PDB-5f73: Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine...

ID or keywords:

Entry

Database: PDB / ID: 5f73

Title

Crystal structure of Mutant S12T of Adenosine/Methylthioadenosine Phosphorylase in APO form

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: 2.06 Å

Authors

Torini, J.R.S. / 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 7, 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	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Apr 17, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	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	5f73.cif.gz	665.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5f73.ent.gz	550.4 KB	Display	PDB format
PDBx/mmJSON format	5f73.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5f73_validation.pdf.gz	489.7 KB	Display	wwPDB validaton report
Full document	5f73_full_validation.pdf.gz	495.3 KB	Display
Data in XML	5f73_validation.xml.gz	67.1 KB	Display
Data in CIF	5f73_validation.cif.gz	96.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f7/5f73 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f73	HTTPS FTP

-
Related structure data

Related structure data	4l5aC 4l5cC 4l5ySC 4l6iC 5f76C 5f77C 5f78C 5f7jC 5f7oC 5f7xC 5f7zC 5fakC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5f7z-2 5f7o-d 5f78-2 5f77-d 4l6i-2 5f78-1 4l5y-2 5f7z-1 4l5y-1 5fak-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

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
Evidence: gel filtration
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
Evidence: gel filtration
106 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	81.440, 82.160, 150.910
Angle α, β, γ (deg.)	90.000, 101.500, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

Trimer confirmed by gel filtration

#1: Protein	Methylthioadenosine phosphorylase Mass: 35273.508 Da / Num. of mol.: 6 / Fragment: Enzyme / Mutation: S12T 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1012 / 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: 2.34 Å³/Da / Density % sol: 47.4 %
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, VAPOR DIFFUSION, HANGING DROP, temperature 291K PH range: 6.3-6.6

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.92 Å

Detector

Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 5, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.92 Å / Relative weight: 1

Reflection

Resolution: 2.06→39.58 Å / Num. obs: 119129 / % possible obs: 98.8 % / Redundancy: 4.2 % / B_iso Wilson estimate: 25.92 Å² / R_merge(I) obs: 0.094 / Net I/σ(I): 11.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	Rejects	% possible all
2.06-2.11	3.8	0.595	1	0	94.3
9.21-39.58	4.3	0.03	1	0	98.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
xia2		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L5Y

4l5y

Resolution: 2.06→39.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2162	6071	5.03 %
R_work	0.1753	114716	-
obs	0.1773	120787	98.59 %

Solvent computation

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

Displacement parameters

B_iso max: 131.59 Å² / B_iso mean: 34.3295 Å² / B_iso min: 14.82 Å²

Refinement step

Cycle: final / Resolution: 2.06→39.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12757	0	30	1012	13799
B_iso mean	-	-	25.13	38.81	-
Num. residues	-	-	-	-	1692

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	13042
X-RAY DIFFRACTION	f_angle_d	0.796	17726
X-RAY DIFFRACTION	f_chiral_restr	0.053	2074
X-RAY DIFFRACTION	f_plane_restr	0.005	2274
X-RAY DIFFRACTION	f_dihedral_angle_d	11.869	7803

