[English] 日本語
Yorodumi
- PDB-7ak8: Structure of Salmonella TacT1 toxin bound to TacA1 antitoxin C-te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ak8
TitleStructure of Salmonella TacT1 toxin bound to TacA1 antitoxin C-terminal peptide
Components
  • GCN5 family acetyltransferase
  • TacA1 antitoxin peptide
KeywordsTOXIN / Acetyltransferase / antitoxin / GNAT / Salmonella
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Vibrio phage ICP1, Orf50 / Antitoxin TacA 1-like / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / GCN5 family acetyltransferase / DUF1778 domain-containing protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGrabe, G.J. / Morgan, R.M.L. / Helaine, S. / Hare, S.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009629/1 United Kingdom
European Research Council (ERC)757369 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Auxiliary interfaces support the evolution of specific toxin-antitoxin pairing.
Authors: Grabe, G.J. / Giorgio, R.T. / Hall, A.M.J. / Morgan, R.M.L. / Dubois, L. / Sisley, T.A. / Rycroft, J.A. / Hare, S.A. / Helaine, S.
History
DepositionSep 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_contact_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 1, 2021Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GCN5 family acetyltransferase
B: GCN5 family acetyltransferase
C: GCN5 family acetyltransferase
D: GCN5 family acetyltransferase
E: GCN5 family acetyltransferase
F: GCN5 family acetyltransferase
G: TacA1 antitoxin peptide
H: TacA1 antitoxin peptide
I: TacA1 antitoxin peptide
J: TacA1 antitoxin peptide
K: TacA1 antitoxin peptide
L: TacA1 antitoxin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,12219
Polymers135,17212
Non-polymers4,9507
Water3,837213
1
A: GCN5 family acetyltransferase
B: GCN5 family acetyltransferase
G: TacA1 antitoxin peptide
H: TacA1 antitoxin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7697
Polymers45,0574
Non-polymers1,7113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-45 kcal/mol
Surface area19210 Å2
MethodPISA
2
C: GCN5 family acetyltransferase
D: GCN5 family acetyltransferase
I: TacA1 antitoxin peptide
J: TacA1 antitoxin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6776
Polymers45,0574
Non-polymers1,6192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-40 kcal/mol
Surface area19390 Å2
MethodPISA
3
E: GCN5 family acetyltransferase
F: GCN5 family acetyltransferase
K: TacA1 antitoxin peptide
L: TacA1 antitoxin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6776
Polymers45,0574
Non-polymers1,6192
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-41 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.140, 96.140, 120.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F
116G
216H
117G
217I
118G
218J
119G
219K
120G
220L
121H
221I
122H
222J
123H
223K
124H
224L
125I
225J
126I
226K
127I
227L
128J
228K
129J
229L
130K
230L

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLNGLNAA3 - 1616 - 164
21ARGARGGLNGLNBB3 - 1616 - 164
12ARGARGPROPROAA3 - 1606 - 163
