PDB-11iz: Crystal structure of HSC-HSC-AMS bound DesD, the desferrioxamine ...

ID or keywords:

Entry

Database: PDB / ID: 11iz

Title

Crystal structure of HSC-HSC-AMS bound DesD, the desferrioxamine synthetase from the Streptomyces griseoflavus ferrimycin biosynthetic pathway

Components

DesD

Keywords

LIGASE / NIS synthetase / NRPS-independent siderophore synthetase / desferrioxamine synthetase / DesD

Function / homology

: / DIPHOSPHATE

Function and homology information

Biological species

Streptomyces griseoflavus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.47 Å

Authors

Patel, K.D. / Gulick, A.M.

Funding support

United States, 1items

Citation

Journal: Acs Bio Med Chem Au / Year: 2026
Title: Modular
Authors: Merrick, C.E. / Patel, K.D. / Kalita, P. / Gulati, N. / Gulick, A.M. / Wencewicz, T.A.

History

Deposition	Feb 26, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	11iz.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb11iz.ent.gz		Display	PDB format
PDBx/mmJSON format	11iz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/1i/11iz ftp://data.pdbj.org/pub/pdb/validation_reports/1i/11iz	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: DesD

A: DesD

D: DesD

E: DesD

C: DesD

hetero molecules

353 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	128.643, 236.822, 331.096
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

-
Protein , 1 types, 5 molecules BADEC

#1: Protein	DesD Mass: 68761.516 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 6 types, 971 molecules

#2: Chemical	... ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-A1C9F / 5'-O-({4-[(5-{4-[(5-aminopentyl)(hydroxy)amino]-4-oxobutanamido}pentyl)(hydroxy)amino]-4-oxobutanoyl}sulfamoyl)adenosine Mass: 746.790 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₈H₄₆N₁₀O₁₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: O₇P₂
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 902 / Source method: isolated from a natural source / Formula: H₂O

-
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: 3.67 Å³/Da / Density % sol: 66.46 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05M Sodium phosphate pH 7.0 0.2M Ammonium sulfate 16% PEG 4000

-
Data collection

Diffraction	Mean temperature: 113 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97935 Å / Relative weight: 1
Reflection	Resolution: 2.47→44.45 Å / Num. obs: 179121 / % possible obs: 100 % / Redundancy: 14.1 % / B_iso Wilson estimate: 43.26 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.2674 / Net I/σ(I): 7.66
Reflection shell	Resolution: 2.47→2.61 Å / R_merge(I) obs: 1.66 / Num. unique obs: 25958 / CC_1/2: 0.39

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.47→44.45 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.0322 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2135	9044	5.05 %
R_work	0.1748	169973	-
obs	0.1768	179017	99.98 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.47→44.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23703	0	287	904	24894

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0105	24531
X-RAY DIFFRACTION	f_angle_d	1.139	33369
X-RAY DIFFRACTION	f_chiral_restr	0.0613	3632
X-RAY DIFFRACTION	f_plane_restr	0.0071	4309
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6966	14433

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 (%)
2.47-2.5	0.3452	305	0.3159	5616	X-RAY DIFFRACTION	99.93
2.5-2.53	0.3123	286	0.2877	5588	X-RAY DIFFRACTION	99.98
2.53-2.56	0.3079	303	0.2821	5646	X-RAY DIFFRACTION	99.98
2.56-2.6	0.3198	314	0.2764	5625	X-RAY DIFFRACTION	100
2.6-2.63	0.3025	290	0.2595	5633	X-RAY DIFFRACTION	100
2.63-2.67	0.3011	320	0.2586	5555	X-RAY DIFFRACTION	100
2.67-2.7	0.2967	312	0.2537	5647	X-RAY DIFFRACTION	100
2.7-2.74	0.2911	295	0.2369	5621	X-RAY DIFFRACTION	100
2.74-2.79	0.2881	286	0.234	5646	X-RAY DIFFRACTION	100
2.79-2.83	0.2659	305	0.2371	5613	X-RAY DIFFRACTION	100
2.83-2.88	0.2868	277	0.2308	5677	X-RAY DIFFRACTION	100
2.88-2.93	0.2777	303	0.2352	5644	X-RAY DIFFRACTION	100
2.93-2.99	0.2606	307	0.2237	5633	X-RAY DIFFRACTION	99.98
2.99-3.05	0.2533	292	0.2111	5615	X-RAY DIFFRACTION	99.98
3.05-3.12	0.2413	303	0.2008	5660	X-RAY DIFFRACTION	100
3.12-3.19	0.2496	294	0.1968	5625	X-RAY DIFFRACTION	99.97
3.19-3.27	0.2479	268	0.1931	5665	X-RAY DIFFRACTION	99.93
3.27-3.36	0.2449	233	0.1952	5719	X-RAY DIFFRACTION	99.97
3.36-3.46	0.2434	288	0.1959	5684	X-RAY DIFFRACTION	99.9
3.46-3.57	0.208	312	0.1843	5641	X-RAY DIFFRACTION	99.95
3.57-3.7	0.1926	334	0.165	5601	X-RAY DIFFRACTION	99.98
3.7-3.84	0.2066	314	0.1554	5716	X-RAY DIFFRACTION	99.98
3.84-4.02	0.1874	328	0.1467	5626	X-RAY DIFFRACTION	99.98
4.02-4.23	0.1658	294	0.1335	5687	X-RAY DIFFRACTION	100
4.23-4.5	0.1583	311	0.1179	5693	X-RAY DIFFRACTION	100
4.5-4.84	0.145	350	0.1128	5645	X-RAY DIFFRACTION	99.98
4.84-5.33	0.1578	276	0.13	5748	X-RAY DIFFRACTION	100
5.33-6.1	0.2029	321	0.1493	5747	X-RAY DIFFRACTION	100
6.1-7.68	0.1967	309	0.1481	5777	X-RAY DIFFRACTION	100
7.68-44.45	0.1689	314	0.1422	5980	X-RAY DIFFRACTION	99.84

