PDB-8soq: S127A variant of LarB, a carboxylase/hydrolase involved in synthe...

ID or keywords:

Entry

Database: PDB / ID: 8soq

Title

S127A variant of LarB, a carboxylase/hydrolase involved in synthesis of the cofactor for lactate racemase, in complex with authentic substrate NaAD

Components

Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

Keywords

LYASE /

Carboxylase /

Hydrolase / LYASE (CARBON-CARBON)

Function / homology

Function and homology information

pyridinium-3,5-biscarboxylic acid mononucleotide synthase / 'de novo' IMP biosynthetic process /

transferase activity /

hydrolase activity /

plasma membrane
Similarity search - Function

Biological species

Lactiplantibacillus plantarum WCFS1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Chatterjee, S. / Rankin, J.A. / Hu, J. / Hausinger, R.P.

Funding support

United States, 2items

Organization	Grant number	Country
National Science Foundation (NSF, United States)	CHE-1807073	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM128959	United States

Citation

Journal: Biochemistry / Year: 2023
Title: Structure of the LarB-Substrate Complex and Identification of a Reaction Intermediate during Nickel-Pincer Nucleotide Cofactor Biosynthesis.
Authors: Chatterjee, S. / Nevarez, J.L. / Rankin, J.A. / Hu, J. / Hausinger, R.P.

History

Deposition	Apr 29, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8soq.cif.gz	441.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8soq.ent.gz	364.4 KB	Display	PDB format
PDBx/mmJSON format	8soq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	8stdC 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: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

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

1

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

A: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

B: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

defined by author&software
Evidence: gel filtration
218 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

C: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

D: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

defined by author&software
218 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

E: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

F: Pyridinium-3,5-biscarboxylic acid mononucleotide synthase

hetero molecules

defined by author&software
215 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.910, 120.910, 212.640
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

#1: Protein	Pyridinium-3,5-biscarboxylic acid mononucleotide synthase / P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB ...P2CMN synthase / Lactate racemase accessory protein LarB / Lactate racemase activation protein LarB / Lactate racemase maturation protein LarB / Lactate racemization operon protein LarB / Nickel-pincer cofactor biosynthesis protein LarB / Nicotinic acid adenine dinucleotide carboxylase/hydrolase / NaAD carboxylase/hydrolase Mass: 26494.227 Da / Num. of mol.: 6 / Mutation: S127A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactiplantibacillus plantarum WCFS1 (bacteria) Strain: ATCC BAA-793 / NCIMB 8826 / WCFS1 / Gene: larB, lp_0105 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: F9UST0, pyridinium-3,5-biscarboxylic acid mononucleotide synthase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+ Mass: 665.418 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₆O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.68 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM Nicotinic acid adenine ...Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM Nicotinic acid adenine dinucleotide sodium salt

Crystal

Density Matthews: 2.44 Å³/Da / Density % sol: 49.68 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM magnesium formate, 20% w/v PEG 3350, 2 mM nitrilotriacetic acid neutralized to a pH of ~7.5 with sodium hydroxide, and 0.7 mM zinc sulfate, 10 mM EDTA, 10 mM Nicotinic acid adenine ...

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 3.1→85.5 Å / Num. obs: 29281 / % possible obs: 99.8 % / Redundancy: 9.7 % / CC_1/2: 0.967 / Net I/σ(I): 8.2
Reflection shell	Resolution: 3.1→3.29 Å / Num. unique obs: 4636 / CC_1/2: 0.767

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→61.15 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2856	1509	5.16 %
R_work	0.2361	-	-
obs	0.2387	29228	99.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→61.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7976	0	218	0	8194

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	8360
X-RAY DIFFRACTION	f_angle_d	1.656	11499
X-RAY DIFFRACTION	f_dihedral_angle_d	13.491	2643
X-RAY DIFFRACTION	f_chiral_restr	0.082	1480
X-RAY DIFFRACTION	f_plane_restr	0.009	1455