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.06-2.0733	0.3457	210	0.2675	3688	3898	96
2.0733-2.0977	0.2686	170	0.2515	3643	3813	93
2.0977-2.1233	0.277	187	0.2259	3566	3753	94
2.1233-2.1502	0.2628	229	0.2187	3825	4054	99
2.1502-2.1785	0.249	183	0.2096	3863	4046	100
2.1785-2.2083	0.2788	179	0.2007	3891	4070	100
2.2083-2.2399	0.237	176	0.2006	3844	4020	100
2.2399-2.2733	0.26	193	0.2094	3852	4045	99
2.2733-2.3088	0.2409	205	0.1919	3825	4030	100
2.3088-2.3467	0.2394	200	0.1882	3880	4080	100
2.3467-2.3872	0.2315	223	0.1867	3824	4047	100
2.3872-2.4306	0.2406	215	0.1874	3832	4047	100
2.4306-2.4773	0.2414	201	0.1878	3878	4079	100
2.4773-2.5279	0.2275	218	0.1813	3853	4071	100
2.5279-2.5829	0.2267	226	0.1742	3801	4027	100
2.5829-2.6429	0.2027	214	0.1708	3852	4066	99
2.6429-2.709	0.2464	216	0.1693	3801	4017	99
2.709-2.7823	0.1969	198	0.1727	3830	4028	99
2.7823-2.8642	0.2288	202	0.1727	3840	4042	99
2.8642-2.9566	0.2362	180	0.1898	3829	4009	98
2.9566-3.0623	0.2449	211	0.195	3643	3854	94
3.0623-3.1849	0.2394	215	0.1929	3827	4042	99
3.1849-3.3299	0.2294	201	0.1825	3904	4105	100
3.3299-3.5054	0.2075	221	0.1759	3845	4066	100
3.5054-3.725	0.2029	204	0.1671	3906	4110	100
3.725-4.0127	0.1735	191	0.1518	3854	4045	99
4.0127-4.4164	0.182	177	0.1358	3889	4066	99
4.4164-5.0554	0.1595	204	0.1323	3881	4085	99
5.0554-6.3689	0.2041	212	0.1676	3781	3993	97
6.3689-79.8656	0.189	210	0.1701	3969	4179	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	1.4981	-0.4847	-0.4014	0.9264	-0.469	0.5699	0.2065	-0.5287	0.0204	0.6419	-0.082	0.6398	0.3576	-0.546	-0.085	0.3898	-0.0968	0.1756	0.4594	0.0298	0.558	-97.9589	-23.6679	74.4565
2	0.8577	0.1815	-0.0223	1.6425	-0.5634	1.476	-0.0381	-0.014	-0.0927	0.1431	-0.0409	0.3063	0.3061	-0.2734	0.0757	0.274	-0.0426	0.1002	0.2546	0.0374	0.4002	-91.497	-26.9932	68.9855
3	1.8614	-0.5732	-0.9123	2.338	0.559	3.1035	0.0282	0.1504	-0.2191	-0.0831	-0.0919	0.0767	0.1473	-0.1346	0.0766	0.1739	-0.0008	0.0048	0.2079	0.0163	0.2504	-84.9185	-18.9845	57.0894
4	1.8055	0.8684	0.46	3.6623	0.8528	2.667	-0.1737	-0.097	0.2037	0.2575	0.0956	0.7274	-0.3654	-0.4967	0.0668	0.2385	0.1195	0.0205	0.3675	0.0498	0.3745	-101.0957	-5.4955	59.9139
5	1.1693	0.6521	0.2596	0.6359	0.3656	1.2923	0.0504	0.1804	0.0336	0.0079	0.0627	0.0335	-0.2127	-0.1019	-0.0993	0.2465	0.0488	0.0591	0.1801	0.0385	0.2456	-83.708	-9.631	61.1565
6	0.9091	-0.271	-0.4349	2.8082	2.7543	5.1504	0.1815	-0.1653	-0.2291	0.0485	0.6413	-1.0663	-0.4878	0.6749	-0.7825	0.3566	0.0024	0.0534	0.3171	-0.0442	0.5323	-83.9381	-6.5805	70.9867
7	2.6608	-0.2454	-0.539	1.7592	-0.2137	2.5303	-0.0056	-0.0885	-0.1231	0.1523	0.053	0.4302	0.0766	-0.4223	-0.0505	0.2255	0.0029	0.0436	0.2892	0.06	0.3871	-96.8831	-17.7967	63.4723
8	0.5608	-1.5008	-0.2684	4.3064	1.5349	3.213	-0.3161	0.3853	-0.3776	0.0188	0.0233	0.3587	0.4782	-0.1604	0.3421	0.2585	-0.0409	0.0188	0.3172	-0.0327	0.2755	-66.8256	-37.5616	30.3483
9	0.7258	0.5925	1.6132	3.7102	3.108	6.6823	-0.2687	0.0593	-0.4741	0.211	-0.04	-0.2218	0.8605	0.1284	0.2568	0.4392	-0.0193	0.0967	0.2284	-0.0047	0.4896	-63.7326	-43.7031	43.0254
10	1.4632	-0.2996	-0.8884	1.0386	0.3509	1.8973	-0.0563	0.204	-0.2751	0.065	-0.0613	0.0965	0.23	-0.1357	0.1183	0.2763	0.0068	0.0298	0.2117	-0.0542	0.2626	-65.9226	-35.5533	37.7644
11	1.5581	-0.2109	0.1217	0.9207	0.5541	1.814	0.067	0.2273	0.1166	-0.142	-0.1083	0.056	-0.2589	-0.1725	0.0388	0.3117	0.0284	0.0304	0.2261	-0.0068	0.2342	-66.728	-19.157	35.7331
12	1.7868	-0.6513	-0.5944	0.8352	0.8913	0.9598	0.0937	0.0732	0.0209	-0.0153	-0.0897	0.0812	-0.0578	-0.1794	-0.0177	0.2847	0.0298	0.042	0.2359	-0.0004	0.2279	-73.9844	-18.4358	44.8397
13	0.2121	0.2597	-0.3058	1.0737	0.0135	0.6546	-0.1481	-0.313	0.1187	0.1921	0.0709	0.482	-0.2259	-0.4567	0.1218	0.3321	0.1108	0.0419	0.4729	-0.0578	0.3775	-77.7114	-23.4248	36.0663