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	2.77636348451	0.209540148732	-0.208702396822	0.845243127526	-0.0185528392753	1.02172737337	-0.118017637644	0.776507140152	-0.190685197214	-0.434974557435	0.136089694402	0.10715967061	0.299438938132	-0.0931137042735	-0.0594238828235	0.560070047211	-0.160532131275	-0.0682322280253	0.452093539315	-0.062794833074	0.369583783917	41.6769651721	3.02327715183	42.8410840684
2	1.3907079766	0.653324974334	0.45315227223	1.60744938493	0.583844821819	0.842533411125	-0.0316562968762	-0.106162934802	0.00733986994152	0.0491862215924	-0.0207461670997	0.211945331264	0.137803976775	-0.0547102982941	0.0474744690688	0.324190387016	-0.0660904409171	-0.0435926862068	0.251932943179	0.0419996257093	0.272202157772	40.3275251959	16.6700212643	72.2550245239
3	2.4422738818	0.235353193615	-0.349685821528	1.48688986165	0.144280916018	0.957693157721	0.00631614138985	0.206570020987	0.04736648853	-0.0752221213689	-0.0707909189272	0.364128062595	-0.0271647692238	-0.148577399938	0.0632917621922	0.413784165213	-0.140465273089	-0.100824096138	0.325252528592	0.0188628723943	0.500491339877	18.6124996672	4.81086923892	59.3471707778
4	6.17643749743	2.53840873245	-0.399603036155	3.03652144421	-0.570016894764	1.99387287328	-0.141795769024	-0.0210767272246	0.93940614599	-0.11921689133	0.124610404547	0.612643271371	-0.441563910831	0.199868241697	0.0280410357704	0.615567259827	-0.103620527045	-0.171514992384	0.556720014423	0.00225365933205	0.533754757808	26.2781119376	15.71479452	47.4780636332
5	2.00241740594	0.254759359262	-0.333429308147	1.64620046583	-0.618132450187	2.41353215848	-0.053823098493	0.103015669387	0.653501547578	-0.0143387250671	0.0676596810572	-0.149295327741	-0.379530205917	0.0444654534849	-0.0207850937258	0.408899870647	-0.0757417426595	-0.150248591674	0.303862747476	0.0368670945313	0.455962536522	57.2019264926	50.9286281109	65.6741527718
6	2.25147127573	-0.0546127744069	-0.54668258495	1.40248577129	-0.0616226233658	0.955229088716	-0.16747269143	0.211895706706	0.406266368595	-0.114326858131	0.159411347903	0.0502088858102	-0.221909274801	-0.0204568367223	-0.00561570656276	0.400482736744	-0.100343100702	-0.116525501742	0.277255067723	0.0667664936348	0.329774902102	60.6903402468	44.0442656606	62.9879558807
7	0.878463910921	0.118723630784	-0.088697866918	1.14576160343	0.344250776339	1.06734992354	-0.105454878556	0.295165613267	0.0470445476016	-0.166193464329	0.113792280239	-0.123046890285	0.0582322265309	0.218444177931	-0.0063045729284	0.41355087609	-0.112348047155	-0.0311949555433	0.477538330519	0.0147372097021	0.230934325183	72.4101972581	20.3967403799	46.5469118683
8	2.92272841716	2.13165025648	2.95102939859	2.16697563389	1.50750114262	3.67305409374	-0.723162025046	1.3785884423	0.108677517447	-0.535554813811	0.49668147678	0.0914449162278	-0.0822154414176	0.241961544432	0.250871480311	0.501492260527	-0.117556256489	-0.0140114455031	0.526160936319	0.00528764687909	0.238241033547	67.8800822063	23.9939423991	41.9320358275
9	1.47362209424	-0.467856520417	-0.452086445408	1.7682666783	0.103622312352	1.14449676394	-0.0314671894145	0.499071033414	0.514813326676	-0.466668374729	0.088771918155	-0.134836769226	-0.367689885796	0.207866701848	-0.0692371458356	0.593102312084	-0.270707957644	-0.0423418669372	0.615445584718	0.204973354518	0.51653928286	77.755265057	49.4155605558	44.2492976358
10	3.0448518322	1.66827415533	-0.209368845983	5.26083601042	-0.931048455343	2.47116872853	-0.329884111214	0.732269875917	0.235128556349	-1.09448741825	0.455934688999	0.137952269567	0.0953986545176	-0.153218528553	-0.100326286817	0.674432183356	-0.120119217875	-0.0725255100375	0.603560894153	0.19309661791	0.405734663286	59.6595107189	47.95470116	43.8876666553
