PDB-4ay0: High resolution crystal structure of the monomeric subunit-free C...

ID or keywords:

Entry

Database: PDB / ID: 4ay0

Title

High resolution crystal structure of the monomeric subunit-free Caf1M chaperone

Components

CHAPERONE PROTEIN CAF1M

Keywords

CHAPERONE / AMINO ACID MOTIFS / BACTERIAL CAPSULES / BACTERIAL PROTEINS / GENE EXPRESSION REGULATION / MOLECULAR CHAPERONES / PROTEIN BINDING / PROTEIN CONFORMATION

Function / homology

Function and homology information

: / protein folding chaperone / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

YERSINIA PESTIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.52 Å

Authors

Yu, X.D. / Dubnovitsky, A. / Pudney, A.F. / MacIntyre, S. / Knight, S.D. / Zavialov, A.V.

Citation

Journal: Structure / Year: 2012
Title: Allosteric Mechanism Controls Traffic in the Chaperone/Usher Pathway.
Authors: Di Yu, X. / Dubnovitsky, A. / Pudney, A.F. / Macintyre, S. / Knight, S.D. / Zavialov, A.V.

History

Deposition	Jun 16, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2012	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ay0.cif.gz	171.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ay0.ent.gz	139.2 KB	Display	PDB format
PDBx/mmJSON format	4ay0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ay0_validation.pdf.gz	429.3 KB	Display	wwPDB validaton report
Full document	4ay0_full_validation.pdf.gz	430.3 KB	Display
Data in XML	4ay0_validation.xml.gz	19.2 KB	Display
Data in CIF	4ay0_validation.cif.gz	29.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ay/4ay0 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ay0	HTTPS FTP

-
Related structure data

Related structure data	4ayfC 4az8C 4b0eC 4b0mC 2os7S 1p5u 1p5v 1z9s C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2ynq-1 3lxr-d 3lwn-1 2nol-d 1vjv-d 5zry-d 1lwv-d 2xhi-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	#32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: CHAPERONE PROTEIN CAF1M

B: CHAPERONE PROTEIN CAF1M

48.8 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)	56.767, 56.767, 248.289
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	CHAPERONE PROTEIN CAF1M / CAPSULE PROTEIN FRACTION 1 Mass: 24420.912 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PTCA1/CAF1MD2-11, D113-129 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26926
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	DELETIONS OF RESIDUES 2-12 AT THE N-TERMINUS AND 113-129 IN THE F1G1 LOOP.

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.41 % / Description: NONE
Crystal grow	pH: 5.5 / Details: 40% PEG 600 AND 0.1 M CITRATE, PH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 10, 2009
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 1.45→62.07 Å / Num. obs: 79538 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 8.52 % / B_iso Wilson estimate: 15.76 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 5.8
Reflection shell	Resolution: 1.45→1.53 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8_1069)	refinement
MOSFLM		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: CHAIN A FROM PDB ENTRY 2OS7

2os7

Resolution: 1.52→28.765 Å / SU ML: 0.13 / σ(F): 1.83 / Phase error: 16.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1879	3446	5 %
R_work	0.1657	-	-
obs	0.1668	69041	99.75 %

Solvent computation

Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46 Å² / k_sol: 0.35 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.52→28.765 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2851	0	0	406	3257

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3085
X-RAY DIFFRACTION	f_angle_d	1.126	4231
X-RAY DIFFRACTION	f_dihedral_angle_d	11.299	1133
X-RAY DIFFRACTION	f_chiral_restr	0.077	474
X-RAY DIFFRACTION	f_plane_restr	0.006	558

