PDB-3m3i: Hypothetical protein from Leishmania major

ID or keywords:

Entry

Database: PDB / ID: 3m3i

Title

Hypothetical protein from Leishmania major

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION / Pfam:PF06172 / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / SGPP / PSI / Protein Structure Initiative

Function / homology

Function and homology information

Cupin domain of unknown function DUF985 / Uncharacterized protein YML079W-like / Cupin superfamily (DUF985) / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology

Biological species

Leishmania major (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Citation

Journal: To be Published
Title: Hypothetical protein from Leishmania major
Authors: Merritt, E.A. / Carruthers, J. / Arakaki, T. / Holmes, M. / Kalyushniy, O. / Napuli, A. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Zucker, F. / Verlinde, L.M.J. / Hol, W.G.J.

History

Deposition	Mar 9, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 23, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3m3i.cif.gz	580.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3m3i.ent.gz	485.1 KB	Display	PDB format
PDBx/mmJSON format	3m3i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3m3i_validation.pdf.gz	514 KB	Display	wwPDB validaton report
Full document	3m3i_full_validation.pdf.gz	569.5 KB	Display
Data in XML	3m3i_validation.xml.gz	50.9 KB	Display
Data in CIF	3m3i_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3i ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3i	HTTPS FTP

-
Related structure data

Similar structure data	6x7v-2 3lzz-d 3lv6-d 4ruw-d 1nh1-d 6lgt-d 3e1v-d 2zb3-d 3gqv-d 2y05-1 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 - HomologyF&H Search
Other databases	TargetDB: Lmaj012795AAA

Similar structure data

Other databases

TargetDB: Lmaj012795AAA

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative uncharacterized protein

B: Putative uncharacterized protein

C: Putative uncharacterized protein

D: Putative uncharacterized protein

E: Putative uncharacterized protein

F: Putative uncharacterized protein

G: Putative uncharacterized protein

H: Putative uncharacterized protein

203 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative uncharacterized protein

H: Putative uncharacterized protein

defined by author&software
50.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative uncharacterized protein

E: Putative uncharacterized protein

defined by author&software
50.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Putative uncharacterized protein

F: Putative uncharacterized protein

defined by author&software
50.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Putative uncharacterized protein

G: Putative uncharacterized protein

defined by author&software
50.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.979, 98.429, 100.758
Angle α, β, γ (deg.)	71.870, 80.190, 89.570
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	15 - 217
2	1	1	4	B	15 - 217
3	1	1	4	C	15 - 217
4	1	1	4	D	15 - 217
5	1	1	4	E	15 - 217
6	1	1	4	F	15 - 217
7	1	1	4	G	15 - 217
8	1	1	4	H	15 - 217

#1: Protein	Putative uncharacterized protein Mass: 25356.342 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF35.1030, LMJ_1035 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4FX13, UniProt: E9AES8*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.42 Å³/Da / Density % sol: 49.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: protein buffer 25 mM HEPES pH 7.5, 500 mM NaCl; crystallization buffer 100 mM Na Acetate, 100 mM KH2PO4, 24% PEG 1500, VAPOR DIFFUSION, temperature 293K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.07811 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07811 Å / Relative weight: 1
Reflection	Resolution: 2.35→46.716 Å / Num. all: 73773 / Num. obs: 73773 / % possible obs: 93 % / Redundancy: 1.9 % / R_sym value: 0.097

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALA	3.3.9	data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
MOSFLM		data reduction
BALBES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.35→46.72 Å / Cor.coef. F_o:F_c: 0.918 / Cor.coef. F_o:F_c free: 0.878 / WR_factor R_free: 0.296 / WR_factor R_work: 0.247 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.685 / SU B: 22.302 / SU ML: 0.274 / SU R Cruickshank DPI: 0.333 / SU R_free: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29	3678	5 %	RANDOM
R_work	0.239	-	-	-
obs	0.242	73637	92.82 %	-

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 max: 221.19 Å² / B_iso mean: 74.223 Å² / B_iso min: 29.52 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.13 Å²	0.86 Å²	0.25 Å²
2-	-	-1.2 Å²	-0.41 Å²
3-	-	-	1.48 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→46.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11321	0	0	121	11442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.021	11643
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7820
X-RAY DIFFRACTION	r_angle_refined_deg	1.223	1.944	15838
X-RAY DIFFRACTION	r_angle_other_deg	0.82	3	18886
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.46	5	1416
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.258	23.203	590
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.036	15	1770
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.963	15	87
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1659
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	13198
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2525

Refine LS restraints NCS

Ens-ID: 1 / Number: 2255 / Refine-ID: X-RAY DIFFRACTION / Type: MEDIUM POSITIONAL / Weight position: 0.5

Dom-ID	Auth asym-ID	Rms dev position (Å)
1	A	0.32
2	B	0.32
3	C	0.27
4	D	0.29
5	E	0.31
6	F	0.32
7	G	0.31
8	H	0.34

LS refinement shell

Resolution: 2.35→2.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	255	-
R_work	0.329	5011	-
all	-	5266	-
obs	-	-	88.98 %

