PDB-5f7j: Crystal structure of Mutant N87T of adenosine/Methylthioadenosine...

ID or keywords:

Entry

Database: PDB / ID: 5f7j

Title

Crystal structure of Mutant N87T of adenosine/Methylthioadenosine phosphorylase from Schistosoma mansoni in complex with Adenine

Components

Methylthioadenosine phosphorylase

Keywords

TRANSFERASE

Function / homology

Function and homology information

S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / nucleus / cytosol
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.66 Å

Authors

Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.M.

Funding support

Brazil, 2items

Citation

Journal: PLoS Negl Trop Dis / Year: 2016
Title: Crystal Structure of Schistosoma mansoni Adenosine Phosphorylase/5'-Methylthioadenosine Phosphorylase and Its Importance on Adenosine Salvage Pathway.
Authors: Torini, J.R. / Brandao-Neto, J. / DeMarco, R. / Pereira, H.D.

History

Deposition	Dec 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 14, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	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	5f7j.cif.gz	700.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7j.ent.gz	576.6 KB	Display	PDB format
PDBx/mmJSON format	5f7j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f7j ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7j	HTTPS FTP

-
Related structure data

Related structure data	4l5aC 4l5cC 4l5yC 4l6iSC 5f73C 5f76C 5f77C 5f78C 5f7oC 5f7xC 5f7zC 5fakC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5fak-1 5fak-2 5f7x-d 4l6i-1 4l5a-2 5f76-d 5f7o-d 4l6i-2 5f77-d 4l5y-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) 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	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Methylthioadenosine phosphorylase

B: Methylthioadenosine phosphorylase

C: Methylthioadenosine phosphorylase

D: Methylthioadenosine phosphorylase

E: Methylthioadenosine phosphorylase

F: Methylthioadenosine phosphorylase

hetero molecules

212 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methylthioadenosine phosphorylase

B: Methylthioadenosine phosphorylase

C: Methylthioadenosine phosphorylase

hetero molecules

defined by author&software
106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Methylthioadenosine phosphorylase

E: Methylthioadenosine phosphorylase

F: Methylthioadenosine phosphorylase

hetero molecules

defined by author&software
106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.493, 82.106, 150.267
Angle α, β, γ (deg.)	90.00, 101.10, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Methylthioadenosine phosphorylase Mass: 35246.484 Da / Num. of mol.: 6 / Fragment: Enzyme / Mutation: N87T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: I0B503, S-methyl-5'-thioadenosine phosphorylase
#2: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₅N₅
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1728 / 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: 2.33 Å³/Da / Density % sol: 47.25 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM Bris-tris or Mes, 14-18% PEG3350, pH 6.5 / PH range: 6.1-6.7

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04 / Wavelength: 0.97949 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 1.66→76.76 Å / Num. obs: 221276 / % possible obs: 96.5 % / Redundancy: 3.8 % / B_iso Wilson estimate: 19.42 Å² / R_merge(I) obs: 0.084 / Net I/σ(I): 7.8 / Scaling rejects: 1153

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Rejects	% possible all
1.66-1.72	2.3	0.737	1	0	75.7
6.21-76.76	4.1	0.049	1	0	99.9

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
xia2		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L6I

4l6i

Resolution: 1.66→73.727 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2263	10728	4.91 %	Random selection
R_work	0.1946	-	-	-
obs	0.1961	218591	95.34 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.66→73.727 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13034	0	60	1728	14822

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13404
X-RAY DIFFRACTION	f_angle_d	0.895	18187
X-RAY DIFFRACTION	f_dihedral_angle_d	14.761	8041
X-RAY DIFFRACTION	f_chiral_restr	0.059	2105
X-RAY DIFFRACTION	f_plane_restr	0.006	2326