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 (%)
1.52-1.5409	0.2268	141	0.1894	2632	X-RAY DIFFRACTION	99
1.5409-1.5629	0.1856	143	0.1795	2631	X-RAY DIFFRACTION	99
1.5629-1.5862	0.2283	142	0.1849	2608	X-RAY DIFFRACTION	99
1.5862-1.611	0.2117	116	0.1792	2612	X-RAY DIFFRACTION	99
1.611-1.6374	0.2115	143	0.1787	2594	X-RAY DIFFRACTION	100
1.6374-1.6656	0.1999	163	0.1767	2616	X-RAY DIFFRACTION	99
1.6656-1.6959	0.197	129	0.1738	2576	X-RAY DIFFRACTION	100
1.6959-1.7285	0.2176	139	0.1684	2656	X-RAY DIFFRACTION	100
1.7285-1.7638	0.2006	129	0.1761	2619	X-RAY DIFFRACTION	100
1.7638-1.8021	0.2079	127	0.1732	2588	X-RAY DIFFRACTION	100
1.8021-1.8441	0.2077	151	0.1718	2627	X-RAY DIFFRACTION	100
1.8441-1.8902	0.2134	131	0.1715	2654	X-RAY DIFFRACTION	100
1.8902-1.9413	0.1789	147	0.1658	2585	X-RAY DIFFRACTION	100
1.9413-1.9984	0.2116	162	0.1728	2589	X-RAY DIFFRACTION	100
1.9984-2.0628	0.1871	147	0.1528	2607	X-RAY DIFFRACTION	100
2.0628-2.1366	0.1751	119	0.16	2667	X-RAY DIFFRACTION	100
2.1366-2.2221	0.1625	144	0.1665	2612	X-RAY DIFFRACTION	100
2.2221-2.3232	0.2041	135	0.1667	2626	X-RAY DIFFRACTION	100
2.3232-2.4456	0.1942	137	0.1677	2639	X-RAY DIFFRACTION	100
2.4456-2.5987	0.1845	145	0.1697	2638	X-RAY DIFFRACTION	100
2.5987-2.7992	0.1936	120	0.1761	2641	X-RAY DIFFRACTION	100
2.7992-3.0806	0.1859	157	0.1767	2608	X-RAY DIFFRACTION	100
3.0806-3.5257	0.2027	129	0.166	2660	X-RAY DIFFRACTION	100
3.5257-4.4394	0.1574	121	0.1456	2647	X-RAY DIFFRACTION	100
4.4394-28.7697	0.166	129	0.1579	2663	X-RAY DIFFRACTION	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	9.142	0.3742	-7.668	0.5561	-0.8008	9.3875	-0.1797	0.0911	-0.1203	-0.051	0.0521	-0.0866	-0.0225	-0.0017	0.1253	0.1319	0.0288	-0.0097	0.0644	-0.0173	0.0803	33.7225	27.8714	-0.8772
2	8.457	2.5864	-7.2694	2.7595	-1.4153	6.8656	-0.0258	-0.395	-0.755	0.1305	-0.2334	-0.3258	-0.03	0.7331	0.2499	0.1105	0.0329	-0.0202	0.2346	0.021	0.1303	41.8096	24.1496	5.3032
3	8.1821	-4.2869	-1.3118	2.2856	0.3641	2.2693	-0.5491	0.0477	0.5209	-0.0239	0.0855	-0.1115	-0.3009	0.8088	0.4298	0.1279	-0.02	-0.1175	0.4553	0.104	0.2694	50.0646	31.4577	10.1301
4	8.1385	-2.6846	7.0088	7.6505	-7.1971	9.6489	-0.6306	-0.324	0.3437	0.633	0.1301	-0.5537	-0.9207	0.2483	0.4888	0.2177	0.0307	-0.0731	0.1662	0.0104	0.237	33.0705	40.1094	7.7228
5	2.0665	1.0507	1.2401	1.0649	-0.2463	1.9517	-0.2682	-0.1634	0.2497	0.1609	0.0847	0.0261	-0.2876	0.1932	0.1787	0.1746	0.0188	-0.0403	0.1892	-0.0117	0.1239	39.0631	31.3524	14.3399
6	8.5227	7.3873	-4.287	7.8959	-1.5445	5.3348	-0.2155	-0.1809	-0.9088	0.2978	0.4102	-0.7171	0.1488	0.9609	-0.1688	0.1562	0.0987	-0.0229	0.478	-0.0097	0.3096	52.3465	22.8984	5.5333
7	6.3452	-3.5529	-4.1099	3.9802	2.4139	5.1242	-0.0478	-0.4146	-0.0153	0.0175	0.0256	0.0769	-0.054	-0.0998	0.0013	0.0978	0.0264	0.0069	0.0974	-0.0048	0.0968	31.4315	27.0228	12.6451
8	5.0679	2.0582	0.9974	1.8037	-0.7671	2.3478	-0.0238	-0.1733	0.244	0.0653	-0.0228	0.0764	-0.1006	-0.1516	0.0312	0.1211	0.056	-0.0153	0.0802	-0.0059	0.1283	24.1397	33.1133	5.0993
