PDB-5vn2: Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase f...

ID or keywords:

Entry

Database: PDB / ID: 5vn2

Title

Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis in complex with NAD

Components

3-oxoacyl-(Acyl-carrier protein) reductase

Keywords

OXIDOREDUCTASE / SDR / short chain dehydrogenase reductase /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity
Similarity search - Function

Biological species

Brucella melitensis biotype 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis in complex with NAD
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Apr 28, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 31, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5vn2.cif.gz	406.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5vn2.ent.gz	333.5 KB	Display	PDB format
PDBx/mmJSON format	5vn2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vn/5vn2 ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vn2	HTTPS FTP

-
Related structure data

Related structure data	4oneS S: Starting model for refinement
Similar structure data	4bnf-1 4bnh-1 2qio-d 4bng-1 4bni-1 4all-d 3k2e-1 4bnj-2 6tbb-2 6oz7-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BrmeA.00010.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (4) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: 3-oxoacyl-(Acyl-carrier protein) reductase

B: 3-oxoacyl-(Acyl-carrier protein) reductase

C: 3-oxoacyl-(Acyl-carrier protein) reductase

D: 3-oxoacyl-(Acyl-carrier protein) reductase

hetero molecules

114 kDa, 4 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)	74.560, 92.710, 129.910
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	3-oxoacyl-(Acyl-carrier protein) reductase Mass: 27733.045 Da / Num. of mol.: 4 / Fragment: residues 47-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria) Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0026 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8YJQ6, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.03 Å³/Da / Density % sol: 39.3 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 F5 (273386f5): 20% PEG3350, 20mM Sodium acetate, 4mM NAD, protein conc. 19.9mg/mL, cryo 15% ethylene glycol: unique puck ID: jif2-4

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2016

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 71305 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.407 % / B_iso Wilson estimate: 21 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.081 / Χ²: 0.976 / Net I/σ(I): 17.22

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.9-1.95	5.407	0.557	2.99	5232	0.858	0.617	99.9
1.95-2	5.414	0.441	3.74	5089	0.905	0.489	99.9
2-2.06	5.404	0.356	4.6	4969	0.936	0.394	99.9
2.06-2.12	5.435	0.28	5.75	4828	0.958	0.31	100
2.12-2.19	5.418	0.226	7.02	4663	0.972	0.251	99.9
2.19-2.27	5.418	0.201	7.83	4533	0.977	0.223	99.8
2.27-2.36	5.437	0.158	9.82	4356	0.986	0.175	99.8
2.36-2.45	5.433	0.138	11.2	4209	0.989	0.152	99.8
2.45-2.56	5.436	0.118	13.04	4051	0.991	0.13	99.8
2.56-2.69	5.437	0.104	14.74	3845	0.993	0.115	99.8
2.69-2.83	5.43	0.087	17.26	3726	0.995	0.096	99.7
2.83-3	5.425	0.069	21.25	3475	0.996	0.076	99.7
3-3.21	5.434	0.056	25.73	3282	0.998	0.061	99.5
3.21-3.47	5.421	0.043	31.95	3069	0.998	0.048	99.4
3.47-3.8	5.413	0.034	38.41	2824	0.999	0.038	99.3
3.8-4.25	5.406	0.029	44.73	2559	0.999	0.032	98.7
4.25-4.91	5.38	0.025	50.09	2272	0.999	0.028	98.8
4.91-6.01	5.314	0.026	47.15	1947	0.999	0.029	98.6
6.01-8.5	5.235	0.025	50.15	1518	0.999	0.027	97.6
8.5-50	4.783	0.02	57.84	858	1	0.022	94.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
Coot		model building
PHENIX	(dev_2744)	refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4one

4one

Resolution: 1.9→50 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.42

	R_factor	Num. reflection	% reflection
R_free	0.1983	1965	2.76 %
R_work	0.1499	-	-
obs	0.1512	71283	99.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 97.32 Å² / B_iso mean: 29.2548 Å² / B_iso min: 9.24 Å²

Refinement step

Cycle: final / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7388	0	196	793	8377
B_iso mean	-	-	23.97	35.55	-
Num. residues	-	-	-	-	1018

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7814
X-RAY DIFFRACTION	f_angle_d	0.773	10619
X-RAY DIFFRACTION	f_chiral_restr	0.054	1258
X-RAY DIFFRACTION	f_plane_restr	0.005	1446
X-RAY DIFFRACTION	f_dihedral_angle_d	14.274	4679

