PDB-3sl7: Crystal structure of CBS-pair protein, CBSX2 from Arabidopsis thaliana

ID or keywords:

Entry

Database: PDB / ID: 3sl7

Title

Crystal structure of CBS-pair protein, CBSX2 from Arabidopsis thaliana

Components

CBS domain-containing protein CBSX2

Keywords

MEMBRANE PROTEIN / CBS-pair protein / redox regulator / plant CBS domain / Thioredoxin / Chloroplast

Function / homology

Function and homology information

detection of redox state / chloroplast stroma / enzyme regulator activity / cell redox homeostasis / chloroplast / plasma membrane
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.905 Å

Authors

Jeong, B.-C. / Lee, M.-R. / Song, H.K.

Citation

Journal: Plant Cell / Year: 2011
Title: Single cystathionine beta-synthase domain-containing proteins modulate development by regulating the thioredoxin system in Arabidopsis
Authors: Yoo, K.S. / Ok, S.H. / Jeong, B.-C. / Jung, K.W. / Cui, M.H. / Hyoung, S. / Lee, M.-R. / Song, H.K. / Shin, J.S.

History

Deposition	Jun 24, 2011	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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	3sl7.cif.gz	133 KB	Display	PDBx/mmCIF format
PDB format	pdb3sl7.ent.gz	106.3 KB	Display	PDB format
PDBx/mmJSON format	3sl7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sl/3sl7 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sl7	HTTPS FTP

-
Related structure data

Similar structure data	4gqw-1 3jtf-d 2p9m-1 2p9m-2 2emq-d 3cni-1 6c8v-d 6yj9-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

Deposited unit

A: CBS domain-containing protein CBSX2

B: CBS domain-containing protein CBSX2

hetero molecules

40.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.045, 73.045, 253.453
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	TYR	TYR	LEU	LEU	chain A and (resseq 77:131 or resseq 155:231 ) and (not element H)	A	A	77 - 131	4 - 58
1	2	TRP	TRP	LYS	LYS	chain A and (resseq 77:131 or resseq 155:231 ) and (not element H)	A	A	155 - 231	82 - 158
2	1	TYR	TYR	LEU	LEU	chain B and (resseq 77:131 or resseq 155:231 ) and (not element H)	B	B	77 - 131	4 - 58
2	2	TRP	TRP	LYS	LYS	chain B and (resseq 77:131 or resseq 155:231 ) and (not element H)	B	B	155 - 231	82 - 158

#1: Protein	CBS domain-containing protein CBSX2 / CBS domain-containing protein 1 / AtCDCP1 Mass: 19846.062 Da / Num. of mol.: 2 / Fragment: resideus in UNP 76-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CBSX2 / Plasmid: pET-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9C5D0
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.98 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Bis-Tris, 0.2M Calcium acetate, 22% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	Photon Factory	AR-NW12A	1	0.97888, 0.97928, 0.95000
SYNCHROTRON	PAL/PLS	6B	2	1.23985

Detector

Type	ID	Detector	Date
ADSC QUANTUM 210	1	CCD	Dec 1, 2008
ADSC QUANTUM 210	2	CCD	Feb 6, 2009

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97888	1
2	0.97928	1
3	0.95	1
4	1.23985	1

Reflection

Resolution: 1.905→50 Å / Num. obs: 31938 / Redundancy: 25 % / R_sym value: 0.057

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
PHENIX	(phenix.refine: dev_589)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 1.905→35.13 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7861 / SU ML: 0.23 / σ(F): 0 / Phase error: 26.73 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2463	1862	6.24 %	RANDOM
R_work	0.223	-	-	-
all	0.2244	-	-	-
obs	0.2244	29856	92.05 %	-

Solvent computation

Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.292 Å² / k_sol: 0.375 e/Å³

Displacement parameters

B_iso max: 130.67 Å² / B_iso mean: 43.3883 Å² / B_iso min: 3.12 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5439 Å²	0 Å²	-0 Å²
2-	-	7.5439 Å²	-0 Å²
3-	-	-	-10.8814 Å²

Refinement step

Cycle: LAST / Resolution: 1.905→35.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2183	0	34	207	2424

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2223
X-RAY DIFFRACTION	f_angle_d	1.153	3009
X-RAY DIFFRACTION	f_chiral_restr	0.106	370
X-RAY DIFFRACTION	f_plane_restr	0.004	380
X-RAY DIFFRACTION	f_dihedral_angle_d	12.044	818

