PDB-8s2r: BzdNO in partially coenzyme A - free state

ID or keywords:

Entry

Database: PDB / ID: 8s2r

Title

BzdNO in partially coenzyme A - free state

Components

BzdN
BzdO

Keywords

OXIDOREDUCTASE / Benzoyl-CoA reductase / reductive dearomatization / iron-sulfur clusters

Function / homology

Function and homology information

iron-sulfur cluster binding / metal ion binding
Similarity search - Function

Biological species

Azoarcus sp. CIB (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Ermler, U. / Boll, M. / Fuchs, J. / Demmer, U.

Funding support

1items

Citation

Journal: To Be Published
Title: X-ray structure of the BzdNO-benzoyl-CoA complex
Authors: Ermler, U. / Boll, M. / Fuchs, J. / Demmer, U.

History

Deposition	Feb 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8s2r.cif.gz	671.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2r.ent.gz	554 KB	Display	PDB format
PDBx/mmJSON format	8s2r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2r ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2r	HTTPS FTP

-
Related structure data

Related structure data	8s02C 8s1tC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: BzdO

B: BzdN

C: BzdO

D: BzdN

hetero molecules

194 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: BzdO

B: BzdN

hetero molecules

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

2

C: BzdO

D: BzdN

hetero molecules

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

Unit cell

Length a, b, c (Å)	208.170, 102.710, 86.900
Angle α, β, γ (deg.)	90.00, 102.48, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-810- HOH

-
Protein , 2 types, 4 molecules ACBD

#1: Protein	BzdO Mass: 51272.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdO / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q68VL9
#2: Protein	BzdN Mass: 43482.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Azoarcus sp. CIB (bacteria) / Gene: bzdN / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q68VM0

-
Non-polymers , 6 types, 804 molecules

#3: Chemical	ChemComp-BYC / benzoyl coenzyme A Mass: 871.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₄₀N₇O₁₇P₃S
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe₄S₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-BJ8 / Double cubane cluster Mass: 735.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₈S₉
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H₂O / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: PEG 3350, bis-tris propane pH 7.5, sodium formate or sodium acetate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 6, 2023

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 201996 / % possible obs: 86.1 % / Redundancy: 3.4 % / CC_1/2: 0.996 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.075 / Net I/σ(I): 10.48

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.6-1.7	0.477	16309	0.735	0.612	1
1.7-1.9	0.29	45741	0.921	0.35	1
1.9-2.3	0.133	60843	0.984	0.156	1
2.3-2.9	0.072	39513	0.992	0.084	1
2.9-3.8	0.053	21864	0.994	0.062	1
3.8-4.6	0.049	7680	0.994	0.057	1
4.6-5.7	0.049	4728	0.993	0.057	1
5.7-8	0.052	3367	0.992	0.062	1
8-12	0.048	1365	0.996	0.056	1
12-50	0.048	586	0.997	0.057	1

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.6→48.45 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2111	10116	5.01 %
R_work	0.1832	-	-
obs	0.1846	201898	86.09 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.6→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13031	0	198	791	14020

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016
X-RAY DIFFRACTION	f_angle_d	1.959
X-RAY DIFFRACTION	f_dihedral_angle_d	6.626	1868
X-RAY DIFFRACTION	f_chiral_restr	0.083	1908
X-RAY DIFFRACTION	f_plane_restr	0.013	2410