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	8.0284	-0.9543	4.8369	4.3211	0.2564	4.7613	-0.3317	0.3585	0.4167	-0.8523	0.175	0.184	-0.4162	0.2629	0.1567	0.3514	0.0029	0.0789	0.0788	0.0213	0.3906	-0.7392	65.4011	-1.349
2	2.5967	1.4259	4.1799	4.2151	8.7721	18.9709	0.0263	-0.3406	0.28	0.177	-0.6466	0.2431	0.4202	-1.3551	0.6203	0.2382	0.1395	0.0633	0.2229	-0.022	0.3699	-6.6757	58.5962	5.7555
3	0.9308	2.6998	-1.8239	9.3578	-2.4916	8.9032	-0.0274	0.1241	0.3312	-0.4745	0.1993	1.2648	-0.511	-0.5907	-0.1718	0.232	0.0967	-0.0259	0.2091	-0.0265	0.4783	-11.5862	40.726	0.9738
4	3.3713	3.2734	-3.4388	7.8425	-3.3782	3.7712	-0.195	-0.0124	-0.2683	0.2067	-0.1306	-0.1913	0.1721	-0.1285	0.3256	0.1624	0.0507	0.0316	0.0999	-0.0096	0.2792	-9.7505	43.0537	5.1805
5	3.4444	1.2166	0.2098	0.82	-1.0666	6.7365	0.0517	-0.2736	0.5171	-0.1958	-0.0742	0.3723	-0.0584	0.0003	0.0225	0.3372	0.0348	-0.0738	0.0801	0.0184	0.4737	-1.9765	55.7126	12.7548
6	0.7051	1.2749	-2.8742	4.6073	-4.3782	13.5358	0.0046	-0.0981	0.1709	-0.2327	-0.0159	0.4149	0.1571	0.3168	0.0113	0.1098	0.0433	0.1058	0.1755	-0.0328	0.3649	6.4966	54.5271	10.213
7	1.1708	-2.6477	-4.1424	9.5822	12.436	17.2965	-0.2732	-0.4855	0.289	-0.3885	0.8842	-0.1805	0.2163	1.4899	-0.6109	0.733	0.2854	-0.1358	0.4351	0.0333	0.6222	4.1886	39.7646	18.4202
8	13.3148	8.8621	-1.7017	6.6492	1.2025	21.1394	0.8721	-2.4117	-1.4139	0.7941	-1.4707	-1.2086	0.1875	2.8181	0.5986	0.2313	-0.0606	-0.1253	0.9189	0.4178	0.5421	4.9297	46.7502	24.2234
9	10.9488	-1.2019	3.2907	1.4451	2.7605	8.4108	-0.134	-0.0819	0.7777	-0.1221	0.1771	-0.2015	-0.3555	0.3872	-0.0431	0.1384	0.0764	0.0449	0.0939	0.0222	0.4066	14.85	53.0944	8.0757
10	2.5598	1.2464	0.3111	6.5591	-2.6217	3.6138	0.1334	-0.1603	0.0438	0.6361	0.121	-0.3455	-0.2335	0.9094	-0.2544	0.1238	0.0657	0.0555	0.5127	-0.1276	0.2726	3.6713	54.1028	14.9129
11	1.0256	-2.695	-2.1586	9.0263	7.1252	5.6324	0.3947	-0.2056	0.0993	-0.3977	-0.1022	-0.446	-0.3466	-0.056	-0.2925	0.423	-0.1886	-0.0106	0.3445	0.0496	0.4708	6.8787	61.1903	5.5178
12	2.3996	0.8509	-0.2395	2.2104	1.4274	1.8453	0.0564	-0.4277	0.3089	0.0917	-0.2457	0.2218	0.0781	0.1931	0.1893	0.0911	0.0607	0.0207	0.211	-0.0208	0.3375	-5.6916	53.2602	21.0417
13	3.7356	-0.0703	1.4297	10.5852	-4.068	14.4808	-0.0225	0.0808	-0.3812	-0.0861	0.137	1.1223	0.2068	-0.7678	-0.1144	0.1242	0.0769	0.0562	0.2115	0.0048	0.4089	0.9362	-4.3597	41.6048
14	10.9354	4.9844	-14.7069	2.3556	-7.5162	41.2698	-0.3015	-0.3338	-0.7863	-0.0917	-0.1612	-0.189	2.1088	0.5253	0.4627	0.4449	0.0424	0.1949	0.0368	0.0126	0.5605	8.3574	-12.1016	45.0614
15	27.4737	-12.7231	7.2748	6.6413	-2.0625	4.2986	-0.0238	-0.7192	-1.9616	-0.0588	0.1994	1.0621	-0.0576	-0.5582	-0.1757	0.3328	-0.0021	0.0674	0.2096	-0.0061	0.558	23.5564	-15.8485	33.5679
16	7.6886	-1.1415	-1.8255	3.0726	-1.9393	2.1334	0.0129	-0.6094	0.3928	-0.3415	0.0955	-0.1494	0.276	0.125	-0.1084	0.246	0.0069	-0.0478	0.0578	0.0177	0.3814	21.3708	-14.3889	40.584