11	2.6320932637	0.0419554195109	-0.237466114286	1.01915243049	0.179067118257	2.41901676568	0.0676039516924	0.419893044603	0.262243468452	-0.137356437116	0.0214796190403	0.119980138542	-0.316014795141	-0.13043185313	-0.0697353054888	0.377163483923	-0.0169835686833	-0.068506311744	0.303273261917	0.0857122412285	0.411082919707	37.0566673448	100.782707142	47.682360747
12	2.21458158826	0.095136666688	0.263046627963	3.07710308692	0.186001131443	0.899273099393	0.098002492916	-0.466385291111	-0.108867937115	0.59200291759	-0.0265701030412	0.0657571718235	-0.116172870442	-0.0351772944797	-0.0504063733041	0.380071509904	-0.0622371139993	-0.0419016841222	0.417163175589	0.0595125485421	0.271934116315	37.4281215173	82.6829862862	77.7103408947
13	5.23136435785	3.48228414878	-1.95884777663	3.66547774196	-1.2130395816	1.34245083877	0.206530666157	-0.488685033131	-0.529749419619	0.425184893719	-0.173462324506	-0.548954446548	-0.237256415689	0.384298609609	-0.0822638181985	0.454033721133	-0.112943121492	-0.201442882825	0.45104717736	0.061640151102	0.444116742512	59.3373768721	85.5467489239	74.575536986
14	3.25095631987	2.22511718628	1.24684308093	2.57037924941	2.19885300171	3.06249352843	0.0102459066192	-0.410826854475	-0.216113024988	-0.210688871318	0.00107061163625	-0.262264614625	-0.342086329785	0.191102197844	-0.21197137291	0.431556931718	-0.087719363219	-0.126307899236	0.400306549515	0.10654336203	0.393890314507	45.3421556212	79.3374935014	71.2506041252
15	2.34436880358	0.433232956963	0.20143434509	1.1923729468	-0.498052812989	1.1777242096	0.111317044292	0.00556811588526	0.077200897945	0.0716085338636	-0.0715604063948	-0.252772124216	-0.0379927349323	0.0478492898713	-0.0506871715807	0.410951763515	-0.133175058451	-0.0939119341837	0.338678899889	-0.0246650087323	0.495078212734	61.0115815851	98.5597359877	60.4927629606
16	2.36247439015	1.01423668099	0.593604146506	2.36532330561	2.36552267501	3.6207145964	-0.102248101957	-0.0609959458147	-0.690029743845	-0.0109645146912	-0.0111916370594	-0.360247605271	0.518496070633	0.0195076018107	0.143059248279	0.45703388259	-0.0395330713317	-0.0559491062359	0.375648373783	0.10611016069	0.477203341409	52.7802604211	88.1271307705	48.5991257072
17	1.90791153952	-0.552707674218	0.424772041425	0.864893297975	-0.78389788863	2.33733541119	0.056430206543	-0.435783163623	0.36949177056	0.313541816192	0.160633726861	0.122765960193	-0.633999594702	-0.697474978744	-0.197475525285	0.714108681489	0.102079684448	0.137812346428	0.664615777595	-0.0636500914893	0.407996459841	63.9110577695	25.4161533268	6.6697360698
18	0.947320280831	-0.0563831594038	0.156666140491	1.86358003523	0.138088041399	1.23308739333	0.151253122214	0.184628033924	0.0827848593401	-0.140975391822	-0.0407891216211	-0.00466238351345	0.0240371803642	-0.122337528257	-0.107284470374	0.439260634205	0.0529951178297	0.0280599720675	0.579918750439	-0.00215579072943	0.27640272116	73.4187490011	6.10564251384	-19.8648905782
19	2.35304873369	-0.263614402866	0.368864225955	1.19712628302	-0.26151723334	2.2541996895	0.19899305144	0.0618315707397	0.345566239465	-0.00222477590977	0.0246591289237	0.267385127353	-0.45698943351	-0.570696419828	-0.216930275771	0.640324334287	0.170897956153	0.154377319085	0.621160172094	0.0981805515723	0.501046987186	59.6436697103	31.1826118249	-17.6728795049
20	1.64484353901	0.333823519159	0.227727440731	0.491652410512	0.17362395374	1.78128325795	-0.0193025484124	-0.317337809379	-0.833118468127	0.145452708096	0.163607580556	0.535296318456	0.34412781365	-0.147485372204	-0.0673343652138	0.517114809503	-0.0916570814662	-0.0396744410525	0.442125130405	0.238396242361	0.815656513618	24.2339220367	51.0562929042	68.603646329