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 (%)
1.66-1.6789	0.3842	246	0.3833	4921	X-RAY DIFFRACTION	68
1.6789-1.6986	0.4077	272	0.3721	5267	X-RAY DIFFRACTION	73
1.6986-1.7193	0.4062	300	0.3676	5550	X-RAY DIFFRACTION	78
1.7193-1.7411	0.3923	311	0.3596	6023	X-RAY DIFFRACTION	83
1.7411-1.764	0.4011	341	0.3407	6379	X-RAY DIFFRACTION	88
1.764-1.7882	0.3498	351	0.3237	6767	X-RAY DIFFRACTION	93
1.7882-1.8137	0.34	396	0.2995	7057	X-RAY DIFFRACTION	98
1.8137-1.8408	0.3592	385	0.2895	7155	X-RAY DIFFRACTION	99
1.8408-1.8696	0.3038	362	0.2866	7168	X-RAY DIFFRACTION	99
1.8696-1.9002	0.3182	382	0.3064	7142	X-RAY DIFFRACTION	98
1.9002-1.933	0.4071	333	0.3578	6748	X-RAY DIFFRACTION	94
1.933-1.9682	0.2981	335	0.2473	7164	X-RAY DIFFRACTION	99
1.9682-2.006	0.2521	389	0.2137	7203	X-RAY DIFFRACTION	100
2.006-2.047	0.2332	367	0.2157	7239	X-RAY DIFFRACTION	100
2.047-2.0915	0.3142	375	0.2422	7073	X-RAY DIFFRACTION	98
2.0915-2.1401	0.2333	343	0.195	7272	X-RAY DIFFRACTION	100
2.1401-2.1937	0.2434	390	0.1916	7190	X-RAY DIFFRACTION	100
2.1937-2.253	0.2514	363	0.2152	7150	X-RAY DIFFRACTION	98
2.253-2.3193	0.2323	352	0.1886	7186	X-RAY DIFFRACTION	98
2.3193-2.3941	0.2106	367	0.166	7239	X-RAY DIFFRACTION	100
2.3941-2.4797	0.2119	359	0.17	7253	X-RAY DIFFRACTION	100
2.4797-2.579	0.1976	377	0.1693	7256	X-RAY DIFFRACTION	100
2.579-2.6964	0.2227	357	0.1748	7272	X-RAY DIFFRACTION	100
2.6964-2.8385	0.2058	382	0.1654	7273	X-RAY DIFFRACTION	100
2.8385-3.0164	0.2194	380	0.169	7287	X-RAY DIFFRACTION	100
3.0164-3.2493	0.1984	406	0.1648	7249	X-RAY DIFFRACTION	100
3.2493-3.5763	0.1971	363	0.1691	7328	X-RAY DIFFRACTION	100
3.5763-4.0937	0.1724	363	0.1529	7334	X-RAY DIFFRACTION	100
4.0937-5.1575	0.1531	362	0.1363	7348	X-RAY DIFFRACTION	100
5.1575-73.8	0.1803	419	0.1788	7370	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	2.1176	0.4128	-0.3278	1.65	-0.7253	1.4786	0.0099	-0.0571	-0.1816	0.1278	0.0031	0.338	0.1683	-0.2734	0.0191	0.1559	-0.0398	0.0372	0.1697	0.0054	0.2489	-11.6523	-21.6973	69.775
2	1.7136	0.3332	-0.1669	1.0755	0.1637	1.3101	0.0444	0.1081	0.0778	-0.0557	-0.0349	0.1437	-0.0862	-0.2074	0.0042	0.12	0.0413	0.0045	0.1287	0.0211	0.1248	-5.6485	-6.9439	59.9535
3	7.8809	2.5631	4.4282	1.537	2.6643	4.8168	0.2407	-1.0843	0.3444	0.2489	-0.2903	0.2286	-0.1124	-0.6091	0.0865	0.259	0.0651	0.0716	0.2216	0.033	0.2781	-9.1426	-3.1721	73.5386
4	3.4156	-0.7041	0.2801	1.5281	-0.9507	0.6061	0.0597	0.6998	-0.7011	-0.4415	-0.2188	0.3956	0.3966	-0.5222	0.1461	0.2451	-0.1018	-0.1222	0.4387	-0.0907	0.4066	-16.5112	-23.7893	49.2505
5	0.9063	-1.0942	-0.6547	8.8321	1.7603	4.7776	-0.3279	0.6235	-0.8477	-0.3734	-0.279	0.7732	0.5661	-0.4599	0.4869	0.3073	-0.026	0.0093	0.3024	-0.0983	0.2719	15.522	-33.8237	30.4705
6	1.1954	-0.351	-0.3451	0.9229	0.3914	1.312	0.0364	0.1815	-0.0565	-0.1038	-0.0599	0.0474	-0.0378	-0.1373	0.0219	0.185	0.0178	0.0161	0.1462	-0.0071	0.111	13.9552	-19.7797	38.1809
7	0.9106	-0.0784	-0.4905	1.3448	0.7428	3.1859	0.1031	0.3447	-0.1708	-0.1949	-0.1279	0.1622	-0.0999	-0.2923	0.0169	0.2735	0.0412	0.0358	0.13	0.0281	0.1692	13.383	-19.9777	33.3852
