PDB-4r83: Crystal structure of Sialyltransferase from Photobacterium damsela

ID or keywords:

Entry

Database: PDB / ID: 4r83

Title

Crystal structure of Sialyltransferase from Photobacterium damsela

Components

Sialyltransferase 0160

Keywords

TRANSFERASE / Rossmann Fold / glycosyltransferase GT-B structural group

Function / homology

Function and homology information

negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / glycosyltransferase activity / metal ion binding
Similarity search - Function

Biological species

Photobacterium damselae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Fisher, A.J. / Chen, X. / Li, Y. / Huynh, N.

Citation

Journal: Febs Lett. / Year: 2014
Title: Crystal structures of sialyltransferase from Photobacterium damselae.
Authors: Huynh, N. / Li, Y. / Yu, H. / Huang, S. / Lau, K. / Chen, X. / Fisher, A.J.

History

Deposition	Aug 29, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 1.2	Jan 14, 2015	Group: Database references
Revision 1.3	Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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	4r83.cif.gz	791.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4r83.ent.gz	658 KB	Display	PDB format
PDBx/mmJSON format	4r83.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4r83_validation.pdf.gz	465.2 KB	Display	wwPDB validaton report
Full document	4r83_full_validation.pdf.gz	479.8 KB	Display
Data in XML	4r83_validation.xml.gz	78.3 KB	Display
Data in CIF	4r83_validation.cif.gz	113.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/4r83 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r83	HTTPS FTP

-
Related structure data

Related structure data	4r84C 4r9vC 2z4tS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4r84-4 4r84-1 4r84-2 6xj7-d 5xf7-d 4qaw-3 4g3e-d 5sy5-1 6m4w-1 2182 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

4r84C

4r9vC

2z4tS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Sialyltransferase 0160

B: Sialyltransferase 0160

C: Sialyltransferase 0160

D: Sialyltransferase 0160

hetero molecules

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

1

A: Sialyltransferase 0160

hetero molecules

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

2

B: Sialyltransferase 0160

hetero molecules

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

3

C: Sialyltransferase 0160

hetero molecules

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

4

D: Sialyltransferase 0160

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.670, 81.340, 111.840
Angle α, β, γ (deg.)	98.60, 92.76, 100.85
Int Tables number	1
Space group name H-M	P1

#1: Protein	Sialyltransferase 0160 Mass: 56832.145 Da / Num. of mol.: 4 / Fragment: UNP residues 16-497 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium damselae (bacteria) / Gene: bst / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O66375, beta-galactoside alpha-(2,6)-sialyltransferase
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1395 / 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: 2.51 Å³/Da / Density % sol: 50.9 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 6000, 0.2M sodium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: May 23, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 1.93→50 Å / Num. all: 156324 / Num. obs: 156324 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / B_iso Wilson estimate: 31.9 Å² / R_merge(I) obs: 0.029 / Net I/σ(I): 18.42
Reflection shell	Resolution: 1.93→1.98 Å / Redundancy: 2 % / R_merge(I) obs: 0.397 / Mean I/σ(I) obs: 2.16 / Num. unique all: 11570 / % possible all: 94

-
Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z4T

2z4t

Resolution: 1.93→34.839 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 24.47 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2192	7869	5.04 %	Random
R_work	0.1787	-	-	-
obs	0.1807	156282	94.19 %	-
all	-	156282	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refine analyze

Luzzati sigma a obs: 0.22 Å

Refinement step

Cycle: LAST / Resolution: 1.93→34.839 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15155	0	4	1395	16554

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15666
X-RAY DIFFRACTION	f_angle_d	1.076	21389
X-RAY DIFFRACTION	f_dihedral_angle_d	12.487	5703
X-RAY DIFFRACTION	f_chiral_restr	0.046	2381
X-RAY DIFFRACTION	f_plane_restr	0.005	2783