17	5.0092	-1.5811	2.627	4.6723	-1.6853	1.6829	0.0831	-0.5197	-0.4184	0.4925	0.0139	0.3414	0.1	-0.2803	-0.0969	0.4915	-0.0063	0.0905	0.1375	-0.0369	0.3443	14.6443	-10.3877	52.7248
18	5.9004	-2.2176	3.7931	2.0515	-3.4367	6.042	-0.035	-0.3323	0.0045	0.2674	0.1573	0.217	-0.205	-0.2644	-0.1223	0.3784	0.038	0.1058	0.0587	0.0054	0.407	15.3211	-0.9834	51.4457
19	15.4267	9.4439	-17.7673	5.8015	-10.8866	20.4679	0.5178	-1.2781	-0.253	0.3941	-0.8556	-0.2797	-0.6485	1.4995	0.3378	0.6688	-0.2164	-0.2438	0.5256	0.1503	1.0922	32.1517	-6.4865	54.5001
20	13.102	-5.2302	-0.1726	11.2072	-1.9829	8.1199	-0.5426	-1.529	0.8193	1.4263	0.1872	-0.8295	-0.6832	0.2193	0.3554	0.4107	0.0517	-0.1064	0.3587	-0.0325	0.3759	25.2777	-5.4538	61.7943
21	8.1478	3.5366	1.745	3.7308	-2.4257	4.9902	-0.2144	-0.9675	1.2443	0.7862	0.2657	0.7769	-1.313	-1.2018	-0.0512	0.4669	0.2528	0.1491	0.3486	-0.1306	0.5081	15.4812	9.9402	52.7643
22	2.5128	-0.2573	1.2881	0.7998	-1.2691	2.3475	0.1779	-0.3999	0.1087	0.1466	0.0229	0.129	-0.1341	-0.1972	-0.2008	0.3308	0.0412	0.0789	0.1374	0.0148	0.2721	14.4124	-1.1566	51.9072
23	0.0739	-0.3519	-0.3689	2.2205	2.4144	2.6372	-0.0969	-0.0192	-0.1077	0.4522	-0.2598	0.3571	0.485	-0.3369	0.3567	0.358	0.0478	0.0849	0.2551	0.0744	0.4143	18.7891	-18.0416	50.0598
24	11.3031	-1.6733	3.862	15.5748	-0.6651	8.5794	-0.2313	-0.393	0.1516	0.7712	-0.143	-0.1833	-0.0519	-0.3642	0.3743	0.4672	0.0365	0.137	0.3176	0.0738	0.1252	16.9322	-14.2039	66.1014
25	7.8934	3.0902	-0.1842	9.7477	-1.4521	2.6098	-0.2701	0.5467	0.8998	-0.7775	0.4014	0.5418	0.128	0.0513	-0.1313	0.3492	0.0939	-0.0123	0.1121	0.0321	0.3196	-7.369	17.0875	-5.0772
26	9.3461	-7.1254	-7.9786	13.2156	13.4172	13.7258	-0.4172	-0.1413	0.0784	0.2259	-0.3154	0.7868	0.2953	-0.2646	0.7326	0.2335	0.129	-0.044	0.1335	0.0599	0.4511	-12.5526	9.1872	3.6267
27	17.7958	25.8468	-7.4972	37.8186	-11.0753	3.2849	0.3959	0.2615	1.2322	1.1169	0.2904	1.9403	-0.5005	-0.071	-0.6863	0.867	-0.0367	0.2215	0.0689	-0.0988	0.4978	-13.1529	-8.2725	-1.7657
28	1.9059	1.9189	-1.2347	5.0655	0.0291	1.7779	-0.1152	-0.0014	-0.1639	-0.0086	-0.0426	0.288	0.2015	-0.1545	0.1578	0.1309	0.058	0.0067	0.1126	0.0127	0.3314	-10.7457	-3.6899	5.1947
29	3.9282	0.4472	-0.4533	5.6065	0.9079	2.5219	0.1503	0.1813	0.1475	-0.171	-0.1592	0.5172	0.1138	-0.1054	0.0089	0.1034	0.0578	0.0116	0.0574	0.0006	0.2702	-7.9122	6.8875	12.6777
30	0.0722	0.0173	-0.5134	0.08	-0.0493	3.7345	-0.0444	-0.0501	0.0236	-0.0227	0.0466	0.182	0.3149	0.4417	-0.0022	0.1516	0.0912	0.0054	0.1758	0.1214	0.4477	1.0762	8.9497	8.7472
31	1.8834	-0.9968	0.8731	5.4201	3.6542	3.8694	0.1507	-0.1739	0.034	0.3061	0.4626	-0.816	0.3818	0.2123	-0.6133	0.3706	0.0805	0.0927	0.2712	0.0445	0.7319	1.8946	-5.3086	19.4151
32	2.4013	5.9027	-1.9346	16.4297	-6.3516	24.9186	-0.0011	-0.701	-0.3387	0.1148	-1.0574	-1.3625	-0.9486	1.8271	1.0585	0.112	0.0241	0.033	0.5926	-0.0049	0.3248	1.5283	3.8316	22.8524
