PDB-2hf0: Bifidobacterium longum bile salt hydrolase

ID or keywords:

Entry

Database: PDB / ID: 2hf0

Title

Bifidobacterium longum bile salt hydrolase

Components

Bile salt hydrolase

Keywords

HYDROLASE / alpha / beta

Function / homology

Function and homology information

L-serine conjugated cholate hydrolase activity / L-alanine conjugated cholate hydrolase activity / L-histidine conjugated cholate hydrolase activity / chenodeoxycholoyltaurine hydrolase / chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase activity / choloylglycine hydrolase / bile acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...
Similarity search - Function

Biological species

Bifidobacterium longum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Suresh, C.G. / Kumar, R.S. / Brannigan, J.A.

Citation

Journal: J.Biol.Chem. / Year: 2006
Title: Structural and Functional Analysis of a Conjugated Bile Salt Hydrolase from Bifidobacterium longum Reveals an Evolutionary Relationship with Penicillin V Acylase.
Authors: Kumar, R.S. / Brannigan, J.A. / Prabhune, A.A. / Pundle, A.V. / Dodson, G.G. / Dodson, E.J. / Suresh, C.G.

History

Deposition	Jun 22, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2hf0.cif.gz	140.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2hf0.ent.gz	113.2 KB	Display	PDB format
PDBx/mmJSON format	2hf0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hf/2hf0 ftp://data.pdbj.org/pub/pdb/validation_reports/hf/2hf0	HTTPS FTP

-
Related structure data

Related structure data	2hezC C: citing same article (ref.)
Similar structure data	2hez-1 3fsu-1 5dhh-d 3fst-1 2quy-2 2fmn-1 2rf8-1 3mji-d 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	#166 - Oct 2013 Proteasome similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #176 - Aug 2014 Dynein similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Bile salt hydrolase

B: Bile salt hydrolase

70.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bile salt hydrolase

B: Bile salt hydrolase

A: Bile salt hydrolase

B: Bile salt hydrolase

defined by author&software
140 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.981, 123.981, 219.565
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Details

The second part of the biological assembly is generated by the two fold axis: -x+1, -y, z+3/2.

#1: Protein	Bile salt hydrolase Mass: 35054.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: bsh / Plasmid: pET 26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KK62, choloylglycine hydrolase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Bile salt hydrolase

Mass: 35054.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bifidobacterium longum (bacteria) / Gene: bsh / Plasmid: pET 26b / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KK62, choloylglycine hydrolase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 251 / 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: 3.47 Å³/Da / Density % sol: 64.58 %
Crystal grow	Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: ammonium sulfate 30% w/v, 0.5 M sodium formate, sucrose (1M) 100ml, 40 uL of b-octyl glucosidase (0.50% w/v), pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 303K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5148 Å
Detector	Detector: CCD / Date: Jan 30, 2004
Radiation	Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5148 Å / Relative weight: 1
Reflection	Resolution: 2.25→107.211 Å / Num. all: 48000 / Num. obs: 46662 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shell	Resolution: 2.25→2.3 Å / % possible all: 99

-
Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.939 / SU B: 10.94 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22835	2264	5.1 %	RANDOM
R_work	0.18481	-	-	-
obs	0.18699	42515	99.74 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 35.781 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.48 Å²	0.24 Å²	0 Å²
2-	-	0.48 Å²	0 Å²
3-	-	-	-0.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4926	0	0	251	5177

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.029	0.021	5027
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	4263
X-RAY DIFFRACTION	r_angle_refined_deg	2.1	1.921	6837
X-RAY DIFFRACTION	r_angle_other_deg	1.096	3	9895
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.945	5	628
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.324	24.196	255
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.138	15	742
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.612	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.196	0.2	721
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	5794
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1090
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	1089
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	4697
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	2427
X-RAY DIFFRACTION	r_nbtor_other	0.103	0.2	2698
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.186	0.2	282
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.047	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.282	0.2	23
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.307	0.2	104
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.158	0.2	29
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	1.709	1.5	3840
X-RAY DIFFRACTION	r_mcbond_other	0.347	1.5	1296
X-RAY DIFFRACTION	r_mcangle_it	1.857	2	5004
X-RAY DIFFRACTION	r_scbond_it	3.157	3	2286
X-RAY DIFFRACTION	r_scangle_it	4.319	4.5	1833
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	154	-
R_work	0.237	3064	-
obs	-	-	99.94 %