9	2.0015	1.46	5.867	1.2083	1.2618	2.9356	-0.0269	1.1468	0.1674	0.3769	-0.2658	-0.9582	-0.4125	1.4379	0.2303	0.2067	-0.043	-0.1292	0.4995	0.1375	0.4289	47.8999	35.2616	8.0151
10	6.3985	1.6088	6.5499	1.4204	1.4855	6.6494	0.0749	0.8456	0.0009	0.2112	-0.1351	-0.3652	-0.0646	0.7387	0.1321	0.1611	0.0434	-0.0435	0.1609	0.0337	0.2051	38.9827	33.3001	3.2527
11	6.2501	5.8943	-1.7606	6.373	0.3788	7.2779	-0.1903	-0.2379	-0.0575	-0.0962	-0.0389	0.1045	0.603	-0.3289	0.2501	0.1285	0.0342	-0.0083	0.0587	-0.0193	0.1454	20.2247	25.8864	2.8591
12	2.0085	-2.5422	0.1924	7.9724	-8.7251	2.0145	-0.0861	0.0071	-0.8323	0.4846	0.1073	0.4488	0.4147	-0.2225	0.0332	0.2203	0.0457	-0.0109	0.1192	-0.0189	0.1995	20.0356	26.2677	-8.5305
13	0.6905	-0.4895	0.3747	8.3311	1.609	1.8096	0.138	0.1113	-0.0459	-0.0976	-0.1268	0.3068	0.1104	-0.0534	0.004	0.1309	0.0698	-0.0091	0.1173	-0.0158	0.1092	17.5872	42.9373	-13.5462
14	1.7795	-1.2616	-0.4016	4.2033	0.7959	1.8803	0.1502	-0.0288	0.0116	0.109	-0.1104	-0.1445	-0.3854	0.2286	-0.0889	0.1141	0.1426	0.0195	0.0686	-0.0292	0.0935	20.833	47.6126	-11.0246
15	1.1118	0.7785	-1.0288	1.1805	-1.5915	3.3922	0.0414	0.0776	-0.1948	-0.1861	-0.16	-0.0957	0.2781	0.1744	0.1187	0.1403	0.069	-0.0217	0.097	-0.0125	0.1156	24.2653	36.5486	-9.9441
16	3.7903	-0.2091	-0.9752	4.0271	0.0523	9.2035	-0.0701	0.2856	-0.1911	-0.2376	-0.2284	-0.2288	-0.1056	0.684	0.281	0.1038	0.0464	-0.0066	0.1511	-0.0025	0.1034	30.8991	44.1315	-14.5454
17	9.0595	-2.4401	1.7998	2.8618	-1.1306	2.7935	0.0864	-0.2094	-0.0572	0.037	-0.1345	-0.1318	-0.0939	-0.1308	0.0372	0.1307	0.0599	-0.0099	0.051	-0.0202	0.1083	20.6331	39.3743	-3.0308
18	3.6206	-0.372	0.881	7.6749	-4.7344	8.6595	0.0368	0.2333	0.143	-0.2015	-0.0356	0.1797	-0.5034	0.3013	-0.0285	0.1511	0.0514	-0.0124	0.1134	-0.0309	0.1152	25.237	49.4659	-12.6366
19	1.3855	-1.0189	0.7997	3.2531	-1.2164	2.1879	0.1382	0.2572	-0.0781	-0.0946	-0.2539	-0.038	0.0377	0.2053	0.0983	0.1424	0.1491	-0.0051	0.1135	-0.0403	0.0947	25.7055	36.0881	-15.8077
20	2.6862	-2.5321	0.8894	7.1576	-2.1783	0.9289	-0.0139	0.0881	-0.0815	-0.0991	0.0863	0.1345	0.1126	-0.375	-0.043	0.1875	0.1149	-0.0287	0.1978	-0.0293	0.129	20.7756	36.2184	-19.3164
21	7.8684	7.8638	7.6844	8.2467	8.1232	7.9985	-0.2237	0.2913	-0.3684	-0.2152	0.1874	-0.5186	-0.1388	0.8519	0.0063	0.1803	0.0213	-0.0386	0.2451	-0.0137	0.1445	42.3135	25.6039	-2.4944
22	4.9062	1.5274	3.5037	2.0848	-0.7636	6.3755	-0.0592	0.2273	-0.0805	-0.2644	-0.0839	0.3799	0.165	-0.0173	0.1675	0.1741	0.0721	-0.0457	0.1123	-0.0432	0.1495	34.0578	17.7585	-16.2355
23	2.0336	7.8202	6.7074	2.0253	8.2264	6.53	0.4285	0.1635	-0.2674	0.2957	-0.1041	-0.2856	0.1796	-0.2344	-0.3096	0.2548	0.0619	-0.0633	0.1717	-0.0437	0.2115	35.0132	26.5919	-18.823
24	9.6257	2.0114	5.2579	2.0002	6.4731	8.8656	0.2486	-0.537	0.3338	0.6504	-0.3765	-0.0549	-0.438	0.5474	0.2602	0.4167	-0.0997	-0.0582	0.229	0.0178	0.1603	47.4108	38.0797	-10.6371