22ARGARGPROPROCC3 - 1606 - 163
13ARGARGPROPROAA3 - 1606 - 163
23ARGARGPROPRODD3 - 1606 - 163
14ARGARGGLNGLNAA3 - 1616 - 164
24ARGARGGLNGLNEE3 - 1616 - 164
15ARGARGGLNGLNAA3 - 1616 - 164
25ARGARGGLNGLNFF3 - 1616 - 164
16GLYGLYGLNGLNBB2 - 1615 - 164
26GLYGLYGLNGLNCC2 - 1615 - 164
17GLYGLYGLNGLNBB2 - 1615 - 164
27GLYGLYGLNGLNDD2 - 1615 - 164
18ARGARGGLNGLNBB3 - 1616 - 164
28ARGARGGLNGLNEE3 - 1616 - 164
19ARGARGGLNGLNBB3 - 1616 - 164
29ARGARGGLNGLNFF3 - 1616 - 164
110GLYGLYGLNGLNCC2 - 1615 - 164
210GLYGLYGLNGLNDD2 - 1615 - 164
111ARGARGPROPROCC3 - 1606 - 163
211ARGARGPROPROEE3 - 1606 - 163
112ARGARGPROPROCC3 - 1606 - 163
212ARGARGPROPROFF3 - 1606 - 163
113ARGARGPROPRODD3 - 1606 - 163
213ARGARGPROPROEE3 - 1606 - 163
114ARGARGPROPRODD3 - 1606 - 163
214ARGARGPROPROFF3 - 1606 - 163
115ARGARGGLNGLNEE3 - 1616 - 164
215ARGARGGLNGLNFF3 - 1616 - 164
116SERSERASPASPGG51 - 872 - 38
216SERSERASPASPHH51 - 872 - 38
117SERSERASPASPGG51 - 872 - 38
217SERSERASPASPII51 - 872 - 38
118SERSERTRPTRPGG51 - 862 - 37
218SERSERTRPTRPJJ51 - 862 - 37
119SERSERTRPTRPGG51 - 862 - 37
219SERSERTRPTRPKK51 - 862 - 37
120SERSERTRPTRPGG51 - 862 - 37
220SERSERTRPTRPLL51 - 862 - 37
121GLYGLYVALVALHH50 - 881 - 39
221GLYGLYVALVALII50 - 881 - 39
122GLYGLYTRPTRPHH50 - 861 - 37
222GLYGLYTRPTRPJJ50 - 861 - 37
123SERSERTRPTRPHH51 - 862 - 37
223SERSERTRPTRPKK51 - 862 - 37
124GLYGLYTRPTRPHH50 - 861 - 37
224GLYGLYTRPTRPLL50 - 861 - 37
125GLYGLYTRPTRPII50 - 861 - 37
225GLYGLYTRPTRPJJ50 - 861 - 37
126SERSERTRPTRPII51 - 862 - 37
226SERSERTRPTRPKK51 - 862 - 37
127GLYGLYTRPTRPII50 - 861 - 37
227GLYGLYTRPTRPLL50 - 861 - 37
128SERSERTRPTRPJJ51 - 862 - 37
228SERSERTRPTRPKK51 - 862 - 37
129GLYGLYASPASPJJ50 - 871 - 38
229GLYGLYASPASPLL50 - 871 - 38
130SERSERTRPTRPKK51 - 862 - 37
230SERSERTRPTRPLL51 - 862 - 37

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

-
Components

#1: Protein
GCN5 family acetyltransferase / GNAT family N-acetyltransferase / N-acetyltransferase / Putative acetyltransferase


Mass: 17988.732 Da / Num. of mol.: 6 / Mutation: Y140F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: A3104_05260, A3S30_03570, A3T81_04110, A3U32_05665, A3V03_13910, A3V89_00850, A3W57_03995, A3W75_07050, A3X15_00850, A3X55_00330, A3Y76_07975, A4N07_08010, A4O05_01330, A4O41_02035, A4R48_ ...Gene: A3104_05260, A3S30_03570, A3T81_04110, A3U32_05665, A3V03_13910, A3V89_00850, A3W57_03995, A3W75_07050, A3X15_00850, A3X55_00330, A3Y76_07975, A4N07_08010, A4O05_01330, A4O41_02035, A4R48_08940, A6D61_12040, AAA76_07490, AAB27_15575, AAB79_05120, AAC35_03630, ADQ28_10180, AF497_21970, AGM99_05605, AHN93_12135, AKH62_19100, AL144_05700, AL168_00240, AL184_01810, AQ530_13120, AU613_00255, AVA38_12920, AVC05_10880, AVL16_07535, AWT30_08435, AXX99_15535, B1265_05365, B1398_03150, B1642_07220, B1P38_10090, B2E31_12125, B4V59_11840, B4W90_05740, B6362_03220, B7Q27_05360, B8Y16_03505, B8Z46_06185, B9C96_10070, B9M14_05170, B9O84_11705, BBQ66_14320, BIC00_08665, BIC13_03225, BK110_05560, BKM50_23080, BMS46_12655, BMU56_14440, BZ203