PDB-6dx7: Crystal structure of chalcone synthase from Physcomitrella patens

ID or keywords:

Entry

Database: PDB / ID: 6dx7

Title

Crystal structure of chalcone synthase from Physcomitrella patens

Components

Chalcone synthase

Keywords

TRANSFERASE / Thiolase / Flavonoid / Polyketide synthase

Function / homology

Function and homology information

chalcone synthase / naringenin-chalcone synthase activity / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function

Biological species

Physcomitrella patens subsp. patens (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.61 Å

Authors

Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.

Funding support

United States, 1items

Citation

Journal: J. Biol. Chem. / Year: 2018
Title: Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants.
Authors: Liou, G. / Chiang, Y.C. / Wang, Y. / Weng, J.K.

History

Deposition	Jun 28, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 17, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 19, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6dx7.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6dx7.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	6dx7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6dx7_validation.pdf.gz	336.9 KB	Display	wwPDB validaton report
Full document	6dx7_full_validation.pdf.gz	364.4 KB	Display
Data in XML	6dx7_validation.xml.gz	80.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/6dx7 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/6dx7	HTTPS FTP

-
Related structure data

Related structure data	6dx8C 6dx9C 6dxaC 6dxbC 6dxcC 6dxdC 6dxeC 6dxfC C: citing same article (ref.)
Similar structure data	3wxy-d 1u0w-2 1i86-1 4wum-1 6dxd-1 1u0u-1 6dxd-2 3wd8-2 1u0u-2 1jwx-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: Chalcone synthase

B: Chalcone synthase

C: Chalcone synthase

D: Chalcone synthase

E: Chalcone synthase

F: Chalcone synthase

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

1

A: Chalcone synthase

B: Chalcone synthase

defined by author&software
Evidence: gel filtration
85.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Chalcone synthase

D: Chalcone synthase

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

3

E: Chalcone synthase

F: Chalcone synthase

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

Unit cell

Length a, b, c (Å)	71.600, 192.830, 195.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Chalcone synthase Mass: 42629.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physcomitrella patens subsp. patens (plant) Gene: PHYPA_029015 / Plasmid: pHis8-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2VAZ3, chalcone synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.69 Å³/Da / Density % sol: 54.36 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.1 M MES (pH 6.9), 18% (v/v) PEG 20000, and 5 mM DTT

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2011
Radiation	Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.61→37.011 Å / Num. obs: 82406 / % possible obs: 98.95 % / Redundancy: 2 % / B_iso Wilson estimate: 47.99 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.03961 / R_pim(I) all: 0.03961 / R_rim(I) all: 0.05602 / Net I/σ(I): 14.31
Reflection shell	Resolution: 2.61→2.703 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.4442 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 7763 / CC_1/2: 0.747 / R_pim(I) all: 0.4442 / R_rim(I) all: 0.6282 / % possible all: 94.6

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
PHENIX	1.13_2998	refinement
PDB_EXTRACT	3.24	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.61→37.011 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2626	1967	2.39 %
R_work	0.181	80409	-
obs	0.183	82376	99 %

Solvent computation

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

Displacement parameters

B_iso max: 358.19 Å² / B_iso mean: 70.8323 Å² / B_iso min: 24.96 Å²

Refinement step

Cycle: final / Resolution: 2.61→37.011 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17592	0	0	59	17651
B_iso mean	-	-	-	58.93	-
Num. residues	-	-	-	-	2322

