PDB-3pig: beta-fructofuranosidase from Bifidobacterium longum

ID or keywords:

Entry

Database: PDB / ID: 3pig

Title

beta-fructofuranosidase from Bifidobacterium longum

Components

Beta-fructofuranosidase

Keywords

HYDROLASE / five-bladed beta-propeller and beta-sandwich domains / glycoside hydrolase family 32 / PROBIOTIC BACTERIA

Function / homology

Function and homology information

beta-fructofuranosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function

Biological species

Bifidobacterium longum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.87 Å

Authors

Bujacz, A. / Bujacz, G. / Redzynia, I. / Krzepkowska-Jedrzejczak, M. / Bielecki, S.

Citation

Journal: Febs J. / Year: 2011
Title: Crystal structures of the apo form of beta-fructofuranosidase from Bifidobacterium longum and its complex with fructose
Authors: Bujacz, A. / Jedrzejczak-Krzepkowska, M. / Bielecki, S. / Redzynia, I. / Bujacz, G.

History

Deposition	Nov 6, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3	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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3pig.cif.gz	438.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3pig.ent.gz	363.2 KB	Display	PDB format
PDBx/mmJSON format	3pig.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3pig_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	3pig_full_validation.pdf.gz	445.4 KB	Display
Data in XML	3pig_validation.xml.gz	49.8 KB	Display
Data in CIF	3pig_validation.cif.gz	76.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pi/3pig ftp://data.pdbj.org/pub/pdb/validation_reports/pi/3pig	HTTPS FTP

-
Related structure data

Related structure data	3pijC 1w2tS 1y4wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3pij-d 2aw5-2 5wi9-2 3d7e-d 3wrh-d 1gll-d 4bwc-1 6urf-2 5vip-d 2xii-d 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

Deposited unit

A: Beta-fructofuranosidase

B: Beta-fructofuranosidase

hetero molecules

119 kDa, 2 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)	87.117, 87.117, 223.942
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Beta-fructofuranosidase Mass: 59165.793 Da / Num. of mol.: 2 / Fragment: fructofuranosidase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: KN29.1 / Gene: EF216677 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: A2TLS9, beta-fructofuranosidase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1167 / 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: 2.07 Å³/Da / Density % sol: 40.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.4M ammonium chloride, 18% PEG 3350, 0.1M MES pH 7.0, protein concentration 11 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2009 / Details: mirrors
Radiation	Monochromator: Double crystal monochromator Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.87→40 Å / Num. obs: 81348 / % possible obs: 98.6 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / B_iso Wilson estimate: 21.6 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 19.19
Reflection shell	Resolution: 1.87→1.94 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.445 / Mean I/σ(I) obs: 2 / Num. unique all: 7152 / % possible all: 87.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0091	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1W2T and 1Y4W

1w2t

1y4w

Resolution: 1.87→75.45 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.952 / SU B: 4.266 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / 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	0.19866	1622	2 %	RANDOM
R_work	0.14889	-	-	-
all	0.14989	81348	-	-
obs	0.14989	79656	98.58 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.469 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	0.03 Å²	0 Å²
2-	-	0.05 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→75.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8295	0	6	1167	9468

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.021	8616
X-RAY DIFFRACTION	r_angle_refined_deg	1.687	1.927	11717
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.452	5	1065
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.632	24.161	435
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.492	15	1368
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.232	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.129	0.2	1193
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	6805
X-RAY DIFFRACTION	r_mcbond_it	0.89	1.5	5232
X-RAY DIFFRACTION	r_mcangle_it	1.38	2	8410
X-RAY DIFFRACTION	r_scbond_it	2.459	3	3384
X-RAY DIFFRACTION	r_scangle_it	3.406	4.5	3299

LS refinement shell

Resolution: 1.869→1.918 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.306	106	-
R_work	0.244	4932	-
obs	-	-	83.6 %