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 (%)
1.6-1.62	0.7775	50	0.6612	1181	X-RAY DIFFRACTION	16
1.62-1.64	0.4698	141	0.4393	2646	X-RAY DIFFRACTION	36
1.64-1.66	0.356	184	0.3351	3523	X-RAY DIFFRACTION	47
1.66-1.68	0.3536	187	0.3007	3973	X-RAY DIFFRACTION	53
1.68-1.7	0.3043	235	0.2728	4285	X-RAY DIFFRACTION	58
1.7-1.72	0.2937	249	0.2519	4619	X-RAY DIFFRACTION	63
1.72-1.75	0.2736	259	0.2368	5088	X-RAY DIFFRACTION	68
1.75-1.77	0.3102	301	0.2256	5547	X-RAY DIFFRACTION	75
1.77-1.8	0.244	313	0.2171	6037	X-RAY DIFFRACTION	82
1.8-1.83	0.2463	348	0.2039	6657	X-RAY DIFFRACTION	90
1.83-1.86	0.2231	384	0.1895	7373	X-RAY DIFFRACTION	99
1.86-1.9	0.2338	400	0.2014	7431	X-RAY DIFFRACTION	100
1.9-1.93	0.2093	415	0.1959	7376	X-RAY DIFFRACTION	100
1.93-1.97	0.2361	390	0.1909	7395	X-RAY DIFFRACTION	100
1.97-2.02	0.2283	412	0.1842	7361	X-RAY DIFFRACTION	100
2.02-2.06	0.212	394	0.1776	7357	X-RAY DIFFRACTION	100
2.06-2.11	0.2192	388	0.1741	7373	X-RAY DIFFRACTION	100
2.11-2.17	0.2054	406	0.1682	7414	X-RAY DIFFRACTION	100
2.17-2.24	0.2079	416	0.1694	7359	X-RAY DIFFRACTION	100
2.24-2.31	0.1966	363	0.1675	7395	X-RAY DIFFRACTION	99
2.31-2.39	0.2043	402	0.1772	7388	X-RAY DIFFRACTION	100
2.39-2.49	0.2224	374	0.1856	7413	X-RAY DIFFRACTION	100
2.49-2.6	0.2209	398	0.1755	7380	X-RAY DIFFRACTION	100
2.6-2.74	0.2175	399	0.1799	7419	X-RAY DIFFRACTION	100
2.74-2.91	0.2245	408	0.1923	7446	X-RAY DIFFRACTION	100
2.91-3.13	0.265	353	0.2012	7423	X-RAY DIFFRACTION	100
3.13-3.45	0.2099	366	0.1938	7452	X-RAY DIFFRACTION	99
3.45-3.95	0.1803	390	0.1696	7439	X-RAY DIFFRACTION	100
3.95-4.97	0.1753	393	0.1529	7470	X-RAY DIFFRACTION	100
4.97-48.45	0.1854	398	0.1814	7562	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.4054	-1.2146	1.1548	3.3898	-2.0467	3.8055	0.0593	0.2715	-0.1935	-0.6073	0.1202	0.1364	0.4252	-0.2128	-0.1214	0.2649	-0.0555	0.0241	0.2656	-0.0363	0.1948	32.0108	-4.0374	-7.4706
2	2.3075	-0.8729	-0.1188	2.4739	0.4187	0.555	-0.0152	0.0365	-0.198	-0.1801	0.0197	-0.1261	-0.0565	0.0922	-0.0339	0.1897	0.0016	0.0237	0.2087	-0.0127	0.2133	43.2278	-7.9742	11.2912
3	0.5042	0.5572	0.0551	1.6276	0.2226	0.5866	0.0206	0.0217	-0.0731	0.0033	-0.0086	-0.0277	0.0507	0.0038	0.0013	0.1816	0.0092	-0.012	0.1856	-0.0042	0.2071	28.6063	-10.827	15.8565
4	1.2875	-1.3195	-0.6638	1.9715	0.9278	1.191	-0.0447	-0.1129	0.0835	0.0485	0.0552	-0.2428	0.0103	0.2078	-0.0315	0.1689	-0.0081	0.0031	0.2454	0.0041	0.2212	44.6215	1.7583	23.3156
5	2.9264	-1.0839	2.1416	0.8642	-0.7214	2.0271	-0.0685	0.1433	0.0463	-0.0269	0.0322	-0.0903	-0.0853	0.1287	0.0886	0.2291	-0.0171	0.0307	0.211	0.0071	0.2094	39.8745	8.0906	4.3625
6	1.4749	-0.9529	1.7077	1.4326	-1.6125	2.2903	-0.0134	-0.1127	-0.1338	-0.1298	0.1592	0.1124	-0.0443	-0.2228	-0.1123	0.282	0.0109	0.0389	0.2636	0.0074	0.2411	28.2103	2.7101	-2.0339
7	1.3731	-0.5761	0.3056	0.6448	0.0508	0.5851	0.0396	0.2088	0.0678	-0.1536	-0.0726	-0.0368	-0.0806	0.0601	0.0466	0.3378	-0.0232	0.0235	0.2643	0.0032	0.1957	27.8058	6.6333	-6.7881
8	0.9045	-0.6902	0.4535	0.7248	-0.287	1.695	0.0009	0.1278	0.0052	-0.0861	-0.0518	-0.065	-0.0349	-0.051	0.0609	0.2004	-0.0026	0.0315	0.1749	0.0047	0.1762	30.279	9.3724	5.2408
9	0.5444	0.0325	0.2326	0.5061	0.0345	0.8256	-0.0377	0.0069	0.0846	-0.045	-0.0108	0.075	0.0156	-0.0478	0.044	0.2065	0.01	-0.0073	0.221	-0.0154	0.2373	16.2765	9.6647	10.4581