25	2.0117	3.4182	0.1091	8.3884	0.4772	4.8759	-0.1245	-0.7236	0.0399	0.1758	-0.3112	-0.279	0.5817	0.42	0.4069	0.2884	-0.0648	-0.03	0.2834	0.0847	0.1978	50.4171	32.5938	-18.6604
26	4.1836	-0.6142	1.7346	4.3215	0.3961	9.8368	0.0315	0.5764	-0.1994	-0.5831	-0.204	-0.6772	-0.0977	1.0074	0.1413	0.288	0.0251	0.0999	0.2975	0.0553	0.3026	48.7965	14.5284	-19.7146
27	8.86	8.4656	-2.4116	9.6619	-5.4592	6.8914	-0.2578	-0.2092	-0.5928	-0.8017	-0.1524	-0.5058	0.3264	0.1023	0.3687	0.1981	0.0546	0.0402	0.1338	0.0014	0.1378	43.374	25.0626	-24.5759
28	2.0097	-0.1701	-0.684	7.0884	9.5478	2.011	-0.1914	0.2472	0.7813	-0.0653	0.1074	0.2719	-0.2078	0.0686	0.0051	0.2767	-0.0497	0.0185	0.196	0.0236	0.1952	47.3041	39.8675	-16.9754
29	6.0943	4.9137	0.8003	2.0115	2.0011	2.007	-0.0216	0.1014	0.3099	-0.7182	0.0817	0.5318	-0.6279	0.1361	-0.0617	0.2354	0.0206	-0.0264	0.1291	0.0038	0.1309	38.5565	29.8681	-20.4326
30	0.2095	0.9793	-0.4128	4.4245	-1.8385	0.7656	0.2732	0.1446	0.0471	-0.5515	0.0605	0.0455	0.3378	0.0397	-0.1816	0.4788	-0.082	-0.1735	0.2034	-0.1604	0.1154	34.5266	10.4925	-22.5077
31	4.4557	3.4881	-1.0319	8.7584	-2.487	2.9242	0.0596	0.1578	-0.2718	-0.2309	-0.2253	-0.4823	-0.0269	0.2536	0.1719	0.1222	0.0743	-0.0163	0.1076	0.0013	0.1045	42.5502	15.7987	-14.9701
32	2.0099	1.9976	-8.3389	2.0063	1.9809	2.003	0.5521	-0.342	0.5177	0.3456	-0.8707	-0.6224	-0.4742	0.8652	0.495	0.2882	-0.1088	-0.1171	0.4121	0.2073	0.4195	53.2192	30.0258	-14.6835
33	2.0679	5.4131	1.456	6.2491	1.0275	3.4453	-0.1869	0.2462	0.2334	-0.2879	0.0312	0.234	-0.0222	-0.1691	0.1178	0.109	0.0719	-0.026	0.1124	-0.0356	0.1396	34.4124	14.4833	-14.3535
34	1.2336	0.7766	2.0867	0.8074	0.33	6.4228	0.001	-0.0672	0.2403	-0.0637	-0.1897	0.6432	-0.1091	-1.1416	0.1914	0.1257	0.0328	-0.0044	0.2305	-0.0485	0.2174	28.3978	9.8552	-5.0712
35	8.7955	-5.8475	0.9345	6.2089	-0.1302	2.2068	-0.0249	0.0032	-0.3988	0.2635	0.0162	0.3144	0.0879	-0.0613	0.0274	0.1508	0.0236	0.0078	0.0603	-0.0163	0.0806	42.8803	-0.0452	2.2408
36	1.5995	-0.0784	1.4712	1.2211	-0.6451	4.0528	-0.0355	-0.0206	-0.0147	0.1566	-0.05	0.0767	-0.0771	0.0996	0.0824	0.0955	0.034	0.0113	0.0614	-0.0107	0.0666	42.3451	8.0284	1.2677
37	1.7328	0.0881	-0.0851	5.2826	1.2494	4.1178	0.1173	0.0244	0.0682	0.0243	-0.1638	0.0885	0.1075	0.1998	0.014	0.0876	0.053	0.0035	0.0633	-0.0239	0.0707	45.3517	5.772	-4.0721
38	8.7477	0.1046	1.0539	6.6694	0.0737	6.2953	0.4465	-0.2856	-0.5056	0.8316	-0.2589	0.0184	0.2477	0.7716	-0.1207	0.295	0.031	-0.0094	0.186	-0.0044	0.1141	48.9112	1.332	11.47
39	2.3394	-2.1079	1.1337	5.0171	-2.428	3.2398	0.0122	-0.0146	0.1621	0.1652	-0.0701	0.2652	-0.1996	-0.1495	0.0245	0.1201	0.0336	0.0082	0.0747	-0.0276	0.1193	36.0958	14.8238	2.7694
40	7.2934	-8.7593	-1.1528	2.0262	0.4353	1.1798	-0.2131	-0.0131	-0.819	0.2691	0.0632	0.6427	0.6026	-0.1094	0.037	0.2857	-0.0136	0.0528	0.0869	0.0048	0.2742	38.7978	0.7377	8.5083