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 (%)
3.1-3.2	0.367	152	0.3013	2441	X-RAY DIFFRACTION	100
3.2-3.31	0.3299	126	0.2734	2492	X-RAY DIFFRACTION	100
3.31-3.45	0.2613	135	0.2515	2491	X-RAY DIFFRACTION	100
3.45-3.6	0.3183	132	0.2498	2481	X-RAY DIFFRACTION	100
3.6-3.79	0.2924	132	0.2384	2514	X-RAY DIFFRACTION	100
3.79-4.03	0.2617	144	0.2247	2492	X-RAY DIFFRACTION	100
4.03-4.34	0.271	153	0.2076	2485	X-RAY DIFFRACTION	100
4.34-4.78	0.2516	120	0.1856	2534	X-RAY DIFFRACTION	100
4.78-5.47	0.2491	128	0.2258	2555	X-RAY DIFFRACTION	99
5.47-6.89	0.3283	136	0.2842	2561	X-RAY DIFFRACTION	99
6.89-61.15	0.2911	151	0.239	2673	X-RAY DIFFRACTION	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	1.4547	-1.5199	-1.5738	1.7326	2.094	2.7957	-0.8952	1.1093	-1.3367	-1.5998	-0.2189	-0.2069	0.9406	0.098	0.5922	1.5952	-0.2699	0.7519	1.4511	-0.5054	1.1412	39.816	-18.786	-0.325
2	7.7296	-0.0151	0.972	6.2782	-0.0698	6.1715	-0.1742	0.6371	0.151	-0.7974	-0.1383	0.2845	0.0963	-0.7351	0.2945	0.3248	-0.0796	-0.037	0.4234	-0.0695	0.3894	35.818	-5.593	14.787
3	2.0927	1.7313	1.5751	2.8539	1.6892	3.6615	-0.0164	-1.484	1.3341	0.7848	-0.2138	1.0746	-0.0822	-0.347	0.6361	1.0118	0.0906	-0.1111	1.2926	-0.5936	0.9466	33.724	-8.18	48.003
4	4.5836	0.3643	-0.1062	5.4444	-0.5723	4.2013	-0.4134	-0.1889	-0.565	0.2577	-0.0954	-0.2862	0.4917	-0.1565	0.4526	0.4179	-0.0263	0.1401	0.2435	-0.0712	0.397	42.976	-20.225	30.096
5	8.5884	1.7965	2.0862	0.3778	0.4363	3.5027	-0.386	1.5267	0.7713	-2.0208	0.1007	1.696	0.6866	-1.3345	0.3932	2.1653	-0.0751	-0.8622	1.4195	-0.0578	1.2478	0.617	-34.773	18.998
6	8.0324	1.8357	-1.6987	8.6531	0.2208	6.4203	0.0284	0.0731	-0.367	-0.9528	-0.1848	-0.3458	-0.092	-0.0342	0.1313	0.3297	0.0044	0.0458	0.3395	-0.0002	0.2989	15.839	-39.441	35.988
7	0.1805	0.2135	-0.7697	0.9985	0.1682	5.197	0.9141	-1.9643	-0.9528	0.8505	-0.87	-0.7522	0.169	-0.3453	0.0114	1.3155	-0.6915	-0.3345	2.5403	0.6172	1.1024	16.757	-38.746	68.948
8	5.9544	0.6884	-0.615	5.9854	-0.3416	5.4894	0.3486	-1.4462	0.5083	0.7328	-0.4064	0.7114	-0.5433	0.4777	0.0588	0.4393	-0.0589	0.0928	0.6211	-0.1212	0.5039	1.445	-33.439	51.22
9	8.061	0.4801	-7.4329	2.4508	-0.7489	6.8955	-0.4638	0.2975	-0.4532	-0.6584	-0.2925	-0.8824	0.6083	1.1579	0.6908	1.5587	-0.2837	0.5792	1.7383	0.2558	1.1336	62.922	-23.02	75.791
10	1.6447	-0.0716	-0.793	0.0025	-0.0135	2.0135	-0.3138	0.1234	-0.4129	-0.1771	-0.4855	-0.1728	0.4617	0.1483	-0.0473	2.1953	0.1863	1.109	1.9916	0.0948	0.8864	61.911	-25.912	70.039
11	4.1298	-1.8357	-0.3963	2.7969	4.2164	8.2814	0.3117	1.7197	-0.5501	-0.7892	-0.4315	-0.5411	-0.1958	0.2309	-0.0055	2.2553	0.2046	1.0297	1.5065	-0.2153	1.2282	55.733	-23.875	64.75
12	7.4688	0.6448	-4.0973	0.9614	-1.9691	5.1127	0.0842	-0.2765	-0.8125	-1.1624	-0.6865	0.2909	2.4025	-1.034	0.6894	2.7258	-0.949	0.523	1.5684	-0.4752	1.1313	44.472	-28.619	77.92
13	1.4843	0.7015	-0.7795	3.5549	1.9772	4.3592	-0.0779	-0.215	-0.1973	-0.2255	-0.7943	0.9903	0.3465	-1.2883	0.7191	1.8531	-0.3247	0.7069	2.0234	-0.833	1.1965	40.139	-20.01	80.346
14	5.1019	-2.4197	0.9325	2.1445	-0.2657	0.1942	-0.6683	-1.336	0.9115	-0.3655	-0.0863	-0.6278	0.7379	-1.109	-0.0115	1.5591	-0.5272	0.8715	1.4754	-0.8123	1.3385	43.508	-14.204	89.718
15	1.2792	2.0894	-0.714	3.6388	-1.5754	1.101	-0.0248	-0.5043	-0.0724	-0.0468	0.1282	-0.0676	0.3933	0.0627	0.1801	2.3034	-0.7634	1.613	1.9503	-0.4221	1.4379	49.889	-22.345	89.759
16	3.0263	3.6828	5.2294	5.5358	7.4958	2.0058	1.4438	-3.4267	1.3321	2.1253	-2.6646	2.5995	1.1202	-1.2176	1.2201	2.2015	-0.4862	0.6107	1.9318	-0.3412	1.6889	38.519	-21.734	117.245
17	3.2907	1.695	-2.051	0.8893	-1.337	6.3885	-0.51	-2.6983	-0.0865	1.3158	-0.1738	1.2862	0.6411	-1.8079	0.7815	3.2134	0.4907	0.9619	3.0223	-0.0393	1.4158	47.786	-23.557	122.427
18	6.2434	-0.0418	-4.7798	2.075	-2.5655	6.8891	-0.7437	-0.1695	-0.8976	-0.4695	-0.0013	0.754	1.7701	-0.6334	0.6438	2.7718	-0.9988	1.0305	1.9296	0.4184	1.7413	51.489	-33.762	106.799
19	0.1167	-0.1749	0.4525	2.0684	0.1844	2.2186	-0.0575	-0.9281	-0.9445	0.1737	-0.9983	-0.1986	1.7342	0.4412	0.7299	3.1901	0.0006	1.2122	1.4062	0.4143	1.3828	60.5	-29.677	103.397
20	4.0847	1.5119	-1.3374	2.5437	-1.3945	3.0683	0.127	0.096	0.0787	0.183	-0.8998	-0.3702	0.9464	-0.6438	0.3163	2.4976	-0.2958	1.1248	1.1523	0.1699	1.2094	55.802	-20.991	98.64
21	3.4745	-2.0675	-1.5438	7.4237	-6.035	9.3322	-0.2485	0.0915	-0.1237	0.4118	-0.111	-0.0094	-0.0544	-0.103	0.2658	0.5707	0.3405	0.4207	0.242	0.3051	0.2889	11.117	-22.074	69.421
22	4.8327	2.8724	-1.5379	4.894	-0.9686	0.452	0.2294	0.1064	0.1431	-0.3633	0.3858	-0.6207	0.2375	-0.0674	-0.4828	0.9898	0.1187	-0.0193	0.4016	-0.2249	0.6766	29.65	-21.161	28.883
23	2.9959	1.8867	2.5222	4.1168	2.9394	4.6223	0.9923	-0.4318	-0.2685	0.0002	-0.6722	0.1136	0.7388	-0.8626	-0.3498	1.2538	0.2966	-0.0111	1.054	0.2309	0.7502	14.262	-35.449	54.822