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 (%)
1.9-1.9475	0.2798	154	0.2332	4877	5031	100
1.9475-2.0001	0.2516	147	0.2119	4909	5056	100
2.0001-2.059	0.2547	147	0.1941	4889	5036	100
2.059-2.1255	0.2222	144	0.1747	4922	5066	100
2.1255-2.2014	0.1989	136	0.1647	4930	5066	100
2.2014-2.2896	0.2204	134	0.1617	4915	5049	100
2.2896-2.3938	0.2171	124	0.1539	4924	5048	100
2.3938-2.52	0.2105	152	0.1547	4916	5068	100
2.52-2.6778	0.2126	157	0.1535	4938	5095	100
2.6778-2.8846	0.2013	141	0.1504	4971	5112	100
2.8846-3.1748	0.2061	147	0.1502	4947	5094	100
3.1748-3.6341	0.1682	125	0.1338	5003	5128	99
3.6341-4.578	0.1781	125	0.1187	5025	5150	99
4.578-48.9925	0.1531	132	0.1375	5152	5284	97

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	3.7766	-0.595	-0.5665	1.4808	-1.1995	2.2947	0.0128	-0.1629	0.1478	0.0327	0.0098	0.0648	0.0293	-0.5901	0.0178	0.1162	0.0187	-0.0246	0.2612	-0.0713	0.1801	-11.2554	-16.2757	19.5991
2	7.1754	1.4282	-2.1163	1.7422	-1.2366	3.9151	-0.1053	0.0786	-0.0435	-0.0415	0.046	0.1998	0.1096	-0.6113	0.0631	0.1319	0.0242	-0.0411	0.269	-0.0516	0.1905	-14.8024	-16.8768	14.0894
3	5.2794	-1.1728	-0.4394	0.9451	0.3208	1.1395	-0.0224	0.2027	0.2029	-0.0909	-0.0136	0.0942	-0.1029	-0.1338	0.0469	0.1731	-0.0039	-0.0508	0.1061	-0.0154	0.1631	-0.441	-13.1821	11.661
4	5.711	-4.1691	-2.2577	5.1325	2.8317	3.2941	-0.0889	0.178	0.1192	-0.1835	-0.0501	0.2089	-0.2831	-0.0804	0.1062	0.1506	0.0106	-0.0578	0.0985	-0.0023	0.179	4.7525	-10.3639	11.3227
5	2.4107	-0.2872	-0.4005	0.9914	0.5082	1.8481	-0.0623	-0.1315	0.2259	0.0332	-0.0995	0.2221	-0.1956	-0.2015	0.0883	0.1477	0.0298	-0.0322	0.1185	-0.0596	0.2031	5.1768	-11.3352	23.2624
6	2.4679	-0.3082	-0.0047	3.9972	-0.5951	5.2277	-0.2084	-0.0268	-0.8903	-0.3612	-0.103	0.0914	1.1362	-0.2813	0.0911	0.3629	-0.0412	0.0523	0.1983	0.0167	0.4117	3.1045	-33.9475	24.7233
7	0.6973	0.5485	0.5194	0.6745	-0.0531	1.2215	-0.026	-0.3862	0.108	0.0145	0.0012	0.1594	-0.0609	-0.3056	0.0349	0.1479	0.0044	0.021	0.2155	-0.0531	0.1568	2.453	-17.7283	32.1768
8	3.5468	-0.5728	-0.7701	3.9636	0.5465	3.6621	-0.0785	0.2948	0.0982	-0.2217	0.0823	-0.2259	-0.1092	0.5063	-0.0193	0.1169	-0.0771	0.002	0.2111	0.0201	0.1344	41.7311	-12.3839	8.5713
9	5.0796	1.2339	1.7114	2.5553	0.2441	1.8303	-0.0463	0.3068	0.3298	-0.0817	-0.1078	-0.4165	-0.3647	0.4046	0.1338	0.2268	-0.0842	-0.0117	0.3601	0.0928	0.1939	41.1845	-8.0152	2.8803
10	3.6614	-1.1129	-0.4771	1.3665	0.3199	1.1221	-0.0605	0.3383	0.2141	-0.0797	0.0288	-0.0045	-0.1859	0.0576	-0.0009	0.1495	-0.0318	-0.0311	0.1117	0.0144	0.1206	24.3471	-12.7816	6.6017
11	3.3083	-0.5596	0.2267	1.6068	0.3145	1.7959	-0.0397	-0.0741	0.0174	0.045	-0.0081	-0.0375	-0.0327	0.0907	0.0449	0.1059	-0.0317	-0.0145	0.0878	0.0126	0.1004	26.5254	-16.5655	18.029
12	1.1323	0.4325	-0.2547	2.1814	0.5021	1.2734	0.0149	-0.0901	0.3234	-0.0147	-0.015	0.0604	-0.3305	0.1395	0.0005	0.2078	-0.0422	-0.0453	0.145	-0.019	0.2008	31.2078	-3.2143	25.223
13	3.0644	-0.5139	-2.1945	2.4967	-2.8782	6.6475	-0.1022	-0.4277	0.0471	0.3324	0.0871	0.2681	0.2076	-0.6569	-0.0209	0.2413	0.0383	0.0482	0.5192	-0.0667	0.1816	-5.8941	-19.5803	56.1145
14	0.8035	-0.349	-0.989	0.556	0.4712	1.235	-0.0529	-0.6933	0.3076	0.1729	-0.1113	0.1611	-0.4511	-0.6252	0.0748	0.3517	0.056	0.0345	0.5688	-0.1443	0.2572	-4.1642	-12.0796	57.8739
15	5.1516	1.4092	0.0631	1.0096	0.2622	1.404	0.0359	-0.5828	0.0099	0.1805	-0.0783	0.0187	-0.0894	-0.0745	0.0667	0.2458	-0.0046	0.013	0.3566	-0.0496	0.1238	9.7547	-16.5716	57.0295
16	1.7165	-0.2486	0.263	0.6405	0.0491	2.2351	0.0252	-0.3992	0.0938	0.1192	-0.1022	0.0602	-0.1337	-0.0499	0.0675	0.1742	0.0028	0.0074	0.2636	-0.0233	0.1211	11.1272	-16.7373	48.588