14	7.5583	0.6124	-1.3015	1.4101	0.2612	2.3668	-0.022	0.7202	-0.1956	-0.2371	-0.2075	0.3218	-0.0064	-0.7049	0.2448	0.3198	0.0273	-0.0338	0.4491	-0.1478	0.3365	-76.6001	-28.6601	25.6799
15	0.841	-0.0138	0.4164	1.6033	1.5635	2.5427	0.0605	0.1854	-0.0686	-0.1542	0.1367	-0.1979	-0.0904	1.3447	-0.1867	0.2485	0.0228	0.0475	0.3486	-0.0152	0.2742	-47.7233	-25.7825	38.3184
16	2.1646	0.2912	2.7196	1.465	-1.4779	6.0413	0.2606	0.0762	-0.1838	0.0065	-0.1914	-0.5292	0.6193	0.8029	-0.0687	0.2994	-0.0041	0.0045	0.2387	0.0366	0.3076	-44.1715	-14.6609	72.9451
17	0.9358	0.1675	-0.1142	1.943	-0.4191	0.6457	0.0236	-0.0768	0	0.084	-0.0189	-0.0044	-0.0648	0.0495	-0.0054	0.2464	-0.0056	0.0259	0.1935	-0.0016	0.1985	-55.8493	-12.355	69.5336
18	0.4682	-0.22	-0.3693	0.2955	0.5667	1.2157	0.0413	0.047	0.1069	-0.1068	-0.0341	0.0455	-0.1667	-0.0119	-0.0279	0.2703	0.0015	0.015	0.1675	0.0175	0.2251	-59.4331	-7.4444	57.7432
19	4.938	0.5669	-3.6326	2.3729	-1.072	6.0599	-0.0244	0.8498	-0.0257	-0.341	0.1152	-0.1813	0.2546	-0.5753	-0.1192	0.291	-0.046	0.0496	0.301	0.0078	0.2416	-51.0209	-8.48	57.7481
20	2.1726	-0.467	-1.7306	2.4821	1.6279	9.2378	0.065	0.0725	0.0935	-0.1314	0.062	-0.5018	0.0354	0.4197	-0.1444	0.2693	-0.0501	0.0209	0.2092	0.0219	0.3076	-41.6082	-6.1231	63.5024
21	7.0133	2.9369	1.7261	2.8186	0.7942	1.8122	0.2752	-0.7851	-0.1422	0.7832	-0.2256	0.1488	0.1139	-0.2608	-0.0183	0.6147	0.0417	0.1614	0.3005	0.0053	0.2664	-65.2997	-8.249	83.9425
22	2.0858	-0.7094	-0.2039	2.4401	0.3843	1.4497	-0.0149	0.1062	-0.2535	-0.06	-0.0641	-0.1859	0.1981	0.1991	0.0693	0.22	0.0283	0.0382	0.2298	-0.0051	0.2892	-85.9111	12.0325	4.5285
23	1.8299	0.6647	0.0391	1.9732	-0.8172	2.6796	0.071	-0.2357	0.0712	0.1795	-0.1496	0.1158	-0.1324	0.1338	0.0868	0.1671	-0.0171	0.0191	0.2156	-0.0297	0.2301	-92.7024	25.6897	14.1317
24	2.232	0.6321	-1.9594	3.8336	-1.1501	1.8076	-0.1823	-0.0647	-0.5603	-0.0795	-0.122	-0.1975	0.3156	0.0585	0.3045	0.2598	-0.0018	-0.0056	0.2877	0.0432	0.3067	-91.6926	10.7021	22.5852
25	1.6187	-0.3109	-0.1378	1.2153	-0.1599	1.0512	0.0157	-0.119	0.1458	0.0897	-0.0098	-0.1963	-0.1746	0.2252	-0.0103	0.2044	-0.0413	-0.0171	0.2389	-0.0222	0.2079	-87.2519	30.453	13.4965
26	0.3989	0.0825	-0.4697	0.4688	-0.0075	0.6036	0.3296	0.2873	-0.0309	-0.2811	0.2309	0.6983	-0.2345	-0.454	-0.1398	0.2427	-0.0183	-0.0456	0.3238	0.0786	0.3963	-93.0291	32.5327	1.8702
27	2.625	1.0931	-0.783	1.0832	0.2579	2.1672	-0.036	-0.0101	-0.2917	0.0877	-0.1451	-0.4712	-0.1192	0.553	0.1307	0.167	0.0484	-0.0189	0.244	-0.0293	0.2928	-79.2897	19.0524	12.1702
28	0.0851	0.5337	-0.0783	3.5799	-1.6094	2.4642	-0.1354	-0.6597	-0.6883	-0.0525	-0.2048	-0.3345	0.1548	0.3892	0.294	0.2768	0.0002	0.0419	0.3665	0.1621	0.3485	-110.6818	2.6391	44.8468
29	0.9914	0.1755	-0.2643	1.2467	0.0815	1.5989	-0.0996	-0.1575	-0.3027	0.0389	-0.0243	0.0723	0.2237	0.0291	0.0988	0.3155	-0.0335	0.0552	0.2402	0.0786	0.3069	-111.8844	2.9121	36.2149
30	3.5102	0.4449	0.5336	1.516	0.1152	1.4058	0.1215	-0.3331	0.0574	0.2188	-0.1129	-0.0783	-0.4271	0.1006	0.009	0.4059	-0.0533	0.0504	0.3004	0.033	0.2349	-102.3638	24.2633	38.9619
31	1.9213	0.3717	-0.018	1.3532	-0.6002	2.5474	0.0901	-0.3643	0.0418	0.2714	-0.1563	0.0692	-0.1952	0.133	0.0584	0.3227	-0.0234	0.0823	0.2522	0.04	0.2805	-111.6893	20.212	39.515
32	1.2394	0.5887	-0.6894	0.6913	-0.2756	1.2886	0.0469	-0.0915	0.0265	0.2454	-0.0054	0.1606	-0.0464	0.0639	-0.0181	0.2379	-0.0157	0.0252	0.1974	0.0265	0.1793	-102.7075	21.352	29.9001
33	0.2246	-0.474	0.3479	1.3054	-0.382	0.7708	-0.2375	0.3713	0.085	0.0989	0.0076	-0.3363	-0.1596	0.5333	0.2434	0.3788	-0.0903	0.0325	0.5849	0.0937	0.3411	-98.7146	16.4121	38.4389
34	6.2426	-0.4064	-1.9299	1.0126	0.4289	1.7344	0.1589	-0.9456	-0.2366	0.4868	-0.3418	-0.211	-0.1224	0.7442	0.1634	0.3676	-0.0515	-0.0287	0.5887	0.23	0.3604	-101.3261	11.0929	49.1917