10	2.0124	-0.7274	0.6345	1.7626	-1.0881	1.4863	0.0128	0.1193	-0.0038	-0.1095	0.0943	0.2126	0.0533	-0.1089	-0.1129	0.1719	-0.0148	-0.0262	0.24	-0.0376	0.2197	5.3912	3.5823	-0.2184
11	1.1534	-0.9367	0.516	2.9703	-1.3769	2.2868	-0.0679	-0.1569	-0.0013	0.2666	0.2633	0.5976	0.0154	-0.5336	-0.1848	0.2283	0.0295	0.0397	0.4069	-0.0234	0.257	2.5991	8.3629	49.1997
12	1.3027	0.5947	0.5116	0.8692	-0.0431	1.1469	-0.0618	-0.0195	0.1242	-0.0394	-0.0541	0.2377	-0.0312	-0.1682	0.0925	0.2504	0.023	0.0188	0.2462	-0.0194	0.2437	11.8718	9.8163	37.9305
13	0.5969	-0.228	0.1145	0.5138	-0.012	0.715	-0.0221	0.0067	-0.0222	-0.0086	-0.0094	0.1214	-0.0209	-0.1499	0.026	0.2143	0.02	0.0078	0.2265	-0.0121	0.2294	13.4772	8.3555	28.4851
14	1.7171	-0.4381	0.4324	1.7403	-0.4373	1.1326	0.0003	-0.0136	0.2421	0.2156	-0.0572	-0.1098	-0.2919	-0	0.0062	0.2539	-0.0063	-0.0129	0.2043	-0.0077	0.2047	27.6713	18.7714	38.5
15	1.0949	0.1609	-0.2637	1.6574	-0.3588	1.2094	-0.0233	-0.1077	-0.0341	0.242	0.0264	0.1034	0.1159	-0.1439	0.0135	0.2852	-0.0052	0.0353	0.2763	-0.0221	0.1699	16.1119	0.4303	51.7472
16	0.7003	-0.3012	-0.1093	1.5843	1.2324	1.8753	-0.0564	-0.2347	-0.0518	0.2447	0.0184	0.088	0.0104	-0.2705	0.019	0.2994	0.0056	0.0498	0.3302	0.0144	0.2066	10.2148	-4.7627	53.3181
17	0.5368	0.2505	0.3624	1.2274	0.6652	0.7723	0.0133	-0.0446	-0.1117	0.1225	-0.0057	0.0924	0.1572	-0.0757	0.0005	0.268	-0.003	0.012	0.2155	0.0161	0.2085	20.5013	-8.4093	39.3632
18	3.2652	0.7963	-0.3405	1.287	0.1387	2.5164	0.0899	0.0418	-0.0164	-0.077	-0.0081	0.4585	0.5501	-0.4661	-0.1135	0.3364	-0.085	0.0192	0.3114	0.0109	0.3793	6.1528	-20.0734	36.1382
19	3.12	2.4932	-1.9532	3.3614	-1.659	1.8424	0.0872	-0.1555	0.2717	0.5967	0.0967	0.3004	-0.1904	-0.2649	-0.1713	0.3751	0.0317	0.042	0.3351	-0.014	0.2276	21.7399	-46.5327	40.5766
20	0.5515	-0.2905	-0.1141	1.1409	-0.1377	0.6961	-0.0164	-0.0465	0.0629	0.0523	0.0158	-0.0165	-0.0291	-0.045	0.0153	0.2021	0.0006	-0.0104	0.1804	-0.0053	0.2125	30.2882	-40.3217	20.1928
21	0.8408	0.8189	0.3791	1.8162	0.9601	1.4761	0.0039	-0.0332	-0.0407	0.0306	-0.0393	-0.0824	-0.0411	0.1021	-0.0333	0.2152	0.0247	-0.0063	0.2419	0.004	0.2212	45.7466	-52.5186	18.1835
22	1.9202	0.5145	-0.8782	1.1039	-0.1971	0.9828	-0.1105	-0.0622	0.0484	0.2055	0.0815	0.1447	0.1184	-0.1319	0.0152	0.3501	0.0041	0.0196	0.2101	0.01	0.1807	26.9134	-56.47	33.6563
23	1.7604	0.4496	-0.0915	0.6221	0.3716	0.7289	-0.0319	-0.2401	-0.0733	0.1572	-0.0229	0.0885	0.0615	-0.1022	0.0469	0.4493	0.0178	0.0752	0.2736	0.0172	0.2306	17.6661	-57.408	38.2009
24	1.3738	0.2962	-0.1281	2.2143	0.0876	1.6854	-0.0072	-0.0087	0.2237	0.2422	-0.0568	0.4424	-0.1735	-0.4379	0.0403	0.3079	0.0386	0.0618	0.2833	-0.0092	0.3071	12.4026	-54.2258	29.6725
25	1.7509	1.3157	-1.1341	1.4365	-0.5437	0.9352	-0.0008	-0.1808	-0.4324	0.1862	-0.0775	-0.2401	0.1259	0.1033	0.0562	0.3032	0.03	-0.0066	0.2328	0.0299	0.2893	37.0682	-65.7123	27.2204
26	1.0472	0.205	-0.3523	0.6289	-0.1092	0.9646	-0.0288	0.0976	-0.0614	0.0576	0.0188	0.1073	0.0681	-0.2007	0.0248	0.2504	-0.0291	0.0107	0.259	-0.0115	0.2602	14.9466	-60.2452	17.8089
27	1.6122	0.7047	0.1283	3.5632	-0.4511	0.4568	0.0252	-0.1755	0.2361	0.3779	0.0021	0.989	-0.1144	-0.5208	-0.0802	0.3357	-0.0342	0.0897	0.4974	-0.0544	0.5229	1.7781	-50.3664	22.3169
28	2.0439	1.0198	-1.1111	4.2627	-1.0933	2.0813	-0.0998	0.4579	0.0152	-0.8294	0.2567	0.4768	0.211	-0.7007	-0.1525	0.3374	-0.0318	-0.0715	0.5247	-0.0366	0.2606	19.099	-58.7215	-23.3542