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.61-2.6753	0.396	121	0.3274	5403	5524	94
2.6753-2.7476	0.3729	133	0.2922	5405	5538	94
2.7476-2.8284	0.3765	141	0.2639	5575	5716	98
2.8284-2.9197	0.3715	142	0.2494	5727	5869	100
2.9197-3.024	0.3098	146	0.2421	5745	5891	100
3.024-3.145	0.3223	137	0.2393	5735	5872	100
3.145-3.288	0.3003	142	0.2318	5757	5899	100
3.288-3.4613	0.2823	140	0.1895	5771	5911	100
3.4613-3.6779	0.2502	146	0.1738	5771	5917	100
3.6779-3.9616	0.2707	145	0.162	5811	5956	100
3.9616-4.3597	0.2063	144	0.138	5805	5949	100
4.3597-4.9893	0.206	140	0.1256	5843	5983	100
4.9893-6.281	0.247	139	0.1556	5918	6057	100
6.281-37.0152	0.2176	151	0.1533	6143	6294	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	1.0788	-0.3989	0.1387	1.2497	0.0025	1.4522	-0.1007	0.1039	-0.1691	0.089	0.1605	-0.1503	0.0943	0.0607	-0.0713	0.282	0.0082	0.0415	0.3159	-0.0514	0.3884	-10.7344	65.2643	-19.3852
2	0.8324	-0.4809	0.4552	0.923	-0.1568	0.962	-0.0354	0.1233	0.0538	0.0382	0.1064	-0.1829	-0.1146	0.2412	-0.0622	0.3256	-0.0243	0.0634	0.3966	-0.0751	0.3866	-7.4697	68.5619	-19.6593
3	0.7887	0.4274	0.5465	2.0954	0.0089	1.5091	-0.1115	0.1103	0.0604	0.1934	0.0625	-0.3522	-0.5362	0.2682	-0.0566	0.3959	-0.058	-0.0145	0.3598	-0.0496	0.4054	-7.6105	82.1557	-15.7546
4	1.9421	1.1019	0.8076	1.9411	-1.0537	2.5458	0.1291	-0.0963	-0.2083	0.6308	-0.1484	-0.7311	-0.3132	0.5	-0.0863	0.4831	-0.1103	-0.0836	0.4351	-0.0986	0.4996	-1.0682	83.0451	-5.4036
5	1.1756	0.1938	0.4876	1.5025	-0.438	1.2299	-0.0589	-0.14	0.0136	0.408	0.1134	-0.2001	-0.2086	0.1878	-0.0705	0.4504	0.0447	-0.0626	0.391	-0.041	0.3369	-7.0079	75.8484	-4.3272
6	1.1986	0.0787	-0.1697	1.3688	-0.3643	0.4321	-0.1938	0.0303	0.1685	-0.0071	0.1671	0.054	-0.3113	-0.3353	-0.0434	0.5253	0.0299	0.0183	0.3355	0.0404	0.406	-25.0035	86.9807	-30.0419
7	0.204	-0.2396	-0.0631	1.8695	0.5595	0.3337	-0.2811	0.2559	-0.2572	-0.7445	0.076	0.1186	-0.1421	-0.0482	0.1103	0.9307	-0.2375	0.0154	0.6486	-0.0118	0.3925	-21.1122	68.6075	-57.9685
8	1.0729	-1.0071	-0.3343	3.1293	0.1277	1.7054	-0.2285	0.287	-0.0522	-0.347	0.22	-0.1031	-0.1577	0.2738	-0.0401	0.6028	-0.1748	0.1282	0.5532	-0.0353	0.4164	-11.3337	78.3202	-44.6626
9	2.0656	0.0236	0.0767	0.2773	0.3577	1.5056	-0.076	0.0921	0.2989	0.053	0.1876	-0.3932	-0.4654	0.1148	-0.0092	0.6762	-0.1035	0.03	0.2977	0.0191	0.3638	-13.3627	87.5393	-29.8525
10	0.3416	0.1563	0.0403	1.1973	-0.4154	1.4163	-0.0891	0.1911	0.0339	-0.1862	0.1441	-0.0177	-0.2064	-0.2545	-0.109	0.3155	-0.0427	0.0187	0.3619	0.0219	0.3449	-21.9134	77.3818	-35.4961
11	0.7328	-0.5606	-0.0384	0.8046	0.6074	1.0305	0.0868	0.1031	0.3586	-0.1299	0.1228	0.8768	-0.4585	-0.1965	-0.2345	0.5778	0.1751	0.0251	0.4651	0.0866	0.5848	-33.6188	90.022	-27.2727
12	3.5659	0.5135	-0.8492	1.4033	0.1577	1.0196	0.5149	-0.2987	-0.3038	-0.2829	-0.0865	0.068	0.0695	-0.0152	-0.2869	0.496	-0.1371	0.0083	0.4391	-0.0044	0.3544	-23.255	60.6707	-37.6063
13	0.8742	0.0542	-0.2436	1.3256	-0.386	0.3868	-0.0355	0.3276	0.0196	-0.4752	0.2329	0.5431	-0.1344	-0.5928	-0.1003	0.4884	-0.0352	-0.1196	0.6341	0.0953	0.5032	-40.6027	74.9995	-39.1339
14	1.388	0.0014	-0.3658	1.5118	-0.2385	1.6395	-0.0556	0.075	0.1332	-0.0981	0.2	0.2994	-0.5303	-0.3876	-0.1594	0.4336	0.0453	0.0125	0.521	0.0989	0.4176	-36.3094	84.4046	-37.4281
15	1.0297	-0.1665	-0.1912	1.3795	0.4077	1.2186	0.0407	0.0159	0.0495	-0.0544	-0.0421	-0.3272	0.0189	0.0871	-0.0251	0.2576	-0.0314	-0.058	0.4312	0.0518	0.4513	-57.7757	39.0908	-1.4849
16	0.572	0.1754	-0.8448	1.5836	-0.3824	1.3948	-0.0577	-0.1943	0.0097	0.3043	0.0269	-0.3057	0.1637	0.272	0.0667	0.4158	-0.0328	-0.1666	0.4804	0.0546	0.4916	-57.0444	31.4565	8.4746
17	1.0455	-0.6108	-0.2272	0.3896	0.1098	2.374	-0.0896	-0.1818	0.0415	0.4366	0.1546	-0.4599	0.6952	0.2579	-0.0515	0.7481	0.1616	-0.1646	0.5678	0.089	0.5771	-51.6302	18.5319	11.5299