_17645, BZZ88_00330, C5W43_16880, CA117_15905, CB102_05785, CB119_09120, CB198_11355, CB380_04135, CB535_00775, CB570_01830, CB646_00875, CBM67_04330, CBM76_05665, CBZ90_17940, CC339_13490, CC403_04175, CC453_00830, CC652_10800, CC971_08245, CCP17_05610, CDZ72_00835, CE70_05380, CED07_09530, CEQ70_11815, CFF58_15565, CFF59_19350, CHN22_12870, CIX60_11715, CPS79_04640, CQO33_02715, CSG22_15800, CVR97_16720, D4361_00885, D4387_02965, D4422_08015, D5823_11465, D5N86_07600, D5N95_00885, D5O82_10095, D5P17_09710, D5X47_03755, D5Y28_11880, D6422_07760, D6J79_03220, D8S24_00880, DD95_16950, DLB93_00885, DLR28_04670, DMI89_02730, DMO92_11770, DNB97_10965, DNM27_08065, DNZ37_00885, DO533_01635, DP680_00885, DPB42_14140, DPD91_14795, DPF41_20260, DPF68_06595, DPS76_07080, DQD22_06095, DQR44_03760, DRM14_09665, DRR75_03365, DRT38_10165, DRT61_12460, DRV05_07100, DSF94_03195, DSG41_05895, DTF68_09770, DU071_11255, DU223_00820, DU657_08775, DU879_06940, DUV75_05410, DWU22_19575, DY580_11360, DYM27_07920, E0935_00860, E1A11_05890, E6W45_05505, EBD14_00865, EBK21_06275, EC404_08075, EEQ30_12975, EER35_04050, EHB09_10530, EL822_04915, ELS01_06380, EPB30_06165, EQG93_08450, EVY71_04550, EW905_00795, F0D96_17680, F2P00_07220, F3Q97_08565, F3R12_09960, F9G02_14050, F9O44_13855, FE758_17765, FEM52_12110, FJM64_04975, FQC24_05145, FQX78_05230, G0038_06520, G0040_06840, G0042_12210, G0045_10425, G0047_05580, G0048_09095, G0051_05650, G0052_10850, G0059_05925, G0061_08175, G0062_08760, G0063_08650, G0067_09255, G0069_08830, G0070_07850, G0071_07190, G0072_20040, G0074_10230, G0076_07485, G0077_09025, G0080_10880, G0084_11640, G0086_11150, G0087_09095, G0088_08180, G0089_05205, G0090_03755, G0094_03985, G0100_14435, G0101_08280, G0102_07980, G0111_07610, G0113_09080, G0117_05815, G0123_09095, G0124_08820, G0148_07855, G0157_08510, G0170_09830, G0A05_14080, G0A28_05470, G0A32_06830, G0A39_18135, G0A43_17515, G0A44_05555, G0A46_06315, G0A50_04845, G0A51_06365, G0A52_16365, G0A53_03435, G0A56_14050, G0A58_04550, G0A60_05595, G0A61_07880, G0A63_17200, G0A66_04930, G0A67_08450, G0A68_18035, G0A70_04845, G0A73_06570, G0A76_16865, G0A79_08460, G0A92_06605, G0A96_06100, G0A97_04970, G0B03_06370, G0B05_02825, G0B07_02730, G0B08_03815, G0B12_00885, G0B96_06340, G0C03_03195, G0C04_07195, G0C34_08570, G0E15_12930, G0E20_13290, G0G84_14090, G0J24_05060, G0J26_08465, G0J27_00100, G0J28_06235, G0J31_03645, G0J33_04730, G0J34_09510, G0J36_06535, G0J37_09250, G0J40_08075, G0J43_05195, G0J44_09365, G0J45_06500, G0J46_07010, G0J47_09130, G0J49_07270, G0J50_09970, G0J51_08110, G0J53_03240, G0J55_05950, G0J58_04235, G0J59_20600, G0J62_02510, G0J65_11730, G0J66_02905, G0J67_06100, G0J69_03035, G0J71_03035, G0J73_12270, G0J76_03045, G0J79_08500, G0J81_05725, G0J85_05725, G0J89_12200, G0J92_11445, G0J94_12610, G0J96_11015, G0J97_05445, G0K00_10910, G0K02_08290, G0K03_06865, G0K04_04255, G0K05_00245, G0K07_03035, G0K10_07460, G0K13_06140, G0K15_04675, G0K16_11385, G0K18_09310, G0K19_03655, G0K20_01180, G0K23_06855, G0K25