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 (%)
1.93-1.9519	0.3165	279	0.2775	4938	X-RAY DIFFRACTION	94
1.9519-1.9749	0.3048	268	0.2723	4884	X-RAY DIFFRACTION	94
1.9749-1.999	0.2922	261	0.263	5014	X-RAY DIFFRACTION	95
1.999-2.0243	0.3193	248	0.2566	4999	X-RAY DIFFRACTION	94
2.0243-2.0509	0.2737	262	0.2449	4898	X-RAY DIFFRACTION	94
2.0509-2.079	0.2848	271	0.2343	4962	X-RAY DIFFRACTION	94
2.079-2.1087	0.2825	269	0.2329	4944	X-RAY DIFFRACTION	95
2.1087-2.1401	0.2627	258	0.2287	4997	X-RAY DIFFRACTION	95
2.1401-2.1736	0.2705	250	0.2157	4999	X-RAY DIFFRACTION	95
2.1736-2.2092	0.2728	242	0.2096	4971	X-RAY DIFFRACTION	95
2.2092-2.2473	0.2524	273	0.2067	4979	X-RAY DIFFRACTION	94
2.2473-2.2882	0.2552	271	0.2154	4920	X-RAY DIFFRACTION	94
2.2882-2.3322	0.2528	273	0.2028	4990	X-RAY DIFFRACTION	95
2.3322-2.3798	0.2448	268	0.1963	5022	X-RAY DIFFRACTION	95
2.3798-2.4315	0.2546	273	0.2008	4960	X-RAY DIFFRACTION	95
2.4315-2.488	0.2408	248	0.1944	5041	X-RAY DIFFRACTION	95
2.488-2.5502	0.2505	279	0.1983	4931	X-RAY DIFFRACTION	95
2.5502-2.6192	0.2412	284	0.1948	4998	X-RAY DIFFRACTION	95
2.6192-2.6962	0.2653	277	0.1967	5015	X-RAY DIFFRACTION	95
2.6962-2.7832	0.2477	254	0.1916	4962	X-RAY DIFFRACTION	95
2.7832-2.8826	0.2344	259	0.1941	4983	X-RAY DIFFRACTION	95
2.8826-2.998	0.224	266	0.1922	4994	X-RAY DIFFRACTION	95
2.998-3.1343	0.2427	261	0.1918	4995	X-RAY DIFFRACTION	95
3.1343-3.2995	0.2335	262	0.1817	4955	X-RAY DIFFRACTION	95
3.2995-3.506	0.2097	239	0.1724	4983	X-RAY DIFFRACTION	94
3.506-3.7764	0.1883	253	0.1593	4965	X-RAY DIFFRACTION	94
3.7764-4.1559	0.1803	268	0.1474	4849	X-RAY DIFFRACTION	93
4.1559-4.756	0.1528	266	0.1256	4828	X-RAY DIFFRACTION	92
4.756-5.9871	0.1674	265	0.1389	4820	X-RAY DIFFRACTION	92
5.9871-34.8449	0.1902	222	0.1517	4617	X-RAY DIFFRACTION	87