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	3.4652	0.8259	-2.7441	0.3941	-0.3353	2.6955	0.4267	0.2294	0.7003	0.0177	-0.1209	0.3095	-0.4966	-0.4902	-0.3058	0.3234	0.0638	-0.0202	0.2892	-0.0442	0.2716	30.7337	69.7892	104.8942
2	8.2615	4.7955	0.8607	4.7381	0.057	1.2152	0.1271	-0.2216	0.1984	0.2056	-0.1471	0.0833	-0.0774	-0.0195	0.0199	0.094	0.0252	0.0273	0.0887	-0.0117	0.0387	26.3795	59.8123	110.089
3	0.717	0.3365	0.432	4.182	3.5941	5.1587	0.0254	-0.0973	-0.063	0.2281	-0.0283	0.2246	0.2567	-0.1948	0.0029	0.0355	-0.0135	0.0256	0.0879	0.0431	0.0652	17.2901	38.3616	99.6161
4	3.0548	0.3402	-0.2408	2.6562	0.7702	3.7823	0.0473	-0.0236	-0.2284	-0.0252	-0.0024	0.0226	0.2635	-0.0452	-0.0449	0.0228	-0.0036	-0.0097	0.0069	0.0085	0.025	24.9737	32.051	82.2837
5	3.2136	-0.1601	0.8368	1.0959	-0.4476	1.3996	-0.0157	-0.0632	0.0541	0.0544	0.0128	-0.0425	-0.0261	0.0108	0.0029	0.0076	-0.0051	0.003	0.0093	-0.0084	0.0085	32.0479	42.5686	93.3614
6	0.179	-0.6514	-0.2567	2.5929	1.6528	5.1893	-0.0139	-0.0332	-0.0955	0.0033	-0.0002	0.4066	-0.1905	-0.4994	0.0141	0.0135	0.0187	0.0068	0.1067	0.0047	0.1053	15.2709	45.3447	90.6073
7	3.7001	-2.5434	-1.4159	4.4146	1.1902	1.3509	-0.0441	-0.0688	-0.1848	0.1691	0.0396	0.0062	0.1862	0.0597	0.0045	0.0399	0.0023	-0.0161	0.0426	0.0077	0.0197	32.3616	36.8369	95.23
8	3.3686	-0.6302	0.1432	1.841	0.1914	1.57	0.0289	-0.0185	0.0978	0.1034	0.0097	-0.0857	-0.0968	0.0212	-0.0386	0.0389	-0.0016	0.0181	0.0016	-0.0011	0.0216	30.4057	53.3053	100.3315
9	7.283	-1.0452	0.6578	7.5423	1.1936	6.8609	0.0176	0.4595	0.0544	-0.2652	-0.0165	0.5348	0.1396	-0.3585	-0.0011	0.0884	0.0343	0.0035	0.1178	0.0157	0.1603	13.1551	60.5817	91.82
10	1.5111	-0.674	0.1216	2.3611	-0.4047	1.3221	-0.0007	-0.0341	0.0759	0.1039	0.0736	0.0754	-0.1464	-0.0863	-0.0729	0.0296	-0.0019	0.0256	0.0509	-0.0181	0.0317	29.0148	56.7965	99.6433
11	2.5473	-0.5191	0.9759	2.0088	-0.4704	2.3922	-0.0385	0.0276	0.1319	0.1366	-0.0061	-0.0709	-0.2339	0.1063	0.0445	0.0662	-0.0219	0.0418	0.0333	-0.0161	0.0648	38.1018	63.9657	91.9167
12	1.4093	-0.4122	0.5357	4.8445	-2.8413	7.6071	0.0641	0.0489	0.1789	0.458	-0.1755	-0.3976	-0.3982	0.5005	0.1114	0.0768	-0.0279	0.0096	0.103	-0.0413	0.1269	40.3005	64.4788	103.1448
13	2.3686	-0.2448	0.9209	2.0377	-0.2029	2.9054	-0.0506	0.1497	0.175	-0.1712	-0.0052	-0.0196	-0.2797	0.0258	0.0558	0.0783	0.0134	0.0433	0.0489	0.0052	0.0953	33.4014	65.872	82.071