_00865, G0K26_09490, G0K28_12270, G0K30_06255, G0K31_02850, G0K32_21515, G0K33_05635, G0K37_00865, G0K38_10405, G0K39_00340, G0K41_00090, G0K42_08450, G0K44_09520, G0K46_05725, G0K47_10445, G0K48_11605, G0K49_12395, G0K52_13590, G0K53_13745, G0K56_12055, G0K58_17235, G0K59_13130, G0K61_08785, G0K65_07075, G0K68_05010, G0K70_08330, G0K72_03980, G0K74_16830, G0K75_06965, G0K78_11505, G0K80_19150, G0K83_05590, G0K84_13790, G0K85_10755, G0K88_003092, G0K89_000477, G0K90_000621, G0K94_000431, G0K95_000291, G0L00_000827, G0L02_000148, G0L03_04550, G0L06_01495, G0L07_01395, G0L10_04815, G0L14_03740, G0L15_14090, G0L18_01840, G0L19_04635, G0L20_03090, G0L24_03305, G0L25_01970, G0L29_02900, G0L31_11000, G0L32_05775, G0L34_00210, G0L35_03000, G0L36_06700, G0L37_03745, G0L38_01890, G0L40_13165, G0L42_04650, G0L48_07895, G0L49_00770, G0L51_03270, G0L52_00210, G0L55_04445, G0L59_01975, G0L62_04770, G0L63_03265, G0L65_18345, G0L67_03000, G0L68_05125, G0L70_10475, G0L73_04825, G0L76_03930, G0L77_17440, G0L78_01725, G0L79_04455, G0L83_11895, G0L86_000813, G0L88_02395, G0L89_04210, G0L91_04735, G0L93_17945, G0L96_03390, G0L98_18585, G0M00_19125, G0M02_16545, G0M05_16250, G0M06_000798, G0M10_10700, G0M13_000387, G0M14_02965, G0M16_02055, G0M18_000980, G0M21_11910, G0M22_000388, G0M25_000387, G0M26_03065, G0M29_000387, G0M30_05725, G0M33_12165, G0M35_05660, G0M36_14215, G0M38_01795, G0M39_00210, G0M41_07035, G0M45_06705, G0M46_000388, G0M48_000387, G0M53_03235, G0M55_04410, G0M56_01965, G0M58_01965, G0M63_03230, G0M65_01600, G0M67_04410, G0N45_04995, G0N48_08875, G0N51_12280, G0N53_04105, G0N55_07640, G0N57_04240, G0N58_04675, G0N59_10620, G0N60_09695, G0N61_05580, G0N62_05155, G0N64_07265, G0N65_06205, G0N66_09415, G0N67_07285, G0N71_08280, G0N75_10635, G0N78_06750, G0N82_06850, G0N84_07820, G0N85_04105, G0N86_11275, G0N88_07700, G0N89_06300, G0N90_07780, G0N92_16345, G0N94_02915, G0N95_11330, G0N98_10690, G0N99_03390, G0O00_03940, G0O03_07585, G0O10_06810, G0O14_02525, G0O15_13900, G0O18_14760, G0O19_09415, G0O20_06680, G0O22_05740, G0O25_08965, G0O27_07640, G0O31_08185, G0O32_05760, G0O36_06600, G0O37_08390, G0O39_05575, G0O40_13495, G0O41_08055, G0O42_08175, G0O43_09120, G0O44_05535, G0O47_08635, G0O52_07980, G0O55_07355, G0O57_07920, G0O58_10055, G0O59_14255, G0O60_09405, G0O63_04990, G0O66_13575, G0O68_07400, G0O70_08830, G0O71_08835, G0O74_07805, G0O75_07520, G0O77_08675, G0O78_08445, G0O80_07570, G0O81_03475, G0O82_10285, G0O84_08830, G0O85_05780, G0O86_10385, G0O87_07975, G0O88_03855, G0O89_06020, G0O92_08940, G0O93_04245, G0O94_13370, G0O97_02245, G0O99_13395, G0P00_15005, G0P01_02700, G0P02_06650, G0P05_12920, G0P06_08360, G0P08_09055, G0P12_13310, G0P13_05685, G0P17_06765, G0P18_07645, G0P19_05480, G0P24_03405, G0P26_08835, G0P28_08905, G0P30_08565, G0P31_10880, G0P36_12770, G0P37_02115, G0P41_15200, G0P44_03660, G0P45_07110, G0P48_07970, G0P49_00340, G0P52_05650, G0P53_00335, G0P56_10015, G0P57_08835, G0P58_04995, G0P63_06780, G0P65_04885, G0P67_10130, G0P68_07250, G0P69_00330, G0P73_13715, G0P75_01830, G0P76_03250, G1N61_05975, G1N64_05890, G1N66_05880, G1N68_05885, G1N71_05900, G1N72_05890, G1N86_05900, G1N87_05900, G1N91_06615, G1O00_03060, G1O02_05895, G1O04_05900, G1O05_05890, G1O08_05880, G1O10_07980, G1O12_05900, G1O16_05895, G1O17_05970, G1O18_05895, G1O20_05900, G1O23_05900, G1O25_05880, G1O26_05900, G1O27_05960, G1O28_05975, G1O29_05960, G1O32_05880, G1O34_05970, G1O38_06305, G1O40_05900, G1O43_05885, G1O46_03055, G1O48_05975, G1O49_05970, G1O51_05895, G1O53_05955, G1O62_05895, G1O63_05885, G1O65_05975, G1O67_07435, G1O68_05900, G1O69_05900, G1O71_09055, G1O72_05975, G1O76_05975, G1O77_05900, G1O80_05970, G1O81_05895, G1O83_05965, G1O84_05975, G1O87_05975, G1O88_05975, G1O89_05900, G1O90_05975, G1O93_05965, G1O94_05960, G1O96_05970, G1P02_05960, G1P03_06000, G1P06_05955, G1P09_03690, G1P10_05900, G1P12_05975, G1P14_00865, G1P15_08095, G1P17_05975, G1P19_05970, G1P23_05970, G1P24_05890, G1P25_05975, G1P26_05895, G1P29_05980, G1P31_05955, G1P35_05900, G1P36_05895, G1P37_05925, G1P40_03130, G1P44_05895, G1P45_05965, G1P47_05970, G1P48_05975, G1P51_05975, G1P52_05925, G1P53_05925, G1P54_05975, G1P55_05970, G1P56_05955, G1P57_05975, G1P58_05960, G1P59_05975, G1P61_08380, G1P64_05975, G1P67_05970, G1P69_05880, G1P72_10270, G1P75_05900, G1P76_05885, G1P78_03705, G1P83_03720, G1P84_05895, G1P87_05965, G1P90_05720, G1P91_05960, G1Q03_05895, G1Q08_05190, G1Q67_05965, G1Q78_05600, G1Q81_05970, G1Q83_05975, G1Q84_05630, G1Q85_05930, G1Q86_05885, G1Q88_03060, G1Q90_05960, G1Q91_05900, G1Q93_04955, G1Q96_05865, G1Q98_05900, G1Q99_05960, G1R01_05880, G1R02_03060, G1R03_05970, G1R04_05975, G1R08_05950, G1R13_05455, G1R15_05050, G1R20_03850, G1R21_05655, G1R22_03135, G1R23_03690, G1R27_05875, G1R28_05975, G1R29_05970, G1R30_05975, G1R31_06170, G1R36_05975, G1R38_05895, G1R40_03135, G1R42_03060, G1R44_05970, G1R45_07655, G1R47_03705, G1R48_03400, G1R51_05885, G1R53_05955, G1R63_05975, G1R69_00865, G1R87_03690, G1R93_05885, G1S02_05975, G2203_08015, G2212_16665, G2218_10050, G2221_14445, G2279_12055, G2290_12655, G2793_13325, G2918_13525, G2951_06215, G3221_002686, G3230_003612, G3231_002107, G3247_003535, G3248_001298, G3254_000042, G3263_002897, G3270_003434, G3275_000731, G3312_001760, G3336_003552, G3357_001663, G3369_000599, G3433_000040, G3460_000172, G3464_002692, G3593_003626, G3A35_06010, G3V06_000997, G3V14_003116, G3V17_000447, G3V21_001923, G3V56_000560, G3V57_001797, G3X03_001805, G4189_001062, G4190_000740, G4192_000813, G4198_000465, G4201_002102, G4202_001476, G4A01_003276, G4A73_001923, G4A83_004289, G4A85_000795, G4A87_001129, G4B68_002272, G4B72_002690, G4B74_000682, G4C74_000732, G4D32_002862, G4D46_002457, G4F88_00975, G4F89_00975, G4F91_00975, G4F92_00975, G4G47_002694, G4G62_000409, G4G67_002617, G4G68_003382, G4G75_001678, G4G76_001465, G4G79_002671, G4G97_002412, G4H00_000794, G4H04_004573, G4H07_003668, G4H08_000531, G4H18_000732, G4H21_000732, G4H24_000731, G4H63_001253, G4I66_003374, G4J07_001210, G4J08_002077, G4J11_000371, G4J12_000194, G4J18_002024, G4J20_003007, G4J37_004095, G4J39_002350, G4J41_001528, G4J45_002734, G4J90_001713, G4K02_000288, G4K03_000467, G4O54_000645, G4O56_001571, G4O59_000813, G4O60_000682, G4O67_000090, G4O69_001285, G4P29_001085, G4P83_001852, G4P85_000794, G4P89_003492, G4P91_001062, G4P93_001763, G4Q12_003650, G4Q28_000731, G4Q31_000729, G4Q50_002143, G4Q52_001802, G4Q59_002807, G4Q60_000794, G4Q63_002241, G4Q67_002884, G4Q94_003298, G4R01_000793, G4R02_002285, G4R15_002693, G4R16_000738, G4W68_003699, G4W73_000556, G4W86_000985, G4W87_000731, G4W88_000731, G4W91_000172, G4Y10_003992, G9269_000835, G9302_000794, G9304_001304, G9305_003573, G9309_000406, G9313_000794, G9314_004792, G9367_001475, G9381_000652, G9C24_000383, G9C41_000997, G9C46_000851, G9C47_000682, G9C49_001055, G9C57_000729, G9C64_002284, G9G03_000498, G9G04_003112, G9G34_001925, G9G36_000578, G9G45_002411, G9G50_002043, G9G62_002043, G9W19_001372, G9W28_001672, G9W45_000066, G9W52_002688, G9W63_002269, G9W65_000729, G9W79_002141, G9W95_000732, G9W96_002671, G9X40_002428, GB021_12050, GB040_11905, GB055_08455, GB076_09500, GB106_05940, GB114_08430, GB120_05565, GB122_13970, GB131_01485, GB139_06880, GB171_04140, GB209_06835, GB221_07875, GB224_00850, GB238_15790, GB280_05650, GB321_07525, GB331_07240, GB339_13215, GB342_05100, GB368_12220, GB372_06140, GB416_14985, GB452_06045, GB459_14225, GB466_12020, GB505_11900, GB510_10155, GB551_04210, GB567_10890, GB645_16185, GBS44_03930, GBS58_06030, GBV53_06500, GBV54_10945, GBV60_02940, GBW03_15450, GBW44_14935, GBW52_04535, GBW76_13770, GBX12_15335, GBX20_14955, GBX46_08295, GBX55_07650, GBX64_03965, GBY13_11230, GBY23_15350, GBY73_06080, GBZ51_19890, GBZ55_00580, GCZ80_15180, GEZ01_02985, GJE27_05660, GJE28_04535, GNA88_002719, GNA97_002866, GNA99_002433, GNB28_002418, GNB36_000625, GNB86_001091, GNC11_000728, GNC19_001071, GNC45_001166, GNC75_002132, GNC95_001306, GT380_05460, GTH60_03855, GTH62_02955, GTH63_08335, GTH66_08440, GTH67_11855, GTH68_08765, GTH70_03980, GTH72_08695, GTH73_05580, GTH75_06310, GTH77_02140, GTH78_08780, GTH79_06415, GTH81_13485, GTH85_09075, GTH87_09405, GTH89_05045, GTH90_06145, GTH91_00200, GTH93_08830, GTH94_05830, GTH99_03650, GXC51_05530, GXC56_05530, GXG40_05530, GYI58_17280, GYI62_000737, GYI77_09255, GYJ04_02115, GYJ24_05830, GYJ27_19110, GYJ28_003980, GYJ30_10040, GYJ32_11345, GYJ53_05970, GYJ59_05490, GYJ60_05960, H8S97_18670, KP44_05625, NG06_06925, R035_07950, SE14_03872, STMLT2P22_CBEKMEGD_04422, Z700_03570, ZV17_16940, ZV33_03595, ZX03_04650, ZY40_05090
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6I609
#2: Protein/peptide
TacA1 antitoxin peptide / DUF1778 domain-containing protein