33	5.7849	-1.8949	4.1039	4.7172	4.3633	10.8651	-0.375	0.4477	0.6099	-0.1244	-0.0174	-0.2465	-0.6236	0.4823	0.3924	0.1829	0.0626	0.0489	0.1097	0.083	0.435	10.4074	10.0968	6.6476
34	0.815	-0.4455	0.0784	0.2835	-0.2876	1.8838	-0.0863	0.0289	0.0398	0.0845	-0.0558	-0.0845	-0.472	0.1625	0.1421	0.2275	0.056	0.0092	0.1128	0.018	0.3525	-0.3755	11.0232	9.391
35	0.7606	-0.0022	0.0432	2.1816	2.4848	3.7392	-0.0714	-0.2111	-0.0041	0.0211	-0.0814	0.1739	0.0781	-0.1995	0.1528	0.0927	0.0474	0.0589	0.1182	0.046	0.3506	-11.8102	3.1793	18.075
36	19.3187	-0.7692	8.8822	3.3751	-6.5502	15.7831	0.0707	-0.2047	1.6235	0.6805	-0.2787	0.3066	-1.0718	0.4316	0.2079	0.3121	-0.0254	0.0885	0.0422	-0.1033	0.4913	-7.7655	14.3124	22.6007
37	3.1798	-0.9019	-0.3763	9.079	-2.2744	2.4801	-0.4603	-0.4921	0.7317	1.3123	0.4114	-0.2429	-0.2237	0.4059	0.0489	0.3308	0.0891	-0.0793	0.1997	-0.0496	0.3927	30.2979	66.2119	45.5458
38	3.5444	0.1341	-1.2214	8.8309	-12.0596	16.7892	0.2065	0.2977	0.04	-0.4009	-0.5934	-0.2685	0.54	0.7142	0.3869	0.2527	0.0477	0.0166	0.1193	-0.016	0.4882	35.3094	58.3376	36.9101
39	9.4371	-0.629	3.3993	6.5967	6.1774	7.4819	0.5348	-0.1721	0.6765	-0.7489	-0.1359	-0.7189	-0.498	-0.2047	-0.3989	0.4017	0.2215	0.0985	0.2143	0.0736	0.4111	35.6414	40.9984	42.2133
40	3.0251	-1.3715	-1.056	3.8217	0.7022	0.4292	0.0395	0.0262	-0.1691	-0.3615	-0.0673	-0.1361	0.0413	0.0498	0.0278	0.2168	0.0939	0.0123	0.1048	-0.0069	0.3124	33.3273	45.493	35.3271
41	2.6065	0.3235	-2.5645	8.6442	0.4983	2.6035	-0.0017	-0.2386	0.0104	0.2063	0.0649	-0.6924	0.0332	0.256	-0.0632	0.1021	0.072	-0.0548	0.0892	0.0109	0.2761	30.6944	56.0683	27.8915
42	0.4678	-1.1983	-2.4055	4.0986	4.4868	15.1238	0.0092	0.0177	0.064	-0.0539	0.1548	-0.2438	0.0816	-0.382	-0.164	0.0762	0.0442	0.034	0.1051	-0.0471	0.3601	21.7203	58.1151	31.7611
43	0.8203	-2.0537	3.4475	5.3818	-8.8736	14.7357	0.1716	-0.1591	-0.058	-0.8578	0.2913	0.3615	1.221	-0.6008	-0.4629	0.7188	0.0651	-0.0254	0.2589	-0.0865	0.7823	20.4909	43.7533	21.2643
44	2.0616	-2.2389	-2.6913	11.6547	6.8278	20.9438	0.3254	0.5492	0.0156	-0.0969	-0.6066	0.5661	-0.202	-0.9085	0.2812	0.0946	0.0676	0.0324	0.1607	-0.036	0.3285	21.6776	52.3597	17.3563
45	4.2517	-3.1371	-0.1316	9.9066	0.2352	9.8771	-0.2628	-0.2738	0.522	-0.3206	0.1539	0.3691	-0.9084	-0.0636	0.1089	0.1742	0.0341	-0.0006	0.0531	-0.0559	0.3928	13.1108	58.5572	33.5039
46	1.2143	0.1142	-0.3408	0.1495	0.447	1.9297	-0.0247	0.0675	0.0597	-0.0618	-0.0277	0.093	-0.2356	-0.1086	0.0524	0.1504	0.0632	0.0203	0.0597	-0.0102	0.3741	23.6971	60.498	31.0545
47	1.9446	-0.1024	-0.5034	2.2901	-1.7431	1.5471	-0.063	0.0638	0.1353	-0.0022	-0.1469	-0.2633	0.0982	0.1598	0.2099	0.1328	0.1112	0.0501	0.1335	-0.0129	0.3364	34.4966	52.3469	22.4535
48	18.6245	2.2219	2.4463	0.7888	2.8254	12.7477	-0.0838	-0.2396	1.3021	-0.2453	-0.1311	0.1101	-1.0219	-0.5084	0.215	0.2664	0.0874	0.1147	0.0399	0.0646	0.5845	30.6526	63.4342	17.9634