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1033	X-RAY DIFFRACTION	POSITIONAL	0.069
1	2	B	1033	X-RAY DIFFRACTION	POSITIONAL	0.069

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9051-1.9732	0.3717	137	0.32	2055	2192	69
1.9732-2.0522	0.3474	168	0.2788	2622	2790	89
2.0522-2.1456	0.2916	183	0.252	2734	2917	91
2.1456-2.2587	0.2873	188	0.2351	2799	2987	95
2.2587-2.4002	0.2627	182	0.2425	2695	2877	90
2.4002-2.5854	0.2817	187	0.2413	2803	2990	93
2.5854-2.8455	0.2712	193	0.2422	2882	3075	95
2.8455-3.257	0.2686	198	0.2311	2983	3181	98
3.257-4.1025	0.2126	208	0.2047	3097	3305	100
4.1025-35.1357	0.2065	218	0.1978	3324	3542	100

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	0.8419	-1.2569	-0.9812	2.9929	1.4484	1.5244	0.2537	0.4216	0.2124	-0.1228	-0.0662	-0.362	-0.074	-0.0592	-0.1443	0.1429	-0.0416	0.024	0.3659	0.0172	0.2204	31.1754	33.3307	96.4978
2	4.8115	0.6643	-0.7822	4.2707	1.1157	2.12	-0.0419	0.5632	-0.0765	-0.3436	-0.1606	-0.187	-0.3704	0.4119	0.1892	0.264	-0.0557	0.0057	0.3386	0.0833	0.2289	37.3035	40.6523	105.0692
3	4.7706	-4.6597	4.1879	6.2645	-4.9534	5.0932	-0.0303	-0.6884	0.3124	-0.1699	0.1339	-0.5103	-0.0579	-0.5702	-0.1061	0.187	-0.0117	0.0613	0.2738	-0.0207	0.2206	40.0108	41.003	114.7308
4	5.9813	3.7661	-0.0068	2.5599	-0.3888	0.7802	0.148	-0.4863	-0.0995	0.066	0.0177	-0.1227	-0.1635	0.4595	-0.2129	0.1816	-0.0412	-0.0215	0.4325	-0.1175	0.1935	44.2036	38.6418	126.3752
5	3.5845	0.616	2.1572	1.4476	-0.3726	1.7118	0.0055	-0.5695	0.5216	0.0178	0.0666	0.1795	-0.0128	-0.6346	-0.0384	0.2608	-0.0575	0.0619	0.5824	-0.0966	0.2812	36.2592	42.3228	124.7088
6	2.6301	-1.0052	0.908	3.2271	0.7841	0.8666	-0.1893	-0.9254	-0.0698	0.2484	0.3264	-0.1526	-0.0378	0.3149	-0.1248	0.1763	0.0187	0.0402	0.3666	-0.0509	0.2763	31.4269	42.0151	119.5747
7	1.0792	1.2276	-0.1192	1.6423	-0.1041	0.1543	0.0074	-0.0114	-0.2817	-0.1024	0.0698	-0.1603	-0.2178	0.16	-0.076	0.2038	-0.11	0.0264	0.3504	-0.0141	0.2168	46.5411	37.0948	115.1283
8	0.3989	-0.5786	0.3712	1.0437	-0.3692	0.4745	-0.0512	0.2124	-0.1291	-0.1034	0.1291	0.2802	0.0353	-0.0759	-0.0782	0.0858	-0.1374	0.014	0.316	-0.0169	0.191	45.5053	34.2341	112.999
9	0.0921	0.0842	-0.2061	0.1229	-0.0883	0.6683	-0.0028	0.311	0.1214	-0.1108	0.1482	0.0317	0.0209	-0.2508	-0.1009	0.1535	-0.0716	0.0573	0.4916	0.0157	0.2863	34.8465	31.6944	125.0304
10	3.3344	-0.0833	0.359	2.9434	-3.0271	3.1365	-0.2299	0.1582	0.1373	-0.1596	-0.2427	-0.055	-0.2503	0.4871	0.4857	0.526	0.2613	-0.1211	0.6192	-0.0457	0.2139	27.6512	31.3683	133.7433
11	5.1464	2.2851	-4.146	3.3084	-0.5484	4.0703	0.2423	-0.3316	0.0334	0.0878	-0.2883	-0.3328	0.5396	1.3011	0.0448	0.2776	0.0996	-0.0564	0.5588	-0.0183	0.2277	28.1108	37.0366	138.4096