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 13:26)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 27:38)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 41:46)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 47:54)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 55:70)
6	X-RAY DIFFRACTION	6	(CHAIN A AND RESID 71:76)
7	X-RAY DIFFRACTION	7	(CHAIN A AND RESID 77:87)
8	X-RAY DIFFRACTION	8	(CHAIN A AND RESID 88:97)
9	X-RAY DIFFRACTION	9	(CHAIN A AND RESID 98:103)
10	X-RAY DIFFRACTION	10	(CHAIN A AND RESID 104:123)
11	X-RAY DIFFRACTION	11	(CHAIN A AND RESID 124:131)
12	X-RAY DIFFRACTION	12	(CHAIN A AND RESID 132:137)
13	X-RAY DIFFRACTION	13	(CHAIN A AND RESID 138:147)
14	X-RAY DIFFRACTION	14	(CHAIN A AND RESID 148:153)
15	X-RAY DIFFRACTION	15	(CHAIN A AND RESID 154:167)
16	X-RAY DIFFRACTION	16	(CHAIN A AND RESID 168:175)
17	X-RAY DIFFRACTION	17	(CHAIN A AND RESID 176:182)
18	X-RAY DIFFRACTION	18	(CHAIN A AND RESID 183:193)
19	X-RAY DIFFRACTION	19	(CHAIN A AND RESID 194:208)
20	X-RAY DIFFRACTION	20	(CHAIN A AND RESID 209:217)
21	X-RAY DIFFRACTION	21	(CHAIN B AND RESID 14:19)
22	X-RAY DIFFRACTION	22	(CHAIN B AND RESID 20:26)
23	X-RAY DIFFRACTION	23	(CHAIN B AND RESID 27:33)
24	X-RAY DIFFRACTION	24	(CHAIN B AND RESID 34:40)
25	X-RAY DIFFRACTION	25	(CHAIN B AND RESID 41:47)
26	X-RAY DIFFRACTION	26	(CHAIN B AND RESID 48:59)
27	X-RAY DIFFRACTION	27	(CHAIN B AND RESID 60:67)
28	X-RAY DIFFRACTION	28	(CHAIN B AND RESID 68:74)
29	X-RAY DIFFRACTION	29	(CHAIN B AND RESID 75:81)
30	X-RAY DIFFRACTION	30	(CHAIN B AND RESID 82:89)
31	X-RAY DIFFRACTION	31	(CHAIN B AND RESID 90:101)
32	X-RAY DIFFRACTION	32	(CHAIN B AND RESID 102:120)
33	X-RAY DIFFRACTION	33	(CHAIN B AND RESID 121:129)
34	X-RAY DIFFRACTION	34	(CHAIN B AND RESID 130:137)
35	X-RAY DIFFRACTION	35	(CHAIN B AND RESID 138:151)
36	X-RAY DIFFRACTION	36	(CHAIN B AND RESID 152:173)
37	X-RAY DIFFRACTION	37	(CHAIN B AND RESID 174:187)
38	X-RAY DIFFRACTION	38	(CHAIN B AND RESID 188:197)
39	X-RAY DIFFRACTION	39	(CHAIN B AND RESID 198:211)
40	X-RAY DIFFRACTION	40	(CHAIN B AND RESID 212:217)

-
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