49	14.8315	-2.2275	-2.0562	3.6003	-0.6897	6.2812	-0.2193	-0.6171	0.6747	0.5128	0.1507	-0.0821	-0.5681	0.2268	0.0686	0.266	0.049	0.0526	0.0522	-0.0547	0.3839	23.7867	16.156	41.9722
50	10.26	4.5399	-2.0144	5.0708	-7.2311	13.5239	-0.083	0.4711	-0.0004	-0.5744	-0.6011	-0.342	1.1445	1.578	0.6842	0.2051	0.1526	0.0835	0.2585	-0.0036	0.4292	29.4992	8.6566	35.5785
51	2.4603	-0.4047	-4.9816	6.7998	11.7771	30.7468	0.139	-0.2268	0.0335	-0.3414	0.1753	-0.1548	-1.2902	0.5378	-0.3144	0.1452	0.0494	0.0513	0.1569	0.0259	0.4715	34.1342	-9.6321	36.4117
52	3.0227	-1.4261	-1.1863	2.4782	0.6695	3.1629	-0.088	0.0343	0.112	0.197	0.0732	-0.2601	-0.0092	0.2903	0.0149	0.052	-0.0045	0.0111	0.0388	-0.0114	0.306	29.7851	-1.0654	36.1449
53	3.9529	1.5554	-1.5698	0.6528	-0.2226	4.5423	0.1637	0.0924	0.0944	0.0617	0.0287	0.0331	-0.146	0.0071	-0.1924	0.0424	0.0294	0.0363	0.107	0.0283	0.3246	25.3673	5.1827	26.3489
54	1.1431	0.9776	1.324	1.2947	3.2583	12.0975	0.1723	0.107	0.1286	0.1717	-0.0042	-0.0562	0.2681	-0.3409	-0.1681	0.1311	0.1156	0.0108	0.1346	0.051	0.3731	16.2277	5.3703	30.3941
55	13.741	12.2637	-16.8926	23.4373	-24.3769	27.7142	-0.3842	0.53	0.0015	0.3645	0.7117	0.4324	0.0298	-0.906	-0.3274	0.5162	-0.1448	0.0324	0.4099	-0.0635	0.4114	18.6206	-9.6533	21.4976
56	18.692	-14.028	-4.1038	14.0925	0.6676	2.5645	1.0587	1.8555	-0.7503	-1.1204	-1.0674	0.8614	-0.0916	-0.689	0.0087	0.3723	0.162	-0.0564	0.4496	-0.1784	0.3626	17.7953	-2.3027	16.0188
57	11.8653	-1.5068	-0.3896	0.493	-1.2232	5.3983	0.2792	0.209	0.731	0.1618	0.0636	-0.0178	-0.8351	-0.4767	-0.3428	0.2594	0.069	0.0632	0.2038	-0.0524	0.4463	5.9332	5.9885	31.9058
58	1.5441	1.2135	-0.0467	0.9895	-0.3236	2.4098	-0.0918	0.2017	0.3845	-0.0544	0.2072	0.3366	-0.0792	-0.4149	-0.1154	0.119	0.0739	0.0384	0.1753	0.0346	0.4049	15.8786	6.0535	29.0337
59	9.3505	-7.1844	-5.1721	5.7287	4.3999	3.7426	-0.0285	0.1878	0.7392	0.1276	-0.0275	-0.3586	0.1933	0.0909	0.056	0.1498	0.1421	0.0172	0.1711	0.0218	0.373	25.9452	0.167	35.2598
60	6.5603	-1.8184	1.8451	2.1039	-0.2182	3.8019	0.1331	0.5277	0.4086	-0.337	-0.3393	-0.0752	0.1656	-0.0396	0.2062	0.1091	0.0727	0.0512	0.1587	0.0468	0.319	28.0809	5.7436	16.5427
61	6.8404	-2.0278	4.6789	18.7565	-2.0556	6.8348	-0.1375	-0.0406	0.0048	0.1599	-0.0482	-0.7512	-0.1274	0.4291	0.1857	0.1897	0.1182	0.0824	0.1936	0.06	0.3257	18.5702	1.6246	-1.1378
62	9.0931	-1.8481	-13.217	0.9879	1.2903	22.4549	-0.7276	0.1069	-0.6098	-0.3103	0.0033	0.1473	2.0214	-0.3141	0.7243	0.4765	0.0739	0.1201	0.165	0.0335	0.4966	10.7491	-8.6226	-0.7087
63	2.9055	3.2766	-0.9036	6.3877	-1.6985	1.689	-0.1334	-0.171	-0.3724	-0.2855	-0.1226	0.0664	0.4413	0.249	0.256	0.2587	0.1012	0.0402	0.0681	0.0248	0.4018	0.5983	-12.5072	1.4905
64	1.7372	0.6218	-0.098	3.6967	0.1359	4.6631	-0.2463	-0.1493	-0.6198	-0.3193	-0.0527	-0.4359	0.4972	0.5147	0.2991	0.4179	0.1283	0.0721	0.1224	0.0035	0.3683	6.4045	-9.1697	-11.6461