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	0.2206	0.147	-0.1136	0.8778	-0.1135	0.6988	0.0493	0.3912	0.0702	-0.372	-0.3938	-0.4012	0.2423	0.5437	0.2184	0.395	0.2417	0.1534	0.7249	0.1609	0.3641	45.0893	15.9156	71.2911
2	2.0711	-0.1878	-0.6816	0.941	-0.3169	0.9553	0.0251	-0.0534	-0.0569	0.0263	-0.1188	0.0142	0.0857	0.0937	0.1076	0.2549	0.036	0.0041	0.2314	-0.0188	0.1894	24.9144	11.312	97.3332
3	2.7036	0.2782	0.1156	0.9147	-0.1135	0.5719	0.0592	0.1826	0.0948	0.0181	-0.0378	0.1874	0.0905	-0.0615	-0.0066	0.2852	0.0376	0.0002	0.1937	-0.0416	0.2207	9.5697	13.8118	97.8816
4	1.8877	-0.4172	-0.4438	1.5496	-0.4185	0.6443	-0.4978	-0.1842	-0.1178	0.6555	0.4071	-0.1202	0.2009	0.0103	0.0494	0.6523	0.0988	-0.111	0.5237	-0.2084	0.6556	-12.9249	-4.5319	99.5316
5	1.0002	0.0616	-0.9662	0.7902	-0.3882	1.0366	-0.2819	0.218	-0.5781	0.0236	0.281	-0.1385	0.4551	-0.1181	-0.0042	0.509	0.0134	-0.0363	0.4391	-0.1925	0.6398	-2.153	-4.9083	95.321
6	1.5738	0.5224	0.4525	2.1216	0.1578	3.2758	0.1874	-0.124	-0.0258	0.373	0.2514	-0.0265	0.3778	0.0701	-0.4078	0.3236	0.0466	-0.0191	0.3336	-0.0134	0.4619	-8.9068	10.1153	103.8664
7	0.9033	-0.2836	0.1392	0.7625	0.2261	2.8043	-0.4709	-0.2343	-0.2602	0.4414	0.1318	0.1988	0.5318	0.0863	0.2305	0.493	0.0511	0.1093	0.5534	0.1339	0.4173	28.7078	16.0707	48.6889
8	2.2588	-0.0372	-0.9388	0.9422	0.2312	1.1215	-0.1138	0.1413	-0.1319	0.0742	0.1255	0.2031	0.0816	-0.3442	-0.0297	0.2361	-0.0399	-0.0181	0.4298	0.1157	0.3253	36.2757	20.8654	29.6862
9	2.1964	-1.0854	-0.3785	1.2137	-0.3341	0.9456	0.0179	-0.1687	0.0667	-0.0813	0.1281	0.0132	0.0129	-0.074	-0.1346	0.2409	-0.0437	-0.0173	0.2631	-0.0039	0.2489	60.1716	26.8677	21.7441
10	1.4084	0.3425	-0.2181	2.5005	0.1005	2.0331	-0.1616	0.2128	0.0971	-0.5065	0.1349	0.249	0.1316	0.264	0.0301	0.4444	-0.034	-0.0112	0.3392	0.1015	0.3808	77.6594	8.2031	16.7722
11	1.2989	-0.1529	-0.4469	2.0671	0.1465	2.4544	0.0239	-0.1753	0.1439	-0.1407	0.1082	0.1985	0.1686	-0.1762	-0.1122	0.2047	-0.0593	0.0097	0.3198	0.0341	0.2847	78.8758	24.381	15.5991
12	0.8146	-0.0044	-0.0457	0.6644	-0.0334	1.2798	-0.0457	-0.2577	-0.1316	0.3267	-0.0688	0.2563	0.114	-0.2621	0.0627	0.3786	-0.0813	0.0884	0.3578	0.0105	0.3317	71.129	-11.9064	-8.7849
13	1.4476	-0.039	0.1584	1.3068	-0.0455	1.1293	-0.0237	0.0184	0.015	-0.0922	0.0956	0.0111	-0.0214	-0.0238	-0.067	0.1876	-0.0006	-0.0093	0.2081	-0.0112	0.1761	92.9051	-3.4274	-34.3164
14	1.8225	0.2178	-0.0684	1.6025	-0.0232	0.8376	-0.1956	0.0459	-0.1771	-0.1346	0.0299	-0.1425	0.0156	0.227	0.1361	0.3355	-0.0192	-0.0454	0.2882	0.0703	0.3011	116.6058	-23.6535	-35.1324
15	1.4825	0.4718	-1.0009	1.3788	-0.906	1.1204	-0.0483	-0.0742	-0.0479	-0.2289	0.0453	0.2032	0.0929	0.0674	-0.0207	0.2952	-0.0279	-0.0618	0.2481	0.0577	0.287	117.4237	-20.2414	-38.3842
16	2.708	-0.5829	-0.7615	1.4547	0.2937	3.4121	0.0646	-0.3687	0.3496	-0.0418	0.0422	-0.1677	-0.3994	-0.0754	-0.0882	0.2266	-0.0218	0.0197	0.282	-0.0585	0.2922	123.9615	-4.9671	-38.7297
17	1.199	0.2386	-0.7653	0.7674	-0.1934	1.1643	-0.0629	0.1605	-0.2602	-0.3201	-0.1154	-0.3297	0.1565	0.1833	0.144	0.3738	0.0615	0.1078	0.4174	0.0472	0.3916	85.7835	-13.1396	20.457
18	2.4703	-0.2985	0.1193	1.1137	0.351	1.3738	-0.2782	0.415	-0.3896	-0.2559	0.0489	-0.0569	0.2235	-0.1445	0.1759	0.3164	-0.0456	0.0639	0.2983	-0.002	0.2788	65.3456	-23.9991	38.0611