Mass: 4539.980 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: N-terminal GS is a vector remnant. / Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: A2O69_07430, A3104_05255, A3111_10580, A3122_13355, A3146_15665, A3R41_08205, A3S30_03565, A3T21_08665, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3W86_ ...Gene: A2O69_07430, A3104_05255, A3111_10580, A3122_13355, A3146_15665, A3R41_08205, A3S30_03565, A3T21_08665, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3W86_05185, A3X15_00845, A3X55_00325, A3Y76_07970, A3Z96_04750, A4J27_00880, A4N07_08005, A4O05_01325, A4O41_02030, A4R48_08935, A6D61_12035, A9C21_08785, A9T17_16030, A9T39_10960, A9U46_09840, A9U64_18200, AAA76_07485, AAB27_15580, AAB39_01350, AAB79_05115, AAC08_13230, AAC35_03625, AAC42_13825, AAC44_01625, AAC95_03230, AAC98_00235, AAK29_18915, AAP89_16385, AAQ24_03585, AB424_08175, ABO94_14755, ABP11_07165, ABP87_00235, ABQ69_11865, ADQ28_10175, ADQ45_06740, AE787_04740, AF480_11855, AF488_13105, AF489_15565, AF497_21965, AGC55_05640, AGM99_05600, AGQ32_00840, AH984_07885, AHN93_12130, AIC76_14410, AKH62_19105, AKH68_08190, AKI16_08145, AL144_05695, AL151_00235, AL166_01580, AL168_00235, AL170_14130, AL174_00235, AL184_01805, APP08_03940, APY91_10580, AQ530_13115, AS118_06315, AT354_08600, AU613_00250, AU805_03955, AU830_17515, AU839_10095, AU951_11905, AU965_09155, AVA38_12925, AVB77_18265, AVB94_02600, AVC05_10875, AVC09_01040, AVD08_04370, AVD75_07515, AVD94_16485, AVG17_05785, AVL02_07520, AVL16_07530, AVM19_07850, AWT30_08430, AXM10_00845, AXM23_12285, AXR84_07290, AXU58_08010, AXX99_15530, B1265_05360, B1398_03145, B1642_07215, B1B86_07505, B1B89_07010, B1I91_11315, B1P38_10085, B1Q82_04335, B2E31_12120, B4V59_11835, B4W90_05735, B5A40_03270, B6362_03215, B6G98_06815, B6M25_05910, B6M43_13380, B7071_06130, B7890_16080, B7J30_00845, B7Q27_05355, B8Y16_03500, B8Y36_18785, B8Z46_06180, B9653_13725, B9C61_18615, B9C71_00845, B9C90_03095, B9C91_03590, B9C96_10075, B9M14_05165, B9O84_11710, B9U29_07155, BBQ66_14315, BEL47_19110, BGP52_05690, BIC00_08660, BIC01_13270, BIC03_04875, BIC13_03220, BK110_05555, BKM50_23075, BLB03_07765, BMG85_04925, BMS46_12650, BMU56_14435, BSC80_12530, BSD55_09725, BZ203_17650, BZ210_09165, BZG47_18420, BZN20_09865, BZZ88_00325, C4E88_13460, C5U54_07580, C5W43_16875, CA117_15910, CB102_05780, CB119_09125, CB161_07230, CB198_11360, CB380_04130, CB383_05320, CB416_08795, CB530_02680, CB535_00770, CB570_01825, CB646_00870, CB657_00830, CBH20_04525, CBM40_17025, CBM67_04325, CBM76_05660, CBN77_00315, CBO42_00830, CBR08_03205, CBU32_01755, CBZ90_17945, CC339_13495, CC403_04170, CC453_00825, CC594_15230, CC652_10795, CC725_03565, CC886_09985, CC918_00830, CC944_03450, CC971_08240, CCF93_05115, CCP17_05605, CCW27_09980, CD48_05455, CD977_17355, CDJ75_03095, CDT37_05600, CDZ72_00830, CE355_04675, CE615_12895, CE70_05375, CE806_17240, CE87_09225, CE896_04015, CEC46_11665, CEC56_02970, CED07_09525, CEQ70_11810, CER78_04015, CET98_06955, CEY64_15580, CFB16_08610, CFB28_16910, CFE76_08800, CFE79_11770, CFF58_15570, CFF59_19345, CFJ48_06400, CGG73_15040, CHN22_12865, CI444_07100, CIX60_11710, CJC42_21280, CPR79_09745, CPS79_04635, CPX68_06625, CQE35_11170, CQG18_03755, CQO33_02710, CR370_17490, CRB02_11240, CSG22_15805, CTJ81_08990, CVR97_16715, D3147_00875, D3174_06325, D3F31_17635, D3T68_14