35	0.8651	0.2409	-0.7079	1.56	-1.3186	1.447	-0.0175	-0.1882	0.008	0.0244	0.0589	0.353	0.0726	-1.2115	-0.0753	0.3271	-0.0123	0.1144	0.4428	-0.002	0.4911	-129.2572	15.3878	36.8018
36	0.9424	-1.1762	-0.8709	2.0085	1.1982	1.7653	-0.1134	0.4502	-0.2704	-0.2169	-0.2846	0.4227	0.8994	-0.754	0.1073	0.365	0.0023	-0.0552	0.3892	-0.1098	0.3093	-129.5481	23.2341	0.7277
37	1.7653	-0.3206	-0.5873	1.6072	0.6031	0.836	0.0961	0.1936	-0.1296	-0.1014	-0.1314	0.139	-0.0575	-0.1877	0.0187	0.1953	0.0258	-0.0448	0.2028	-0.0228	0.1795	-121.0371	28.9918	6.2592
38	0.809	-0.2092	-0.0732	0.5827	-0.0247	1.0457	0.0277	-0.0528	0.0159	0.0822	-0.0501	0.0786	-0.1056	-0.128	0.0145	0.2156	0.0083	0.0102	0.1709	-0.0034	0.2194	-118.8114	33.0626	17.2507
39	2.5804	-0.9592	-0.4148	2.1013	0.3477	1.3448	0.153	0.3724	0.1495	-0.1826	-0.1253	0.1296	-0.1326	-0.1948	-0.0223	0.2616	0.0172	-0.0606	0.1734	-0.0424	0.2013	-124.2345	33.5243	2.5273

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 26 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 90 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 91 through 139 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 164 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 220 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 221 through 238 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 239 through 291 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 23 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 24 through 38 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 39 through 90 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91 through 182 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 183 through 217 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 218 through 241 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 242 through 269 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 270 through 291 )	B
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 3 through 23 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 24 through 164 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 165 through 220 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 221 through 242 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 243 through 269 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 270 through 291 )	C
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 3 through 89 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 90 through 120 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 121 through 139 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 140 through 220 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 221 through 242 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 243 through 291 )	D
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 2 through 23 )	E
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 24 through 90 )	E
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 91 through 110 )	E
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 111 through 182 )	E
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 183 through 217 )	E
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 218 through 241 )	E
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 242 through 270 )	E
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 271 through 291 )	E
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 3 through 29 )	F
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 30 through 164 )	F
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 165 through 242 )	F
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 243 through 292 )	F

-
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

-
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