19	1.4292	0.3478	-0.1421	1.4719	-0.5218	1.3431	-0.1681	0.0041	-0.3891	-0.0021	-0.2128	-0.3742	0.256	0.4428	0.3431	0.3071	0.0419	0.0684	0.3586	0.106	0.3554	73.1151	-23.0248	45.8355
20	1.7146	-0.3978	0.1263	1.4105	-0.2511	2.2403	-0.1589	-0.2655	0.0055	0.1615	0.0421	0.0967	-0.2296	-0.1391	0.0525	0.2497	0.03	-0.0188	0.2232	0.0094	0.2002	61.4278	-11.0405	51.747
21	2.1551	0.1185	0.0275	1.0718	-0.6364	1.442	-0.2354	-0.1459	0.4285	0.1218	0.1124	0.2095	-0.496	-0.3052	0.1012	0.3469	0.0779	-0.0531	0.2835	-0.0109	0.3269	57.3884	-4.2939	50.7087
22	1.2937	-0.322	0.5039	1.6518	-0.0069	0.2557	0.115	0.3088	-0.5469	-0.7449	0.1566	0.4574	0.2874	-0.3292	-0.1952	0.601	-0.0646	-0.2128	0.508	-0.0731	0.5403	47.8874	-30.3978	32.7793
23	0.5669	0.0504	0.209	0.2121	0.214	0.2765	-0.0077	0.1589	-0.0824	0.9398	0.3768	-0.336	0.6021	-0.7558	-0.0903	1.1422	-0.1592	-0.3858	0.8872	0.1096	0.8358	28.1735	-34.2866	46.2488
24	0.4769	0.4557	-0.4338	0.5058	-0.3017	0.4364	0.7464	-0.1194	-0.3226	-0.0381	0.3106	0.6682	1.0391	-0.0209	-0.494	0.8003	-0.1761	-0.4516	0.5769	-0.0272	0.9677	41.9612	-35.0576	39.3262
25	0.9223	0.3622	0.4466	1.2901	0.4273	0.894	0.2635	-0.0931	-0.3015	0.7283	0.7049	-0.2955	0.466	-0.3395	-0.6304	0.7158	-0.0012	-0.2247	0.6072	0.0969	0.8507	36.2706	-23.4519	47.4314
26	1.9613	0.0585	0.2914	1.8504	-0.5386	2.4006	0.0293	-0.3112	-0.1119	0.3793	0.4147	0.5487	0.6255	-0.9338	-0.2603	0.3909	-0.0568	0.0117	0.8115	0.2492	0.656	32.3992	-17.2837	50.7076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 98 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 245 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 246 through 366 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 367 through 404 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 405 through 443 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 444 through 497 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 52 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 53 through 218 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 219 through 366 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 367 through 443 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 444 through 497 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 24 through 122 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 123 through 313 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 314 through 393 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 394 through 469 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 470 through 497 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 24 through 122 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 123 through 154 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 155 through 198 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 199 through 245 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 246 through 313 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 314 through 363 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 364 through 394 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 395 through 438 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 439 through 469 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 470 through 497 )

-
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