8	2.8127	0.4981	4.5034	1.7706	-0.6226	8.5147	0.2244	0.2755	-0.1889	0.0747	-0.1074	-0.6422	0.5652	0.987	-0.1378	0.1914	0.0083	-0.018	0.2099	0.0229	0.3082	38.4638	-9.9728	72.8868
9	7.7181	1.8718	-0.4157	3.0395	-1.4311	1.4495	-0.0402	-0.4602	-0.2875	0.2241	-0.0974	-0.3706	0.0881	0.3848	0.1251	0.2071	0.035	-0.0113	0.1795	0.0183	0.2113	30.6324	-22.0186	75.7218
10	0.8674	0.0595	-0.2293	1.5261	-0.257	0.7056	0.0549	-0.0171	0.081	0.0022	-0.0193	-0.0703	-0.078	0.0633	-0.0391	0.141	-0.0054	0.0036	0.1028	-0.0072	0.1142	25.8532	-4.4176	67.4584
11	0.7378	0.1405	0.3981	1.3365	-0.2065	1.9611	0.0509	0.1173	0.0118	-0.1685	0.0169	-0.0466	-0.0991	0.0288	-0.0572	0.1492	0.0092	0.0264	0.1025	-0.0069	0.1393	22.8165	-5.74	57.8464
12	2.8384	-0.2045	-2.4306	2.1703	0.9799	2.9579	0.0501	0.054	0.0776	-0.2472	0.1003	-0.4956	-0.014	0.4542	-0.1262	0.1937	-0.0305	0.0368	0.1247	0.0282	0.2551	40.2417	-1.3014	63.0718
13	6.3556	2.0519	-0.7812	3.2708	-0.3718	2.5302	0.1015	-0.5257	0.0203	0.2783	-0.0746	0.3166	0.0503	-0.3644	-0.0418	0.2879	0.0191	0.0627	0.2031	0.0296	0.1617	11.7141	-5.1274	84.1399
14	4.5324	-2.299	-1.3661	3.8296	-2.3312	3.8572	0.1183	-0.2002	0.2138	0.4359	0.2178	0.6564	-0.0519	-0.5427	-0.2083	0.1826	-0.0427	0.0662	0.3011	0.0307	0.414	-3.6956	-22.1281	-0.8958
15	2.0469	0.5038	-0.3586	1.9457	-0.5609	1.6703	0.0153	-0.1158	-0.3551	0.2002	-0.0268	0.2316	0.2353	-0.2566	0.0369	0.1777	-0.0361	0.0231	0.1823	0.035	0.2557	5.461	-23.853	-4.7244
16	1.8161	0.0516	-0.052	1.1834	-0.0985	1.5845	0.015	0.0841	-0.0294	-0.1092	0.0014	0.0963	-0.1419	-0.2187	-0.0078	0.1217	0.041	-0.0093	0.1485	0.0183	0.1113	7.9367	-8.4948	-14.1367
17	7.3386	0.061	0.3439	1.9747	-2.84	6.9168	0.0793	-0.6892	2.0424	0.3403	0.1854	-0.166	-2.1619	0.1957	-0.1817	0.6491	-0.0386	0.052	0.3024	-0.0808	0.5908	19.5862	4.7518	-1.0082
18	3.4378	0.4005	-0.0593	2.8138	0.8444	2.4481	0.0781	-0.0836	-0.2489	0.0319	-0.0991	0.3732	0.0595	-0.5793	0.0812	0.1664	0.0246	-0.0435	0.206	0.1353	0.2332	-0.7837	-15.9153	-10.9743
19	0.5092	-1.0796	-0.3946	2.5374	1.7407	6.6989	-0.2328	0.2043	-0.6354	0.0747	-0.0664	0.5827	0.564	-0.3713	0.3725	0.3609	0.0196	0.1462	0.2728	-0.0589	0.494	29.5299	-34.9949	-44.0544
20	1.3381	-0.4705	-0.7287	1.1804	0.5485	1.8018	-0.0156	0.0555	-0.1309	-0.1353	-0.0331	-0.0673	-0.0367	-0.0154	0.048	0.1894	0.0062	0.0507	0.1711	-0.0271	0.1796	27.4333	-20.5728	-36.5692
21	1.0454	-0.0069	-0.4204	1.7846	1.0766	4.2419	-0.0322	0.2209	-0.2147	-0.2358	-0.15	0.1485	-0.0488	-0.3879	0.1376	0.3229	0.0281	0.0746	0.142	0.0113	0.2678	26.4362	-21.2143	-41.5177
22	1.0606	-1.002	-0.4471	2.8695	0.9908	1.9336	0.2003	-0.4171	-0.3235	0.226	-0.1284	-0.4228	0.2555	0.4296	-0.0033	0.1833	-0.0724	-0.0399	0.4433	0.1846	0.3468	48.3532	-10.0003	-1.9797
23	1.828	0.2122	-0.4804	1.6026	-0.4985	0.3386	0.0755	-0.7117	-0.4999	0.394	-0.2951	-0.2925	0.0427	0.5136	0.1601	0.2854	-0.0297	-0.0512	0.5626	0.2457	0.4208	48.0341	-15.2973	1.6568
24	1.7018	0.3157	0.0659	2.0131	-0.3746	2.0854	-0.0317	-0.3351	-0.4264	0.0704	-0.2324	-0.2657	0.215	0.3651	0.218	0.1621	-0.0003	0.0225	0.2586	0.1189	0.3035	42.0185	-13.8745	-6.0059
25	2.4634	0.7633	-0.86	1.4179	-0.3241	1.5739	0.155	-0.1144	0.0693	0.0295	-0.0889	-0.1002	-0.2073	0.1749	-0.0628	0.1576	-0.0204	0.0056	0.1531	0.0171	0.147	36.8289	-0.2278	-9.9817