18	0.5959	-0.0178	-0.2114	1.4332	0.0128	1.9881	-0.0502	-0.0355	-0.0325	0.0536	0.0555	-0.3701	0.3143	0.2684	0.018	0.4007	0.0689	-0.0768	0.4209	0.0163	0.511	-52.8528	21.1295	0.5427
19	0.5041	-0.1795	-0.0588	1.2495	0.1147	1.3673	-0.0978	-0.2113	0.172	0.4664	-0.0015	-0.1964	-0.2948	-0.1241	0.088	0.5641	-0.0203	-0.1559	0.5369	-0.0561	0.4062	3.7537	58.7708	20.0811
20	0.8411	0.7033	0.0937	1.7611	0.3494	0.084	-0.0398	-0.3	-0.0323	0.6772	-0.0728	-0.3276	-0.1829	0.1698	0.114	0.5787	0.0285	-0.2201	0.609	-0.0126	0.4087	9.8127	47.7059	25.0015
21	0.5658	0.0677	0.034	0.9457	0.4162	0.4798	-0.0706	-0.2275	0.0372	0.4041	-0.0781	-0.236	-0.0408	0.0376	0.1641	0.531	-0.0203	-0.1204	0.4798	0.0427	0.3407	4.7339	44.0548	18.4251
22	1.2523	0.2271	-0.0253	1.1695	-0.0862	0.0053	0.1087	-0.1344	-0.1744	0.4452	0.0226	-0.0598	0.1947	-0.3127	-0.0726	0.5385	-0.0983	0.0478	0.6162	-0.0124	0.3739	-9.7588	33.2973	23.2718
23	2.4807	0.8506	1.0003	0.5471	0.1744	0.5132	0.1598	-0.0201	0.0046	-0.247	-0.2179	0.0335	0.041	-0.1561	-0.0132	0.4998	-0.0306	-0.1154	0.4713	0.0256	0.396	0.4484	57.3323	2.8469
24	1.5564	0.0663	0.6175	0.9336	-0.6806	1.4215	-0.1098	-0.2377	0.0709	0.3477	-0.0492	0.4508	-0.4053	-0.5074	0.1053	0.4065	0.0826	0.0373	0.675	-0.0558	0.4284	-16.9921	51.3501	16.0174
25	0.781	0.0235	-0.0352	1.6215	0.1509	1.6754	0.0389	-0.2992	0.0316	0.663	-0.0614	0.1708	0.1314	-0.443	0.0232	0.497	-0.0706	0.0345	0.7418	-0.0421	0.3561	-12.6993	45.2788	23.3775
26	1.3221	0.3489	0.0511	1.4641	-0.0079	1.6711	-0.3922	0.2059	-0.1855	-0.2644	0.2774	0.1211	0.3319	0.1226	0.1532	0.8174	-0.1197	-0.0122	0.367	-0.0521	0.5547	-46.6478	13.2148	-39.4196
27	0.6162	0.6787	-0.1323	1.7159	-0.0283	1.2682	-0.1616	0.0805	-0.3049	-0.4141	0.179	-0.1319	0.5408	0.1094	0.0392	0.6397	0.0177	0.0577	0.3565	-0.0616	0.5468	-43.1238	13.303	-35.4447
28	2.6818	-1.2536	-0.0156	0.6232	-0.0478	0.534	-0.1015	-0.6257	0.9046	-0.0026	0.1801	-0.0461	-0.0283	0.0409	-0.0825	0.4345	0.085	0.0229	0.392	-0.0501	0.5578	-46.9425	24.1913	-20.2318
29	0.5148	-0.1589	-0.5092	0.9271	-0.0288	0.7263	0.0646	-0.228	-0.0023	-0.4723	0.1104	0.5933	0.2618	-0.5217	-0.0657	0.4761	-0.1228	-0.1193	0.5418	0.0139	0.7266	-66.1638	20.9228	-33.9212
30	0.9787	-0.3017	0.4357	1.3273	0.1719	1.4938	-0.1599	0.1735	-0.2633	-0.3942	0.1209	0.4339	0.7039	-0.3596	0.0379	0.7206	-0.1784	-0.0591	0.4363	0.0037	0.633	-60.9627	11.1589	-36.3951
31	1.0005	0.7532	-0.4097	1.4711	-0.3171	0.7947	-0.4153	0.1466	0.0244	-0.3958	0.3135	-0.0129	-0.3112	0.2687	-0.141	0.4941	-0.0552	-0.0828	0.4031	-0.0534	0.4396	-36.7012	39.5448	-39.093
32	1.0736	1.0924	-0.2679	1.2881	-0.3947	1.4171	-0.114	-0.2284	-0.2261	-0.0493	-0.1367	-0.3291	0.0093	0.5333	0.191	0.3017	0.0385	-0.0226	0.5303	0.0033	0.5267	-24.721	38.7556	-27.2939
33	1.1536	0.4029	0.0125	1.6784	-0.3947	1.0012	-0.2114	0.0357	-0.0249	-0.4952	0.2222	-0.0095	0.054	0.0626	0.05	0.4172	-0.0616	-0.0307	0.3518	-0.0328	0.417	-40.4447	36.2173	-39.6271
34	1.2009	0.1638	0.5033	1.1111	0.4377	3.5819	-0.4003	-0.0779	-0.736	-0.383	0.0747	-0.6113	0.4718	0.6483	0.0767	0.5591	0.1048	0.0487	0.5697	-0.0871	0.798	-22.1036	23.3212	-38.9614
35	4.7211	0.0816	1.4676	1.1748	0.4299	2.5968	-0.5571	0.5925	-0.4684	-1.2761	0.3396	-0.4845	-0.0712	0.1242	0.1123	1.1742	-0.2178	0.3058	0.5479	-0.0709	0.6084	-27.1543	31.6831	-59.1038
36	1.7847	0.0851	-1.1414	2.0837	0.1593	0.7522	-0.212	0.4211	0.15	-0.6996	0.0718	-0.382	-0.1893	0.4913	0.0813	0.7878	-0.2077	0.1331	0.6192	-0.1171	0.4118	-24.7695	40.501	-55.5482
37	1.0579	0.4421	-0.2212	1.375	-0.3923	1.0401	-0.3235	0.2707	0.0968	-0.6242	0.1906	-0.1313	-0.0025	0.1118	0.1058	0.6177	-0.1499	-0.0047	0.444	-0.0252	0.3944	-30.4835	45.0044	-50.2965