12	3.4517	-0.5191	1.1484	3.5241	-2.2663	1.6535	0.0361	-1.1697	-0.116	-0.1019	-0.717	-0.4703	0.303	0.8012	0.5946	0.2101	0.2856	0.1081	0.8567	0.1716	0.324	35.3878	35.4972	137.8589
13	4.6547	-0.7883	0.554	4.9877	-0.6955	0.1404	-0.4954	-0.7542	0.0575	0.5623	0.8698	-0.0543	-0.0793	-0.217	-0.3374	0.2077	0.0597	0.0033	0.6724	-0.0163	0.2549	44.2243	36.0738	131.5014
14	3.4677	1.0394	1.4644	1.0718	-0.2405	2.2827	0.0383	-0.4217	0.0458	0.0733	-0.1713	-0.0052	0.0464	0.1669	0.1577	0.1002	-0.0734	0.0398	0.3811	-0.0242	0.186	43.5292	27.9436	120.53
15	5.4956	2.6335	-1.0129	4.6557	-2.2954	4.9959	0.2347	0.6196	-0.1543	0.0868	0.0809	-0.052	0.0588	0.3125	-0.1461	0.1205	-0.0534	-0.0311	0.3567	-0.0301	0.1795	39.3775	28.5931	102.1445
16	3.5691	1.9175	1.7279	1.7675	0.3892	1.7744	0.2544	-0.159	-0.7819	-0.0505	0.0953	-0.0423	0.5196	-0.7571	-0.29	0.2844	-0.0697	-0.0169	0.3978	-0.0402	0.3786	29.9488	24.492	103.0026
17	3.0058	-2.2816	-0.8317	2.003	-0.842	8.2393	-0.3505	-0.3019	-1.4178	-0.7394	0.0898	-0.9141	1.4311	-0.4198	0.284	0.5988	-0.0246	0.088	0.5366	0.1203	0.6868	31.759	25.5618	114.6789
18	0.8566	0.8486	0.5383	1.5617	-0.0463	1.0069	0.0457	-0.0634	-0.1424	0.0115	-0.1285	-0.1825	-0.0237	0.221	0.0959	-0.0628	-0.1409	0.1132	0.3844	0.0178	0.1639	42.5366	33.213	106.4019
19	0.0974	0.079	0.0379	0.6422	0.2826	0.1256	0.1371	-0.0612	0.1616	0.1404	-0.0976	0.2504	-0.0474	-0.2716	-0.1418	0.139	-0.0035	0.0854	0.3561	-0.0127	0.234	28.185	34.344	106.2154
20	5.2063	4.7274	3.9077	6.2031	2.334	6.2488	0.3013	0.8948	1.3433	-0.3297	-0.5349	0.2143	0.0266	-0.1892	0.2605	0.2414	0.131	0.0379	0.4951	0.0701	0.3896	20.518	35.4584	97.2607
21	1.8068	-0.5172	1.5907	0.3261	-0.2042	1.7556	-0.0745	-0.407	0.2443	0.0759	-0.1215	0.0242	0.076	-0.4545	0.1894	0.3724	0.1291	0.0787	0.3052	-0.0049	0.1851	22.0938	49.49	133.476
22	1.3842	0.055	-0.2956	0.1341	-0.2536	0.5233	0.1666	0.3923	0.0906	-0.1525	-0.0399	0.0055	-0.503	0.0336	-0.1466	0.5184	0.1989	0.0535	0.4409	0.0152	0.2309	18.029	50.0939	118.6287
23	0.6628	-0.6621	-0.6735	1.1022	1.3491	1.723	0.1122	0.1762	0.0182	-0.0668	-0.0689	0.1123	-0.4081	-0.647	0.0512	0.2763	0.3276	0.0423	0.8842	0.0036	0.1862	7.5081	42.9447	108.6179
24	3.949	0.9494	3.6279	4.6143	3.509	5.1154	-0.0539	0.2747	-0.0222	-0.5914	-0.1599	-0.0274	-0.0954	0.447	0.1491	0.3597	0.2362	0.0138	0.4834	-0.0148	0.1825	15.7663	41.0492	105.5226
25	2.1336	0.5956	2.9128	2.8227	2.4459	4.9795	0.2934	0.116	0.2054	0.1771	0.1899	0.193	-0.1349	-0.3349	-0.4139	0.2696	0.0978	0.1065	0.4593	0.0855	0.1231	22.9821	42.3946	109.5497