26	3.7691	-0.4148	-1.0043	4.0054	0.0745	3.7624	-0.077	0.3697	0.0961	-0.3556	-0.1197	-0.3338	-0.2528	0.0383	0.1597	0.1993	-0.0299	0.0138	0.1905	-0.0236	0.1658	32.8077	-7.5214	-27.1282
27	2.3968	0.9537	-0.5804	2.427	-1.1739	4.3208	-0.0185	0	-0.131	-0.2285	-0.1002	-0.2184	-0.0859	0.2407	0.0887	0.1548	-0.0064	0.0269	0.1362	0.0239	0.1847	37.6675	-5.0856	-13.2933
28	4.4906	0.1089	-3.3314	3.0807	1.2198	3.5722	0.1472	-0.3654	0.0179	-0.2055	-0.0775	-0.3337	-0.1565	0.6425	-0.0687	0.2097	-0.0544	-0.0103	0.2587	0.1129	0.2891	54.0147	-0.6429	-11.3401
29	6.0962	2.8193	-0.0595	3.0192	0.0721	2.1482	0.4617	-0.9919	0.2275	0.5259	-0.4369	0.1128	-0.3177	0.1141	-0.0398	0.3629	-0.0904	0.0221	0.3679	0.0168	0.1508	29.7004	-4.4515	8.9523
30	0.4411	-0.1307	-1.8031	0.0031	0.4772	6.6646	-0.2741	0.1358	-0.1479	0.0596	-0.0797	0.0321	1.1722	-0.2097	0.3803	0.3505	0.0305	0.0323	0.3108	-0.0275	0.2165	8.3454	-11.5535	17.5427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 235 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 236 through 269 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 270 through 292 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 26 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 27 through 230 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 231 through 291 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 3 through 23 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 24 through 38 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 39 through 182 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 183 through 242 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 243 through 269 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 270 through 299 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 3 through 26 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 27 through 90 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 91 through 235 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 236 through 242 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 243 through 291 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1 through 26 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 27 through 230 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 231 through 291 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 3 through 27 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 28 through 53 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 54 through 91 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 92 through 182 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 183 through 198 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 199 through 243 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 244 through 269 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 270 through 293 )
30	X-RAY DIFFRACTION	30	(chain 'A' and resid 301) or (chain 'B' and resid 301) or (chain 'D' and resid 301) or (chain 'E' and resid 301)

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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