14	5.7791	-1.7848	-0.7136	1.4782	-0.2052	1.2464	0.0181	-0.1543	0.0935	0.0039	-0.0002	-0.1472	0.0075	0.1759	-0.0179	0.0668	-0.0116	0.0143	0.0505	-0.0175	0.0704	46.4945	56.7004	81.9319
15	1.724	0.1524	0.435	1.6961	0.691	2.8296	0.0731	0.146	0.1806	-0.2188	-0.0676	0.048	-0.2806	-0.1642	-0.0055	0.0555	0.0259	0.0164	0.041	0.0135	0.0408	30.0587	56.0081	70.2504
16	2.4648	1.3743	1.693	2.6585	1.6147	5.738	-0.0968	-0.0058	0.1669	-0.1943	0.1374	-0.0626	-0.6178	0.2455	-0.0406	0.0791	-0.016	0.0307	0.0652	0.0067	0.1283	46.3527	64.7843	81.3011
17	0.6691	0.2426	0.2358	1.1278	-0.1993	1.5687	0.0047	-0.0962	0.0416	0.0248	-0.031	-0.099	0.0188	0.0772	0.0264	0.0059	0.0022	0.0031	0.0323	-0.0071	0.0219	37.6699	47.9737	81.6317
18	0.3921	0.1559	-0.4679	2.5368	-2.5432	2.8201	0.0182	0.0988	0.0205	-0.0362	0.1512	0.1909	0.0093	-0.2487	-0.1694	0.01	0.0074	-0.021	0.0658	-0.0211	0.0836	17.8807	41.7115	78.1987
19	3.8719	2.0702	-1.4084	2.389	-0.5038	1.3385	-0.0333	0.1211	-0.0546	-0.1528	0.0145	-0.1863	0.0921	0.1945	0.0188	0.0289	0.0381	0.0209	0.0851	0.0138	0.0211	44.2986	45.426	77.3742
20	4.8208	3.2369	2.4374	7.4855	5.3164	5.7266	0.1528	0.0375	-0.302	0.0806	-0.0896	-0.3357	0.3506	0.1126	-0.0632	0.0776	0.044	-0.0023	0.0823	0.0313	0.0649	43.4077	28.6825	79.698
21	0.585	-0.1921	-0.1862	0.6117	0.064	1.2022	0.0139	0.0931	-0.0914	-0.0646	0.0035	-0.0401	0.1308	0.0901	-0.0173	0.0245	0.0117	-0.003	0.0524	-0.0032	0.0469	35.2875	35.6954	63.3284
22	4.1511	2.5661	1.2655	4.4652	1.6091	0.6357	0.1511	0.2956	-0.4096	0.2258	-0.2805	0.7423	0.1407	-0.0693	0.1294	0.2978	-0.064	-0.0169	0.3007	-0.0884	0.4296	27.8018	24.6066	85.333
23	1.5553	0.3842	-1.6688	0.0986	-0.4109	1.7919	0.0872	-0.1252	-0.0252	0.0153	-0.0658	-0.0416	-0.1224	0.1476	-0.0213	0.3644	-0.0124	0.0287	0.3272	-0.0087	0.3815	44.2319	54.5754	7.7223
24	0.9119	1.6894	0.1606	7.4778	-1.772	1.0959	-0.1376	0.0842	0.0465	0.0548	0.0863	-0.1146	-0.1214	0.015	0.0513	0.1643	0.0134	0.0164	0.184	-0.0074	0.1314	35.8673	45.563	2.61
25	1.6844	0.6878	-2.025	1.1691	-0.6817	3.4175	-0.1056	0.1477	-0.1507	-0.2076	0.0049	-0.0379	0.2673	-0.0151	0.1007	0.1264	0.0338	-0.0202	0.125	-0.0304	0.1118	22.4225	28.4991	16.2421
26	1.301	-0.8227	-0.5539	2.9514	-0.0467	2.4261	0.0651	0.0942	-0.1276	0.0102	-0.0873	0.1568	0.1759	-0.1651	0.0222	0.0409	-0.0031	-0.0241	0.0541	-0.0154	0.0346	15.2144	33.9496	34.08