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	0.7344	0.3548	0.4501	1.8321	0.5452	0.3405	0.0469	0.2994	-0.3503	-0.3194	-0.0306	-0.1512	0.097	0.0505	-0.0163	0.1645	-0.0575	0.0195	0.056	-0.0701	0.077	-46.262	19.7718	3.4631
2	1.117	1.6738	-1.5375	6.158	-0.3439	3.1689	-0.0892	-0.3138	-0.2919	0.147	0.0427	-0.0513	0.516	0.1888	0.0465	0.126	-0.0094	0.0278	0.0586	0.0211	0.1342	-41.7265	17.5599	24.8353
3	2.9981	-0.1329	-0.4392	0.8863	0.1666	0.0889	-0.1026	-0.1298	-0.3188	0.091	0.0521	0.2388	0.4027	-0.3325	0.0505	0.2808	-0.1403	0.0646	-0.0173	-0.0612	0.1436	-54.2207	0.9161	15.6213
4	3.2339	-3.6366	-4.4463	4.0896	5.0001	6.1132	0.7141	-1.2975	-1.2278	1.1001	-1.0326	-0.7526	1.0035	-0.0796	0.3185	0.3649	-0.2253	-0.0075	-0.0767	-0.1146	0.1056	-55.5275	0.6001	6.0876
5	4.853	3.2382	-0.2567	4.3259	-0.5182	8.8677	0.0348	-0.3292	-0.5679	0.523	0.0267	0.5324	0.5117	-0.3087	-0.0615	0.2608	-0.0267	0.0787	-0.0432	-0.0452	0.1896	-48.5467	3.7616	19.9291
6	1.0972	-1.4294	-1.2962	1.8907	1.4757	3.1243	-0.0402	-0.0178	-0.2833	-0.09	0.0552	-0.0049	0.3823	-0.0152	-0.0151	0.1695	-0.1092	0.0181	0.0466	-0.0263	0.122	-52.2652	14.7694	16.3163
7	3.1177	-1.569	0.2245	4.2385	0.9488	1.7605	0.0357	0.016	-0.5046	0.1644	0.0312	0.3884	0.3417	-0.483	-0.0669	0.1711	-0.1891	0.0235	0.106	0.0429	0.1102	-67.4925	10.9624	22.6434
8	5.5837	0.913	5.2742	2.0139	-0.6669	6.2362	-0.0666	-0.1105	-0.3322	-0.1672	0.0929	0.1713	0.3852	0.0831	-0.0263	0.2279	-0.1363	0.0373	0.0536	-0.0302	0.1202	-57.2676	7.2025	14.9868
9	2.2949	-1.6559	-1.6569	7.2173	-1.2452	2.1854	0.2909	0.3239	-0.3482	-0.3773	-0.2696	0.2386	0.278	-0.2873	-0.0214	0.2083	-0.1594	-0.0803	0.097	-0.0866	0.0732	-61.4475	12.5301	5.0332
10	9.7188	-3.3102	-0.8032	6.2208	2.0871	0.7121	0.5491	0.9252	0.0783	-0.8503	-0.0288	0.5484	-0.229	-1.6799	-0.5203	-0.0994	-0.6145	0.0022	-0.1278	0.026	-0.3835	-66.3573	13.0702	17.8758
11	6.5278	-2.2802	7.1339	9.0769	-4.8398	8.462	-0.2924	-0.8096	-0.1903	0.8509	0.5265	0.0219	-0.4108	-0.5776	-0.2341	0.2012	-0.0395	0.0663	0.1107	0.0764	0.1276	-57.0833	12.4613	33.4085
12	1.28	-0.0721	-1.0479	0.8039	0.5288	4.7759	0.0249	0.0336	-0.1081	-0.0787	0.1399	0.2778	0.0442	-0.391	-0.1648	0.1265	-0.1102	-0.0237	0.0644	-0.0076	0.0722	-59.4141	20.9147	13.8355
13	1.8433	-0.8844	-0.591	1.7769	-0.7044	1.78	0.0147	0.1275	-0.1788	-0.0245	0.0445	0.2094	0.1746	-0.3407	-0.0593	0.0721	-0.0576	-0.0116	0.0795	-0.0295	0.0446	-55.0818	32.318	13.1251