65	7.6259	0.7072	2.5128	11.8644	0.5104	0.9444	-0.047	0.3361	-0.068	-0.5397	0.1744	-0.289	0.1251	0.1887	-0.1274	0.3025	0.1086	0.0045	0.0968	-0.0298	0.3493	6.2116	3.7653	-8.6438
66	3.7357	7.6569	0.8459	20.6429	-3.828	8.0288	-0.4322	-0.4095	0.0397	-1.3945	-0.3105	0.387	0.7628	-0.6554	0.7427	0.5387	0.1492	0.0907	0.1853	0.0083	0.7601	-2.2976	-8.5643	-17.1573
67	29.8044	9.2865	-16.3847	3.0168	-5.0907	9.0096	-0.5375	2.797	1.5648	-0.5686	1.2451	0.56	0.3595	-1.4975	-0.7076	2.0342	-0.0192	-0.38	1.1145	-0.0197	0.916	-11.9792	-8.9528	-16.2373
68	10.9971	0.6625	2.6347	0.1184	0.8306	6.9866	-0.9785	0.4614	1.6156	-0.1913	-0.0757	0.1912	-0.7886	-1.0778	1.0542	1.0271	0.0507	-0.3097	0.3985	-0.0891	0.55	-2.9044	-6.0495	-20.9022
69	7.9845	-2.3119	0.1978	8.6672	2.959	6.5748	-0.105	0.4336	0.8041	-1.3209	0.0767	-0.219	-0.5737	0.5391	0.0282	0.3427	0.0289	0.0417	0.1371	0.0589	0.3438	0.8923	9.4638	-12.4595
70	3.0026	0.5934	-0.9547	1.5719	1.7397	4.3586	0.0565	0.3859	0.1971	-0.3432	-0.008	-0.0413	0.0869	0.1462	-0.0485	0.3392	0.1605	0.008	0.158	0.0715	0.2745	6.4468	-0.3701	-12.382
71	2.3963	-2.1062	-2.4944	13.0162	0.3361	2.9089	0.0337	-0.0304	-0.2369	-0.4842	-0.3471	-0.1242	0.0139	0.0994	0.3135	0.3542	0.0569	-0.0237	0.1037	-0.0573	0.4248	2.9346	-14.8859	-2.1707
72	7.1876	-2.7838	1.9345	2.5071	0.4999	2.5782	-0.1982	0.1981	-0.411	-0.6315	0.0905	-0.0825	0.1391	-0.1162	0.1077	1.1766	-0.1966	0.4032	0.366	-0.1796	0.4488	6.2827	-14.8493	-23.122
73	5.8341	1.1781	-3.0145	15.3951	-4.2516	8.7219	0.0579	-0.0522	-0.0856	0.1397	-0.018	1.0491	0.1622	-0.5014	-0.0399	0.1858	0.0473	0.0565	0.174	-0.0323	0.324	4.1252	50.8621	41.6963
74	20.7058	7.0256	-24.9727	5.0333	-5.8443	32.7312	-0.952	-0.1583	-0.8678	0.3372	-0.1608	-0.2365	1.7956	0.1084	1.1128	0.501	0.0508	0.1379	0.1771	-0.0653	0.4816	8.8563	41.0232	45.1193
75	23.6822	-21.2257	-4.6096	19.027	4.1359	0.9141	-0.8846	-0.7456	-0.9051	0.803	0.6482	0.8394	0.2587	0.1326	0.2364	0.6139	0.0234	0.1535	0.1725	-0.055	0.5975	21.0732	37.2694	32.1943
76	1.7921	-0.8559	-1.314	4.4772	0.5273	2.0174	-0.1659	0.1205	-0.1642	0.2293	-0.0346	-0.2725	0.3656	-0.0844	0.2004	0.263	0.014	0.0142	0.0164	0.0042	0.3415	21.3148	37.0294	40.3694
77	1.2199	-0.0586	-2.7445	3.5064	1.8258	6.9987	-0.1876	0.3792	-0.0424	0.6117	-0.1139	0.4843	0.6937	-0.887	0.3015	0.4913	0.0176	0.1005	0.1898	0.0276	0.438	16.1184	40.0901	52.169
78	1.5345	-0.6671	1.1979	9.0166	-4.1967	2.5271	0.0151	-0.0495	0.0086	0.9326	0.0923	0.4555	-0.3617	0.0228	-0.1074	0.3543	0.0976	0.0648	0.2442	0.0409	0.3625	18.2663	49.8598	51.9358
79	21.2779	15.5725	-18.9561	11.52	-13.9055	16.9002	1.0144	-0.7218	0.5243	1.0962	-0.5143	-0.037	-1.115	0.5744	-0.5001	1.2838	0.5423	-0.5046	0.5716	-0.0952	1.7863	33.3001	40.5245	54.8705
80	18.6686	-2.6091	7.1977	1.8717	-4.9147	13.878	-0.6217	-1.3397	0.8824	0.4352	0.0468	-0.3591	-0.32	0.2765	0.5749	0.9517	0.369	-0.2264	0.4006	-0.0786	0.5576	26.4504	42.1163	61.89