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 9 through 185 )	A	9 - 185
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 186 through 232 )	A	186 - 232
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 233 through 296 )	A	233 - 296
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 297 through 323 )	A	297 - 323
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 324 through 395 )	A	324 - 395
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 9 through 41 )	B	9 - 41
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 42 through 79 )	B	42 - 79
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 80 through 123 )	B	80 - 123
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 124 through 160 )	B	124 - 160
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 161 through 232 )	B	161 - 232
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 233 through 252 )	B	233 - 252
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 253 through 276 )	B	253 - 276
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 277 through 343 )	B	277 - 343
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 344 through 395 )	B	344 - 395
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 9 through 232 )	C	9 - 232
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 233 through 276 )	C	233 - 276
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 277 through 312 )	C	277 - 312
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 313 through 395 )	C	313 - 395
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 9 through 96 )	D	9 - 96
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 97 through 123 )	D	97 - 123
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 124 through 231 )	D	124 - 231
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 232 through 252 )	D	232 - 252
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 253 through 276 )	D	253 - 276
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 277 through 343 )	D	277 - 343
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 344 through 395 )	D	344 - 395
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 9 through 49 )	E	9 - 49
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 50 through 252 )	E	50 - 252
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 253 through 276 )	E	253 - 276
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 277 through 312 )	E	277 - 312
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 313 through 395 )	E	313 - 395
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 9 through 49 )	F	9 - 49
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 50 through 123 )	F	50 - 123
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 124 through 252 )	F	124 - 252
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 253 through 276 )	F	253 - 276
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 277 through 296 )	F	277 - 296
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 297 through 322 )	F	297 - 322
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 323 through 395 )	F	323 - 395

-
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