14	0.2068	0.5498	-0.2672	1.9955	-1.2915	0.9779	-0.0247	0.2968	0.1336	-0.1822	-0.0597	-0.1706	-0.0952	0.0863	0.0844	0.1127	-0.0173	-0.0022	0.1155	-0.0152	0.0789	-41.4356	46.1921	2.2954
15	1.6483	0.9087	0.2543	0.5391	0.3535	1.2313	0.0681	0.2424	0.2651	-0.2718	-0.137	-0.2126	-0.1343	0.0629	0.0688	0.056	-0.0094	0.0142	0.0892	0.0033	0.0547	-35.505	55.8901	5.9182
16	0.635	0.0085	-0.5082	0.2068	-0.4171	1.2209	0.0011	0.0606	-0.018	-0.0486	-0.0027	-0.0378	0.0879	-0.0347	0.0016	0.074	-0.0131	0.0092	0.0619	-0.0194	0.0454	-44.1272	35.2145	12.2005
17	5.2593	12.2218	2.5971	28.9726	9.1561	18.3417	-0.386	-0.143	-0.2513	0.4574	0.0414	0.8728	0.4258	-0.5021	0.3446	0.1158	-0.025	0.0452	0.0703	-0.0708	0.0617	-39.9533	24.9837	-3.9993
18	2.0788	-0.3185	-0.5068	2.301	0.3309	0.152	-0.0421	0.0781	-0.3281	-0.1127	0.0139	-0.2115	0.3699	0.1178	0.0282	0.1437	-0.0186	0.0432	0.0399	-0.0236	0.0867	-38.0469	22.8518	6.9509
19	0.5919	0.1217	0.0781	1.4377	1.041	1.7215	-0.0286	0.151	-0.2844	-0.0499	-0.0217	-0.0513	0.3647	0.0015	0.0503	0.154	-0.0105	0.0316	0.0291	-0.0075	0.1172	-38.4317	16.9906	16.866
20	1.3481	1.4419	-0.6071	6.0142	1.124	3.8216	-0.0345	0.031	-0.4239	0.0157	0.1148	-0.4552	0.2497	0.158	-0.0802	0.2755	-0.008	0.0619	-0.0047	-0.0594	0.1857	-43.1782	-2.3741	13.7373
21	2.6497	-0.7586	1.9011	2.7417	-0.8176	4.0135	-0.0228	0.073	-0.2973	0.093	-0.081	-0.1857	0.2405	0.3265	0.1039	0.0745	0.0247	0.0489	0.1037	-0.0145	0.1523	-20.4855	32.2568	19.2884
22	8.9989	2.8048	-0.9144	1.6227	0.8057	1.6823	-0.1255	0.4411	-0.0124	-0.0459	-0.1012	-0.1789	-0.0908	0.1157	0.2267	0.1429	0.0855	0.1424	0.044	-0.0843	0.1888	-10.8183	27.8619	5.7811
23	0.109	-0.8221	-0.0778	6.2011	0.5868	0.0555	0.0323	0.1149	-0.287	-0.3712	-0.0789	-0.9256	0.2587	0.755	0.0466	-0.0726	0.0432	0.105	0.2122	0.0218	0.2851	2.6452	37.8174	8.74
24	43.2893	1.8865	-13.3404	8.2166	6.0834	13.5351	0.4969	1.0885	0.1794	0.369	0.0288	-0.5062	-0.4206	0.9766	-0.5257	0.0537	0.0772	-0.0346	0.127	0.1102	0.2411	1.6358	31.2421	17.8417
25	3.8674	1.169	-4.2305	2.0412	1.2978	8.5603	0.0593	0.5665	0.0527	-0.3399	0.1089	-0.4714	-0.3249	0.4135	-0.1682	0.1177	0.0678	0.0909	0.1881	-0.0366	0.2328	-7.4979	31.1284	4.2289
26	0.9047	0.3879	-0.5024	1.5097	-0.4807	1.4006	-0.0396	0.0367	-0.1867	-0.0873	-0.029	-0.2919	0.1301	0.3752	0.0686	0.0329	0.0169	0.0341	0.1286	-0.0106	0.1088	-9.0381	41.9793	10.7389
27	3.1635	0.0863	-1.3554	1.9588	-2.6201	5.8324	-0.0057	-0.1264	-0.0631	0.2845	-0.0617	-0.2943	-0.055	0.5185	0.0674	-0.0046	0.0256	-0.0297	0.2018	-0.0014	0.1494	-4.2022	42.3485	21.7909