81	10.2174	2.1026	1.9919	5.643	-6.9152	10.7109	-0.2163	-0.4468	1.0375	0.74	0.3002	0.3822	-1.0335	-0.7255	-0.0839	0.6239	0.0189	0.0556	0.166	-0.0283	0.3089	22.3097	57.6056	52.8574
82	1.8857	-0.8322	-0.6308	1.478	0.1412	5.2341	-0.0706	-0.3782	0.0593	0.6166	0.02	0.0991	0.0586	-0.2609	0.0506	0.3872	-0.0493	0.0563	0.1361	-0.0185	0.3434	15.5341	48.9126	53.1123
83	1.1321	-0.7471	-1.3552	1.7339	0.7972	1.6447	-0.1466	-0.2654	-0.2639	0.7773	-0.1147	0.3616	0.0684	0.2992	0.2613	0.6308	0.0319	0.1161	0.2468	0.0852	0.4984	18.4214	32.5865	52.9708
84	17.4769	-0.0113	-3.06	2.245	3.9517	8.6612	-0.5315	-1.236	0.2515	0.8547	-0.3448	0.6605	0.657	-0.8746	0.8763	1.1449	0.2347	0.3295	0.4113	0.0987	0.4485	14.9524	38.3077	64.8933
85	3.4364	1.4732	0.842	15.0377	4.9115	5.9959	-0.1987	0.0909	-0.0316	-0.1699	0.1273	-0.975	0.0257	0.4453	0.0713	0.1462	0.0619	0.068	0.2147	0.0029	0.4471	21.7082	45.2557	-1.2188
86	3.1686	-5.3996	-2.1864	10.0646	6.6311	11.4263	0.1564	0.3988	-0.2376	0.1001	-0.859	0.5307	1.4051	-0.8065	0.7027	0.5446	0.0112	0.2635	0.1849	-0.09	0.3606	14.1449	37.113	-4.496
87	1.6862	7.3667	1.452	32.3724	6.4142	1.2814	-0.2699	0.0284	-0.3688	-2.0858	0.2527	-1.2503	-0.4145	0.0304	0.0172	0.6257	0.1141	-0.0154	0.2206	0.1258	1.1425	0.7549	33.9195	7.7492
88	13.0945	5.2509	1.3369	7.058	4.4357	3.312	0.007	0.5003	0.2948	0.5363	0.0158	0.3013	0.4932	-0.0679	-0.0228	0.2662	0.0816	-0.0264	0.076	0.0146	0.4052	-1.6883	33.2294	1.0828
89	0.5242	-0.0898	1.2231	3.7931	-0.5501	2.9232	0.0139	0.1513	-0.071	-0.3148	0.0467	-0.3335	0.1676	0.3476	-0.0606	0.3908	0.0909	0.104	0.1411	-0.0759	0.3257	8.6007	39.5143	-11.4669
90	2.6059	2.4809	4.6635	2.5769	4.5514	10.5805	-0.1782	0.0221	0.1202	-0.3143	-0.0103	-0.1407	0.0292	0.1979	0.1885	0.297	0.106	0.0763	0.0443	0.0005	0.4153	7.3202	48.2834	-10.8427
91	10.7362	-5.8026	-7.9577	9.4252	8.0969	8.1967	0.6994	1.3589	0.1058	-0.9772	-0.6966	-0.0412	-0.8137	-1.0245	-0.0027	0.8993	0.1901	0.0878	0.5012	-0.0221	0.7263	-9.7288	42.997	-14.0682
92	15.9238	-0.9907	6.1573	5.4715	1.5777	10.6704	-0.5711	1.0741	0.8289	-1.1303	0.2718	1.0684	-0.777	-0.2965	0.2993	0.5422	0.0228	-0.0986	0.3699	0.1662	0.4499	-2.6753	43.9188	-21.1774
93	29.8356	-22.0631	-2.4583	23.8399	8.4199	17.3136	0.6044	0.1199	2.4304	-1.5953	-1.1386	0.1323	-0.7694	1.418	0.5342	0.3455	0.2814	-0.1481	0.6487	-0.3951	0.8512	7.2673	59.2238	-12.1496
94	0.6479	0.1726	1.4556	2.3021	0.5382	3.4947	-0.0209	0.1983	0.1249	-0.5692	-0.0751	-0.056	-0.2593	0.3631	0.096	0.3454	0.1303	0.0817	0.1256	0.0453	0.2857	8.3794	48.4684	-11.4932
95	0.943	2.1423	-1.3484	16.0854	-0.5057	2.5501	0.0619	-0.1099	-0.264	-0.0174	-0.3398	-1.2135	-0.0249	0.2043	0.2779	0.3162	0.1369	0.0199	0.1639	0.0649	0.2807	2.6442	32.8227	-3.4875
96	2.75	-1.3675	2.1221	9.1007	-5.8849	9.7353	-0.3055	0.1824	-0.411	-0.8633	0.184	0.0905	0.3609	0.0594	0.1215	0.5606	0.0697	0.0889	0.2829	-0.0742	0.2662	5.1782	34.0656	-24.2841