26	3.9145	0.0573	-1.2894	0.0437	0.0061	1.9225	0.2694	0.4051	-0.156	0.0075	-0.1978	0.0122	-0.2598	-0.2173	-0.0389	0.1892	0.2268	-0.0195	0.3328	0.0711	0.1688	15.9857	40.8804	116.0783
27	0.0207	0.1112	0.0283	0.6815	-0.0811	0.8743	0.0682	0.1145	0.0921	-0.2546	-0.1405	0.0985	-0.3663	-0.4053	0.0258	0.4915	0.7439	0.0016	0.8077	0.0777	0.2507	6.2029	50.4769	117.7861
28	1.2648	0.5778	0.0749	0.4592	-0.5218	1.5771	-0.2209	-0.0412	-0.3258	0.0786	-0.0473	0.1591	-0.0485	-0.5005	0.2677	0.0486	0.1601	0.0662	0.5391	-0.1105	0.203	12.768	33.1303	113.8037
29	2.6927	-1.1378	2.7704	5.4374	1.2369	5.0937	0.0651	0.8183	-1.076	0.0976	-0.0996	0.3953	0.3211	-0.3387	0.029	0.2632	-0.126	-0.0257	0.5007	-0.0206	0.4564	21.0631	24.674	103.5885
30	5.1129	5.9163	-2.976	6.8754	-3.5944	2.4787	0.0717	0.7431	-0.0276	-0.3129	0.0733	0.8594	0.0845	-0.7326	-0.0932	0.2177	0.021	-0.0843	0.6541	-0.1603	0.4195	15.3718	28.3119	100.0708
31	5.2452	-0.3596	0.0533	2.0588	1.6605	2.6298	-0.152	-0.9892	-0.2004	0.0438	-0.0413	0.2717	-0.2994	-0.3699	0.1441	0.2735	0.2851	-0.0688	0.7028	-0.0338	0.215	7.3326	34.3984	101.9841
32	3.9668	-2.4458	-1.3404	3.024	-0.7193	2.0296	0.2097	0.0491	-0.3827	-0.2182	-0.0232	0.363	0.0231	-0.4353	-0.1702	0.1348	0.3316	-0.2118	0.892	0.011	0.1033	5.7439	36.8003	113.8781
33	3.4312	0.5572	-2.0118	1.4551	-1.0512	1.5642	0.1684	0.9372	-0.0685	0.0669	0.1906	0.0845	-0.1145	-0.4507	-0.2923	0.2163	0.2311	-0.0095	0.4732	-0.0516	0.1634	8.3231	40.347	126.7423
34	0.1998	-0.1962	-0.365	1.7482	-0.2737	0.9304	-0.0591	-0.0384	0.086	0.1351	0.2387	-0.0521	-0.4155	-0.2114	-0.1295	0.409	0.1841	0.0602	0.3131	0.0181	0.1802	14.4343	48.3612	135.46
35	2.4656	1.1684	0.8202	2.3186	1.0596	0.7186	-0.1036	-0.4558	0.0697	-0.1184	-0.112	0.0979	-0.1618	-0.2449	0.2191	0.2316	0.1526	-0.0079	0.4443	-0.0009	0.1589	18.8957	39.2657	136.7375
36	0.3639	0.1442	0.7868	0.0614	0.3374	1.7955	0.091	0.1512	-0.0102	0.0316	0.0706	-0.2461	0.1052	0.1829	-0.0772	0.024	0.1417	-0.0229	0.3479	0	0.2037	16.6412	33.9386	126.7534
37	3.4654	-1.8711	-0.087	2.1831	-0.2898	0.6027	0.0687	0.1431	-0.207	0.0521	-0.047	0.2736	-0.1188	-0.0524	0.034	0.1889	0.2429	0.0478	0.3688	0.0199	0.2151	14.6415	43.503	126.0023
38	0.2354	-0.2298	0.2507	0.4331	0.0275	0.5737	0.0557	0.0441	0.1696	-0.1198	-0.1319	0.1672	-0.6507	-0.7423	-0.0491	0.5223	0.5396	0.258	0.4714	-0.0846	-0.0352	9.9582	51.2228	125.7292
39	4.1283	-2.2447	-1.8144	2.1211	-0.5964	3.5869	0.3447	0.4319	-0.299	0.0661	-0.0483	0.185	-0.1547	0.5163	-0.3237	0.2213	0.0444	-0.0067	0.359	-0.04	0.2362	24.6514	41.2203	128.1269
40	1.3867	1.0696	-0.5096	3.8169	2.5509	3.0818	-0.1703	0.3628	0.0403	-0.1024	0.3962	-0.2575	-0.5282	1.9799	-0.2447	0.3497	-0.1176	0.0243	0.6623	-0.0983	0.3682	32.3076	45.8446	133.9412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 76:82)	A	76 - 82