29	0.4103	-0.1021	-0.1788	0.6937	0.0194	0.8462	0.0124	0.125	-0.0633	-0.084	-0.0293	0.0924	0.0235	-0.1713	0.0134	0.2261	-0.0138	-0.01	0.2389	-0.0184	0.212	25.8342	-58.7752	-7.0822
30	1.0911	-0.364	-0.4173	1.4003	0.8059	1.8175	0.0688	0.3902	0.0546	-0.2095	-0.1116	0.0364	-0.2138	-0.3358	0.032	0.3885	0.0263	-0.0043	0.3671	0.036	0.2317	27.2696	-45.0117	-23.5227
31	0.5269	-0.3128	-0.4685	0.9876	0.2108	0.8719	0.0762	0.1336	0.0871	-0.1696	-0.0248	0.0241	-0.1616	-0.1385	-0.0449	0.2787	0.009	-0.0017	0.2466	0.0178	0.2324	31.3316	-43.9959	-8.3114
32	2.8438	-0.8166	0.8319	1.6885	-0.7784	2.7093	0.1418	0.1437	0.2576	-0.0919	0.0555	0.378	-0.4182	-0.3804	-0.1552	0.3868	0.0878	0.0072	0.2893	0.0178	0.3342	20.8133	-31.8411	-5.9791

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 58 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 59 through 160 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 161 through 187 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 188 through 213 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 214 through 237 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 238 through 276 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 277 through 343 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 344 through 397 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 398 through 442 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2 through 27 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 28 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 133 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 134 through 158 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 159 through 206 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 207 through 243 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 244 through 344 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 345 through 376 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 6 through 31 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 32 through 160 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 161 through 187 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 188 through 237 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 238 through 276 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 277 through 308 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 309 through 343 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 344 through 396 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 397 through 434 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 2 through 27 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 28 through 206 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 207 through 243 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 244 through 327 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 328 through 376 )

-
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

-
Protein , 2 types, 4 molecules ACBD

-
Non-polymers , 6 types, 804 molecules

-
Details

-
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

-Protein , 2 types, 4 molecules ACBD

-Non-polymers , 6 types, 804 molecules

-Details

-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

-
Protein , 2 types, 4 molecules ACBD

-
Non-polymers , 6 types, 804 molecules

-
Details

-
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