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 44:125 )	A	44 - 125
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 126:246 )	A	126 - 246
3	X-RAY DIFFRACTION	3	( CHAIN B AND RESID 46:107 )	B	46 - 107
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 108:246 )	B	108 - 246
5	X-RAY DIFFRACTION	5	( CHAIN C AND RESID 47:107 )	C	47 - 107
6	X-RAY DIFFRACTION	6	( CHAIN C AND RESID 108:246 )	C	108 - 246
7	X-RAY DIFFRACTION	7	( CHAIN D AND RESID 35:107 )	D	35 - 107
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 108:250 )	D	108 - 250
9	X-RAY DIFFRACTION	9	( CHAIN E AND RESID 49:58 )	E	49 - 58
10	X-RAY DIFFRACTION	10	( CHAIN E AND RESID 59:86 )	E	59 - 86
11	X-RAY DIFFRACTION	11	( CHAIN E AND RESID 87:103 )	E	87 - 103
12	X-RAY DIFFRACTION	12	( CHAIN E AND RESID 104:125 )	E	104 - 125
13	X-RAY DIFFRACTION	13	( CHAIN E AND RESID 126:162 )	E	126 - 162
14	X-RAY DIFFRACTION	14	( CHAIN E AND RESID 163:218 )	E	163 - 218
15	X-RAY DIFFRACTION	15	( CHAIN E AND RESID 219:244 )	E	219 - 244
16	X-RAY DIFFRACTION	16	( CHAIN F AND RESID 46:83 )	F	46 - 83
17	X-RAY DIFFRACTION	17	( CHAIN F AND RESID 85:107 )	F	85 - 107
18	X-RAY DIFFRACTION	18	( CHAIN F AND RESID 108:125 )	F	108 - 125
19	X-RAY DIFFRACTION	19	( CHAIN F AND RESID 126:190 )	F	126 - 190
20	X-RAY DIFFRACTION	20	( CHAIN F AND RESID 191:246 )	F	191 - 246
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 )	D	301
22	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 )	E	301
23	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 302:302 )	A	301 - 302
24	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 302:302 )	B	301
25	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 302:302 )	C	301
26	X-RAY DIFFRACTION	22	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 302:302 )	D	302
27	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 302:302 ) OR ( CHAIN C AND RESID 302:302 ) OR ( CHAIN D AND RESID 303:303 ) OR ( CHAIN E AND RESID 302:302 )	B	302
28	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 302:302 ) OR ( CHAIN C AND RESID 302:302 ) OR ( CHAIN D AND RESID 303:303 ) OR ( CHAIN E AND RESID 302:302 )	C	302
29	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 302:302 ) OR ( CHAIN C AND RESID 302:302 ) OR ( CHAIN D AND RESID 303:303 ) OR ( CHAIN E AND RESID 302:302 )	D	303
30	X-RAY DIFFRACTION	23	( CHAIN B AND RESID 302:302 ) OR ( CHAIN C AND RESID 302:302 ) OR ( CHAIN D AND RESID 303:303 ) OR ( CHAIN E AND RESID 302:302 )	E	302

-
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