28	1.5693	0.7943	-1.8361	2.8837	-1.2744	9.4513	-0.2056	0.5737	-0.2762	-0.3745	0.1868	0.1787	0.4094	0.1289	0.0188	0.0341	-0.0142	0.0517	0.1581	-0.0301	0.1689	-9.2597	47.2772	0.8922
29	1.4005	0.6964	-0.1104	1.7283	-1.9834	4.4957	0.0227	-0.004	0.0069	0.0674	0.0175	-0.1935	-0.0926	0.2479	-0.0402	0.0287	0.0118	0.0341	0.1108	-0.0082	0.1233	-14.8415	45.9496	16.5326
30	2.1822	-0.7329	-0.7071	1.4952	0.3034	2.0122	-0.0188	-0.095	-0.0511	0.1294	-0.0302	-0.1171	-0.0319	0.1029	0.049	0.0438	-0.0109	-0.0041	0.0525	-0.0087	0.0685	-27.6506	47.0002	21.8293
31	8.865	-0.9993	-4.288	5.2898	0.3704	9.362	-0.1187	-0.2605	-0.0228	0.1949	-0.0206	0.0545	0.0563	-0.4341	0.1393	0.0771	-0.0199	0.007	0.0915	-0.001	0.0118	-43.3411	35.5584	33.559
32	2.0532	-0.8527	-0.304	1.4834	-0.1839	0.7264	-0.0978	-0.2047	-0.03	0.3398	0.0414	0.1714	0.0565	-0.2212	0.0564	0.0703	-0.032	0.0123	0.0873	-0.0071	0.0363	-52.6705	38.8053	30.9951
33	5.3101	1.7877	-8.5644	1.2973	-2.9895	14.2547	0.0878	-0.0822	0.1332	0.1876	0.085	0.0401	0.0904	-0.1726	-0.1728	0.0743	-0.008	-0.0097	0.0722	-0.0005	0.0658	-38.8703	41.1743	17.0137
34	1.5474	0.4994	-1.3314	2.6548	-2.8568	3.5079	0.0518	-0.0133	-0.1337	-0.0145	-0.0255	-0.0279	0.2053	-0.0072	-0.0263	0.0681	0.0031	-0.0061	0.053	-0.0171	0.0595	-31.1297	38.4231	21.4553
35	12.5773	-1.5876	-1.6883	6.6394	-4.2638	3.3393	-0.2488	-0.4044	0.1755	0.397	0.3377	-0.6197	-0.034	0.3786	-0.089	0.0851	0.0009	-0.0317	0.04	0.0192	0.1049	-25.1539	25.8949	31.996
36	1.2277	0.8629	-0.5653	1.5395	-0.643	0.8981	0.0119	-0.1586	-0.2826	0.0626	-0.0214	-0.2918	0.3119	0.1938	0.0094	0.1002	0.0225	0.0244	0.0446	-0.0038	0.1194	-25.8409	26.4302	21.6153
37	2.6957	0.0334	0.2069	4.6204	-0.798	3.9695	0.0894	0.3609	0.0594	-0.4334	-0.1337	-0.4268	0.1041	0.3239	0.0443	0.1129	-0.0047	0.0486	0.0928	-0.0367	0.0904	-33.8379	36.467	1.6948
38	3.248	0.2584	2.2026	0.502	0.439	3.328	0.0788	0.0935	-0.3563	-0.0747	-0.0256	-0.2317	0.3822	0.2219	-0.0532	0.105	0.0376	0.0669	0.0571	-0.0143	0.1311	-21.2782	25.0491	12.5208
39	0.4517	-0.1688	-0.7796	2.3281	-1.5387	2.8239	0.015	-0.2098	-0.3448	-0.1459	-0.0202	-0.6957	0.346	0.4426	0.0052	0.1192	0.0817	0.057	0.1165	-0.0382	0.2666	-4.7531	20.055	13.283
40	6.0924	-0.6675	-0.9067	1.1796	-0.2347	3.561	-0.2762	-1.1371	0.4298	-0.1493	-0.0737	0.4662	0.1589	-0.0844	0.35	0.096	0.1068	0.1546	0.0195	-0.0798	0.1768	-7.2636	22.3183	4.1069