2	X-RAY DIFFRACTION	2	(chain A and resid 83:87)	A	83 - 87
3	X-RAY DIFFRACTION	3	(chain A and resid 88:93)	A	88 - 93
4	X-RAY DIFFRACTION	4	(chain A and resid 94:99)	A	94 - 99
5	X-RAY DIFFRACTION	5	(chain A and resid 100:106)	A	100 - 106
6	X-RAY DIFFRACTION	6	(chain A and resid 107:112)	A	107 - 112
7	X-RAY DIFFRACTION	7	(chain A and resid 113:119)	A	113 - 119
8	X-RAY DIFFRACTION	8	(chain A and resid 120:125)	A	120 - 125
9	X-RAY DIFFRACTION	9	(chain A and resid 126:132)	A	126 - 132
10	X-RAY DIFFRACTION	10	(chain A and resid 133:157)	A	133 - 157
11	X-RAY DIFFRACTION	11	(chain A and resid 158:162)	A	158 - 162
12	X-RAY DIFFRACTION	12	(chain A and resid 163:167)	A	163 - 167
13	X-RAY DIFFRACTION	13	(chain A and resid 168:174)	A	168 - 174
14	X-RAY DIFFRACTION	14	(chain A and resid 175:181)	A	175 - 181
15	X-RAY DIFFRACTION	15	(chain A and resid 182:188)	A	182 - 188
16	X-RAY DIFFRACTION	16	(chain A and resid 189:198)	A	189 - 198
17	X-RAY DIFFRACTION	17	(chain A and resid 199:203)	A	199 - 203
18	X-RAY DIFFRACTION	18	(chain A and resid 204:215)	A	204 - 215
19	X-RAY DIFFRACTION	19	(chain A and resid 216:225)	A	216 - 225
20	X-RAY DIFFRACTION	20	(chain A and resid 226:231)	A	226 - 231
21	X-RAY DIFFRACTION	21	(chain B and resid 77:83)	B	77 - 83
22	X-RAY DIFFRACTION	22	(chain B and resid 84:92)	B	84 - 92
23	X-RAY DIFFRACTION	23	(chain B and resid 93:98)	B	93 - 98
24	X-RAY DIFFRACTION	24	(chain B and resid 99:104)	B	99 - 104
25	X-RAY DIFFRACTION	25	(chain B and resid 105:109)	B	105 - 109
26	X-RAY DIFFRACTION	26	(chain B and resid 110:115)	B	110 - 115
27	X-RAY DIFFRACTION	27	(chain B and resid 116:122)	B	116 - 122
28	X-RAY DIFFRACTION	28	(chain B and resid 123:154)	B	123 - 154
29	X-RAY DIFFRACTION	29	(chain B and resid 155:161)	B	155 - 161
30	X-RAY DIFFRACTION	30	(chain B and resid 162:166)	B	162 - 166
31	X-RAY DIFFRACTION	31	(chain B and resid 167:172)	B	167 - 172
32	X-RAY DIFFRACTION	32	(chain B and resid 173:178)	B	173 - 178
33	X-RAY DIFFRACTION	33	(chain B and resid 179:184)	B	179 - 184
34	X-RAY DIFFRACTION	34	(chain B and resid 185:189)	B	185 - 189
35	X-RAY DIFFRACTION	35	(chain B and resid 190:196)	B	190 - 196
36	X-RAY DIFFRACTION	36	(chain B and resid 197:203)	B	197 - 203
37	X-RAY DIFFRACTION	37	(chain B and resid 204:208)	B	204 - 208
38	X-RAY DIFFRACTION	38	(chain B and resid 209:217)	B	209 - 217
39	X-RAY DIFFRACTION	39	(chain B and resid 218:224)	B	218 - 224
40	X-RAY DIFFRACTION	40	(chain B and resid 225:231)	B	225 - 231

-
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

-
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