	21 - 50
21	X-RAY DIFFRACTION	21	G	51 - 61
22	X-RAY DIFFRACTION	22	H	1 - 21
23	X-RAY DIFFRACTION	23	H	22 - 45
24	X-RAY DIFFRACTION	24	H	46 - 58
25	X-RAY DIFFRACTION	25	I	1 - 22
26	X-RAY DIFFRACTION	26	I	23 - 53
27	X-RAY DIFFRACTION	27	I	54 - 60
28	X-RAY DIFFRACTION	28	J	1 - 15
29	X-RAY DIFFRACTION	29	J	16 - 53
30	X-RAY DIFFRACTION	30	J	54 - 59
31	X-RAY DIFFRACTION	31	K	1 - 20
32	X-RAY DIFFRACTION	32	K	21 - 55
33	X-RAY DIFFRACTION	33	K	56 - 62
34	X-RAY DIFFRACTION	34	L	1 - 16
35	X-RAY DIFFRACTION	35	L	17 - 46
36	X-RAY DIFFRACTION	36	L	47 - 54

-
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://pdbjlvh1.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