27	1.6941	-1.2043	0.5511	3.0663	-1.0452	1.3712	0.0334	0.0934	0.0806	-0.1014	0.0111	-0.0324	-0.0077	-0.0076	-0.0446	0.0636	0.0339	0.0216	0.0723	-0.004	0.0237	19.9685	44.3948	21.4548
28	4.7081	1.4914	-2.2699	5.0965	-1.3852	2.2207	0.1221	-0.0968	-0.1316	0.1115	-0.0883	-0.4048	-0.0358	0.3219	-0.0337	0.1038	0.0707	-0.009	0.1169	-0.0356	0.089	30.8123	31.5715	24.6479
29	4.2434	-1.483	-1.4518	1.9513	1.1994	1.6885	0.0754	0.1909	-0.1176	-0.1101	-0.0441	0.1772	0.0313	-0.1951	-0.0313	0.0998	0.0482	-0.0247	0.0975	0.0234	0.0387	14.8757	41.5088	20.2419
30	1.0934	0.0703	0.1075	1.6713	-0.1292	0.8283	0.0257	0.1677	0.0289	-0.1302	0.0172	-0.0554	-0.0672	0.0668	-0.0429	0.1298	0.0333	0.0488	0.1583	-0.0243	0.0713	29.5843	46.7357	12.9523
31	1.9856	0.1735	0.1127	7.9629	1.0309	3.9655	0.0345	-0.13	-0.1175	0.1358	-0.0854	-0.0941	0.0072	-0.1411	0.0509	0.1808	0.0427	0.0254	0.1907	-0.0164	0.233	45.0798	35.8227	20.6894
32	1.5674	-0.1793	-0.0422	1.1253	0.0013	1.1651	-0.0221	0.234	0.0229	-0.118	0.0743	-0.1261	-0.1129	0.2194	-0.0521	0.1474	0.0371	0.0636	0.1448	-0.0088	0.1026	33.9763	47.3324	13.2874
33	1.8065	-0.1114	1.218	2.235	-0.3577	2.2315	0.0078	0.0678	0.0666	-0.1089	0.0633	-0.0316	-0.1107	0.1662	-0.0711	0.1319	0.0008	0.0803	0.1567	0.0033	0.0898	36.3454	59.131	19.3471
34	4.5323	-0.204	1.9133	1.4994	-0.2712	3.3825	-0.2134	0.1474	0.1278	-0.2026	0.1404	-0.0059	-0.31	0.1992	0.0729	0.2316	-0.0004	0.0548	0.1765	0.0105	0.1444	34.4456	60.143	8.4011
35	1.8077	-0.2081	1.5942	1.935	-0.8495	1.8642	-0.0402	-0.0239	0.0564	0.0939	-0.0576	-0.1746	-0.1401	0.1884	0.0978	0.1388	-0.0027	0.0497	0.2162	-0.0268	0.1352	41.359	56.8718	28.9508
36	1.8193	-0.8965	-0.1377	2.7099	0.2138	1.2905	0.026	-0.0073	0.1771	-0.2024	0.0236	0.0451	-0.1923	-0.0207	-0.0496	0.1401	-0.0177	0.0397	0.1381	0.0213	0.0983	26.9002	63.5596	29.9309
37	1.1069	-0.0519	0.4482	0.5029	-0.9935	2.1242	0.0599	0.0624	0.1156	0.0563	-0.1373	-0.0592	-0.1095	0.3533	0.0774	0.0364	-0.0046	0.0374	0.1367	-0.0473	0.1441	35.333	50.6264	42.091
38	0.9893	0.3736	0.8031	1.1965	-1.3511	3.8988	0.0378	0.0833	0.0948	0.0413	-0.1392	-0.0889	-0.3521	0.4753	0.1014	0.1982	-0.0347	0.0626	0.1635	0.0052	0.1601	34.6179	67.8146	29.5476
39	0.6859	0.3084	0.1733	0.6886	0.3299	0.8969	0.0256	0.1347	0.1349	-0.1144	-0.044	0.0413	-0.0879	0.0888	0.0185	0.0497	0.0282	0.0294	0.0714	0.0276	0.0527	23.9981	52.2457	32.0023
40	1.5075	0.8902	1.204	1.7095	0.4882	1.0833	0.1277	0.0347	-0.1886	0.007	-0.0023	-0.156	0.1911	0.1182	-0.1254	0.0895	0.0746	0.0075	0.1164	-0.0018	0.0714	27.2318	32.3525	36.5323