17	1.7408	0.1998	-0.4676	2.403	-0.7509	1.0852	0.0254	-0.1759	0.3629	0.2545	-0.0319	0.0524	-0.2773	-0.1019	0.0136	0.2344	0.0435	-0.0344	0.2491	-0.0836	0.2182	5.5208	-4.8949	38.6302
18	3.8375	-0.0609	0.7793	3.392	0.1354	4.3302	0.114	-0.5172	-0.217	0.0722	-0.2346	-0.3056	0.0273	0.6938	0.1275	0.1548	0.0477	-0.0317	0.5711	0.1028	0.2131	47.8012	-20.4802	41.6141
19	2.0313	-2.6911	-1.1011	3.9713	1.1685	4.8358	-0.0053	-0.541	-1.1985	0.5149	-0.0833	-0.3588	0.4621	1.2646	0.0804	0.3806	0.0504	-0.058	0.632	0.1089	0.703	52.0093	-27.7843	47.0896
20	2.8628	0.4986	-0.5052	0.9248	-1.0978	1.2982	0.0124	-0.6663	0.1176	0.262	-0.1552	-0.197	-0.338	0.5635	0.1114	0.2613	-0.0476	-0.0591	0.6037	0.0063	0.2229	45.8532	-15.2654	51.2625
21	4.8085	1.5637	-1.4594	0.6483	-0.102	1.4847	0.0567	-0.354	-0.7928	0.1027	0.0055	-0.0431	0.2883	0.2485	0.0063	0.3	0.0284	0.003	0.3674	0.1719	0.3255	22.7729	-31.2569	50.6248
22	1.6233	-0.0945	-0.1278	0.4608	-0.113	1.6311	0.0309	-0.3834	-0.0292	0.1156	-0.0828	-0.0662	-0.1014	0.2458	0.0558	0.1728	-0.0088	-0.0235	0.2674	0.014	0.1282	31.5406	-16.4514	44.2099
23	4.6155	-0.9571	0.7337	3.41	-2.837	3.3767	0.1519	-0.1177	-0.7565	0.0403	-0.1876	0.0212	1.5108	0.103	-0.0537	0.4181	0.0797	0.0837	0.2283	0.046	0.3471	29.3664	-38.7381	36.7976
24	1.61	-0.6448	-0.0021	0.8354	-0.1043	1.6875	-0.0779	-0.1033	-0.2572	-0.0603	0.0189	-0.0702	0.1716	0.2991	0.0504	0.1623	0.0411	-0.0003	0.1824	0.0359	0.1419	33.0914	-23.0542	29.609

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 3 through 40 )	A	3 - 40
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 63 )	A	41 - 63
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 102 )	A	64 - 102
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 103 through 130 )	A	103 - 130
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 131 through 188 )	A	131 - 188
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 189 through 219 )	A	189 - 219
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 220 through 254 )	A	220 - 254
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 40 )	B	0 - 40
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 41 through 63 )	B	41 - 63
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 64 through 130 )	B	64 - 130
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 131 through 188 )	B	131 - 188
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 189 through 254 )	B	189 - 254
13	X-RAY DIFFRACTION	13	chain 'C' and (resid -4 through 15 )	C	-4 - 15
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 16 through 63 )	C	16 - 63
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 64 through 102 )	C	64 - 102
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 103 through 199 )	C	103 - 199
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 200 through 254 )	C	200 - 254
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 2 through 36 )	D	2 - 36
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 37 through 50 )	D	37 - 50
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 51 through 86 )	D	51 - 86
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 87 through 102 )	D	87 - 102
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 103 through 193 )	D	103 - 193
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 194 through 209 )	D	194 - 209
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 210 through 254 )	D	210 - 254

-
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

-
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