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	1 - 16	1 - 16
2	X-RAY DIFFRACTION	2	A	A	17 - 26	17 - 26
3	X-RAY DIFFRACTION	3	A	A	27 - 48	27 - 48
4	X-RAY DIFFRACTION	4	A	A	49 - 52	49 - 52
5	X-RAY DIFFRACTION	5	A	A	53 - 63	53 - 63
6	X-RAY DIFFRACTION	6	A	A	64 - 86	64 - 86
7	X-RAY DIFFRACTION	7	A	A	87 - 101	87 - 101
8	X-RAY DIFFRACTION	8	A	A	102 - 111	102 - 111
9	X-RAY DIFFRACTION	9	A	A	112 - 121	112 - 121
10	X-RAY DIFFRACTION	10	A	A	122 - 129	122 - 129
11	X-RAY DIFFRACTION	11	A	A	130 - 138	130 - 138
12	X-RAY DIFFRACTION	12	A	A	139 - 163	139 - 163
13	X-RAY DIFFRACTION	13	A	A	164 - 186	164 - 186
14	X-RAY DIFFRACTION	14	A	A	187 - 197	187 - 197
15	X-RAY DIFFRACTION	15	A	A	198 - 210	198 - 210
16	X-RAY DIFFRACTION	16	A	A	211 - 236	211 - 236
17	X-RAY DIFFRACTION	17	A	A	237 - 240	237 - 240
18	X-RAY DIFFRACTION	18	A	A	241 - 257	241 - 257
19	X-RAY DIFFRACTION	19	A	A	258 - 304	258 - 304
20	X-RAY DIFFRACTION	20	A	A	305 - 316	305 - 316
21	X-RAY DIFFRACTION	21	B	B	1 - 22	1 - 22
22	X-RAY DIFFRACTION	22	B	B	23 - 35	23 - 35
23	X-RAY DIFFRACTION	23	B	B	36 - 48	36 - 48
24	X-RAY DIFFRACTION	24	B	B	49 - 52	49 - 52
25	X-RAY DIFFRACTION	25	B	B	53 - 63	53 - 63
26	X-RAY DIFFRACTION	26	B	B	64 - 109	64 - 109
27	X-RAY DIFFRACTION	27	B	B	110 - 124	110 - 124
28	X-RAY DIFFRACTION	28	B	B	125 - 136	125 - 136
29	X-RAY DIFFRACTION	29	B	B	137 - 163	137 - 163
30	X-RAY DIFFRACTION	30	B	B	164 - 189	164 - 189
31	X-RAY DIFFRACTION	31	B	B	190 - 195	190 - 195
32	X-RAY DIFFRACTION	32	B	B	196 - 213	196 - 213
33	X-RAY DIFFRACTION	33	B	B	214 - 221	214 - 221
34	X-RAY DIFFRACTION	34	B	B	222 - 236	222 - 236
35	X-RAY DIFFRACTION	35	B	B	237 - 240	237 - 240
36	X-RAY DIFFRACTION	36	B	B	241 - 256	241 - 256
37	X-RAY DIFFRACTION	37	B	B	257 - 270	257 - 270
38	X-RAY DIFFRACTION	38	B	B	271 - 298	271 - 298
39	X-RAY DIFFRACTION	39	B	B	299 - 309	299 - 309
40	X-RAY DIFFRACTION	40	B	B	310 - 316	310 - 316

-
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