41	0.8936	1.2004	0.3003	4.6159	0.6394	1.424	0.0643	-0.0768	0.2379	0.1022	-0.0686	0.1195	-0.1467	-0.0918	0.0042	0.0365	0.0302	0.0363	0.0833	0.0144	0.0953	18.7118	57.2301	36.0399
42	5.0959	4.3622	-4.2083	4.737	-2.5629	6.5102	0.1039	0.0327	0.3501	0.0141	0.0443	0.3663	-0.1602	-0.2209	-0.1482	0.0424	0.0317	-0.0227	0.1062	0.0249	0.1016	4.1389	49.1079	35.9776
43	1.1486	0.0623	0.1474	0.5146	0.2585	1.274	0.0254	-0.0307	0.0496	0.0507	-0.0039	0.0847	-0.0327	-0.0847	-0.0215	0.0186	0.0077	0.0077	0.0275	0.02	0.0406	15.3654	46.6816	51.4041
44	0.0371	0.2901	0.1118	3.2022	1.1781	0.4382	0.053	-0.0422	-0.0195	0.2252	-0.1435	0.2145	0.1028	-0.0802	0.0905	0.1995	0.0076	-0.0013	0.2078	0.0173	0.2246	7.6685	28.6857	28.9076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 14
3	X-RAY DIFFRACTION	3	A	15 - 35
4	X-RAY DIFFRACTION	4	A	36 - 49
5	X-RAY DIFFRACTION	5	A	50 - 73
6	X-RAY DIFFRACTION	6	A	74 - 81
7	X-RAY DIFFRACTION	7	A	82 - 102
8	X-RAY DIFFRACTION	8	A	103 - 133
9	X-RAY DIFFRACTION	9	A	134 - 144
10	X-RAY DIFFRACTION	10	A	145 - 182
11	X-RAY DIFFRACTION	11	A	183 - 210
12	X-RAY DIFFRACTION	12	A	211 - 219
13	X-RAY DIFFRACTION	13	A	220 - 236
14	X-RAY DIFFRACTION	14	A	237 - 259
15	X-RAY DIFFRACTION	15	A	260 - 275
16	X-RAY DIFFRACTION	16	A	276 - 291
17	X-RAY DIFFRACTION	17	A	292 - 319
18	X-RAY DIFFRACTION	18	A	320 - 335
19	X-RAY DIFFRACTION	19	A	336 - 356
20	X-RAY DIFFRACTION	20	A	357 - 365
21	X-RAY DIFFRACTION	21	A	366 - 513
22	X-RAY DIFFRACTION	22	A	514 - 523
23	X-RAY DIFFRACTION	23	B	1 - 6
24	X-RAY DIFFRACTION	24	B	7 - 14
25	X-RAY DIFFRACTION	25	B	15 - 35
26	X-RAY DIFFRACTION	26	B	36 - 49
27	X-RAY DIFFRACTION	27	B	50 - 73
28	X-RAY DIFFRACTION	28	B	74 - 81
29	X-RAY DIFFRACTION	29	B	82 - 102
30	X-RAY DIFFRACTION	30	B	103 - 133
31	X-RAY DIFFRACTION	31	B	134 - 144
32	X-RAY DIFFRACTION	32	B	145 - 182
33	X-RAY DIFFRACTION	33	B	183 - 210
34	X-RAY DIFFRACTION	34	B	211 - 219
35	X-RAY DIFFRACTION	35	B	220 - 236
36	X-RAY DIFFRACTION	36	B	237 - 259
37	X-RAY DIFFRACTION	37	B	260 - 275
38	X-RAY DIFFRACTION	38	B	276 - 291
39	X-RAY DIFFRACTION	39	B	292 - 319
40	X-RAY DIFFRACTION	40	B	320 - 335
41	X-RAY DIFFRACTION	41	B	336 - 356
42	X-RAY DIFFRACTION	42	B	357 - 365
43	X-RAY DIFFRACTION	43	B	366 - 513
44	X-RAY DIFFRACTION	44	B	514 - 526

-
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