21	1.93952748151	-0.0734694304926	-0.154437289059	1.76350043943	-0.0492818514131	1.77847304416	0.0231231760925	-0.159859758226	-0.473395943962	0.0847842342486	0.140116534828	0.442459927553	0.207482903099	-0.368610666803	-0.11369292531	0.357732129852	-0.106296708737	-0.0467036097512	0.404233955301	0.190139049522	0.61326093572	20.5807688462	58.4067395908	67.218599324
22	2.20707639949	0.435001558408	0.320499163788	2.01877998853	-0.117043935659	0.967611225249	-0.0674990087839	-0.0406548051409	0.0228680932514	-0.0576145557127	0.205153861525	0.59280094213	-0.117117325112	-0.437707009967	-0.0772344605418	0.283915720491	0.0132192445213	-0.0353514165923	0.559704773172	0.122989517441	0.506304047834	6.92007230159	83.46171237	55.3659955186
23	6.64097089647	1.85441438613	-1.74326815796	2.19248490941	-0.716877973392	2.2396666341	-0.233106059898	0.274944528443	-0.207656803281	-0.18702265907	0.23537865561	0.508897505471	0.0569455411101	-0.44129261752	0.00265030108216	0.349334873583	0.00238954787684	-0.10917590146	0.483995645785	0.133079882889	0.530452578832	9.17732501452	80.3655871397	49.3886567505
24	1.91228328811	-0.814299755979	0.362468028498	1.67231184841	0.156386058664	0.767271565047	0.194539461374	-0.0122368968397	-0.873719603346	-0.394005307472	0.16326124293	0.900953198967	0.403579057148	-0.475199260891	-0.189191540667	0.492669220951	-0.243216227586	-0.238222640423	0.714471266921	0.153565968004	1.19422909873	0.575294062832	54.8030430429	51.1616481067
25	5.40248096114	2.41154054699	1.34639291831	2.17646689733	2.67184653703	4.38327665355	0.176270862586	0.672229229836	-0.499379961238	-0.999019116525	-0.0411310502929	0.506127003378	-0.204828991037	0.0426177282443	-0.129984970847	0.493518643995	-0.0103467584341	-0.279434475777	0.474690001765	0.057385176453	0.806535816586	18.2535499405	56.1096687805	48.0343429556

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 158 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 159 through 398 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 399 through 558 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 559 through 592 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1 through 66 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 67 through 158 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 159 through 346 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 347 through 380 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 381 through 557 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 558 through 592 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 2 through 158 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 159 through 306 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 307 through 346 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 347 through 380 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 381 through 557 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 558 through 592 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 158 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 159 through 381 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 382 through 592 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 2 through 66 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 67 through 158 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 159 through 339 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 340 through 381 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 382 through 557 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 558 through 592 )

-
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 , 1 types, 5 molecules BADEC

-
Non-polymers , 6 types, 971 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 , 1 types, 5 molecules BADEC

-Non-polymers , 6 types, 971 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 , 1 types, 5 molecules BADEC

-
Non-polymers , 6 types, 971 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