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 25
2	X-RAY DIFFRACTION	2	A	26 - 34
3	X-RAY DIFFRACTION	3	A	35 - 43
4	X-RAY DIFFRACTION	4	A	44 - 56
5	X-RAY DIFFRACTION	5	A	57 - 75
6	X-RAY DIFFRACTION	6	A	76 - 90
7	X-RAY DIFFRACTION	7	A	91 - 98
8	X-RAY DIFFRACTION	8	A	117 - 126
9	X-RAY DIFFRACTION	9	A	127 - 140
10	X-RAY DIFFRACTION	10	A	141 - 157
11	X-RAY DIFFRACTION	11	A	158 - 168
12	X-RAY DIFFRACTION	12	A	169 - 204
13	X-RAY DIFFRACTION	13	B	11 - 25
14	X-RAY DIFFRACTION	14	B	26 - 34
15	X-RAY DIFFRACTION	15	B	35 - 42
16	X-RAY DIFFRACTION	16	B	43 - 58
17	X-RAY DIFFRACTION	17	B	59 - 75
18	X-RAY DIFFRACTION	18	B	76 - 90
19	X-RAY DIFFRACTION	19	B	91 - 117
20	X-RAY DIFFRACTION	20	B	118 - 126
21	X-RAY DIFFRACTION	21	B	127 - 135
22	X-RAY DIFFRACTION	22	B	136 - 168
23	X-RAY DIFFRACTION	23	B	169 - 186
24	X-RAY DIFFRACTION	24	B	187 - 205
25	X-RAY DIFFRACTION	25	C	8 - 25
26	X-RAY DIFFRACTION	26	C	26 - 34
27	X-RAY DIFFRACTION	27	C	35 - 40
28	X-RAY DIFFRACTION	28	C	41 - 60
29	X-RAY DIFFRACTION	29	C	61 - 75
30	X-RAY DIFFRACTION	30	C	76 - 90
31	X-RAY DIFFRACTION	31	C	91 - 117
32	X-RAY DIFFRACTION	32	C	118 - 126
33	X-RAY DIFFRACTION	33	C	127 - 139
34	X-RAY DIFFRACTION	34	C	140 - 167
35	X-RAY DIFFRACTION	35	C	168 - 194
36	X-RAY DIFFRACTION	36	C	195 - 204
37	X-RAY DIFFRACTION	37	D	8 - 25
38	X-RAY DIFFRACTION	38	D	26 - 34
39	X-RAY DIFFRACTION	39	D	35 - 40
40	X-RAY DIFFRACTION	40	D	41 - 60
41	X-RAY DIFFRACTION	41	D	61 - 75
42	X-RAY DIFFRACTION	42	D	76 - 90
43	X-RAY DIFFRACTION	43	D	91 - 117
44	X-RAY DIFFRACTION	44	D	118 - 126
45	X-RAY DIFFRACTION	45	D	127 - 140
46	X-RAY DIFFRACTION	46	D	141 - 167
47	X-RAY DIFFRACTION	47	D	168 - 194
48	X-RAY DIFFRACTION	48	D	195 - 204
49	X-RAY DIFFRACTION	49	E	10 - 25
50	X-RAY DIFFRACTION	50	E	26 - 35
51	X-RAY DIFFRACTION	51	E	36 - 45
52	X-RAY DIFFRACTION	52	E	46 - 60
53	X-RAY DIFFRACTION	53	E	61 - 75
54	X-RAY DIFFRACTION	54	E	76 - 90
55	X-RAY DIFFRACTION	55	E	91 - 117
56	X-RAY DIFFRACTION	56	E	118 - 125
57	X-RAY DIFFRACTION	57	E	126 - 135
58	X-RAY DIFFRACTION	58	E	136 - 163
59	X-RAY DIFFRACTION	59	E	164 - 175
60	X-RAY DIFFRACTION	60	E	176 - 204
61	X-RAY DIFFRACTION	61	F	11 - 25
62	X-RAY DIFFRACTION	62	F	26 - 37
63	X-RAY DIFFRACTION	63	F	38 - 60
64	X-RAY DIFFRACTION	64	F	61 - 75
65	X-RAY DIFFRACTION	65	F	76 - 85
66	X-RAY DIFFRACTION	66	F	86 - 92
67	X-RAY DIFFRACTION	67	F	93 - 118
68	X-RAY DIFFRACTION	68	F	119 - 126
69	X-RAY DIFFRACTION	69	F	127 - 139
70	X-RAY DIFFRACTION	70	F	140 - 167
71	X-RAY DIFFRACTION	71	F	168 - 179
72	X-RAY DIFFRACTION	72	F	180 - 204
73	X-RAY DIFFRACTION	73	G	11 - 25
74	X-RAY DIFFRACTION	74	G	26 - 33
75	X-RAY DIFFRACTION	75	G	34 - 40
76	X-RAY DIFFRACTION	76	G	41 - 60
77	X-RAY DIFFRACTION	77	G	61 - 75
78	X-RAY DIFFRACTION	78	G	76 - 90
79	X-RAY DIFFRACTION	79	G	91 - 117
80	X-RAY DIFFRACTION	80	G	118 - 126
81	X-RAY DIFFRACTION	81	G	127 - 140
82	X-RAY DIFFRACTION	82	G	141 - 167
83	X-RAY DIFFRACTION	83	G	168 - 192
84	X-RAY DIFFRACTION	84	G	193 - 204
85	X-RAY DIFFRACTION	85	H	10 - 25
86	X-RAY DIFFRACTION	86	H	26 - 34
87	X-RAY DIFFRACTION	87	H	35 - 40
88	X-RAY DIFFRACTION	88	H	41 - 56
89	X-RAY DIFFRACTION	89	H	57 - 75
90	X-RAY DIFFRACTION	90	H	76 - 90
91	X-RAY DIFFRACTION	91	H	91 - 117
92	X-RAY DIFFRACTION	92	H	118 - 126
93	X-RAY DIFFRACTION	93	H	127 - 135
94	X-RAY DIFFRACTION	94	H	136 - 167
95	X-RAY DIFFRACTION	95	H	168 - 179
96	X-RAY DIFFRACTION	96	H	180 - 204

-
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