225, D3Y48_15375, D4361_00880, D4369_00880, D4380_10135, D4387_02960, D4422_08010, D4E62_06950, D4E68_00880, D4E74_02815, D4X64_02820, D4X79_06330, D4Y62_06565, D5823_11460, D5949_11280, D5B48_05645, D5C67_00880, D5C71_12120, D5N86_07595, D5N95_00880, D5O82_10090, D5P17_09705, D5X47_03750, D5X51_14880, D5Y28_11875, D6360_00910, D6367_03355, D6371_05540, D6373_13080, D6395_00875, D6421_11315, D6422_07755, D6J79_03215, D6K10_11010, D6P67_04805, D6Q64_06505, D6S43_06005, D6T00_08410, D6T40_11365, D7F20_07790, D7H43_11190, D7N92_03765, D7O44_11380, D8Q90_03915, D8S24_00875, D8W49_14545, D9O84_06205, DJ388_00205, DJ702_12035, DK061_07035, DK631_12445, DK641_08320, DK642_03945, DK689_01285, DK696_05985, DK698_03630, DKJ10_11495, DKR95_03680, DKS55_00215, DKU45_08040, DKU57_08860, DKU80_01710, DLB14_09795, DLB57_07130, DLB93_00880, DLR28_04665, DM322_13010, DM708_18505, DMI89_02725, DMO92_11765, DMV40_03225, DMZ93_12650, DN165_06005, DN204_12055, DN359_04035, DNB97_10970, DNL62_00875, DNM27_08060, DNM63_05840, DNU59_07240, DNV08_09565, DNV12_04210, DNV30_10880, DNY92_02035, DNZ37_00880, DO350_16635, DO533_01630, DO585_00880, DO640_00870, DO698_04645, DO766_08740, DO828_06170, DO960_15640, DOC60_05660, DOH72_08650, DOI32_06930, DOI53_00915, DOI92_08220, DOJ39_03765, DOJ91_17535, DOQ54_08145, DOQ88_07235, DOR12_09835, DOV43_06050, DOW25_06610, DP680_00880, DPB42_14145, DPB45_07580, DPB48_10095, DPB57_08600, DPD91_14800, DPD95_03375, DPD99_04265, DPF41_20265, DPF68_06590, DPJ93_15635, DPK32_09070, DPK79_03180, DPL02_09685, DPP13_07860, DPP94_11760, DPP97_09085, DPS76_07075, DPT18_06895, DPU20_08890, DPY58_02180, DQ848_00880, DQ947_11435, DQC39_12965, DQC52_22465, DQD03_09235, DQD22_06090, DQE64_00880, DQE65_03185, DQK42_06775, DQQ98_05140, DQR10_16255, DQR44_03755, DQR61_02975, DQS14_04090, DQY10_06940, DQZ46_13555, DQZ56_05945, DR982_16565, DRL45_04255, DRM14_09660, DRM16_03120, DRR75_03360, DRT38_10160, DRT61_12455, DRT65_06785, DRV05_07095, DRV83_19365, DRW84_09815, DRX66_00880, DS270_05640, DS296_12670, DS451_02255, DS453_00880, DS521_06785, DS619_08010, DSF69_08865, DSF94_03190, DSG41_05900, DSM38_04975, DSN15_04670, DSR36_09055, DTE73_02045, DTF68_09765, DTG22_12765, DTG27_13190, DTW13_08230, DTW14_14180, DTW26_03215, DU071_11260, DU223_00815, DU657_08780, DU821_00880, DU879_06935, DU924_09400, DUQ28_08425, DUQ56_13420, DUQ92_08185, DUR36_08615, DUV75_05405, DUW10_03165, DUW48_08950, DVF14_05690, DVF88_07330, DVG01_09235, DVZ53_03735, DWU22_19580, DWU62_11335, DY580_11365, DYM27_07925, DYS82_00350, DZG11_00335, E0584_01250, E0595_11730, E0935_00855, E0989_05990, E0M34_10705, E0U75_04125, E0V94_07290, E1336_11680, E1A11_05885, E1A20_05840, E2A46_17665, E5196_05965, E6W45_05500, EBB93_03040, EBC01_21145, EBD14_00860, EBD99_10295, EBK21_06270, EBL31_13265, EBO41_03425, EBP31_09100, EC404_08070, EC52_14745, ECA50_00445, ECC89_00860, ED424_07445, ED467_11060, EDL18_03060, EEK73_12420, EEQ30_12970, EER35_04045, EGL32_10090, EGN81_04765, EGU67_11950, EGU98_03095, EHB09_10535, EHB24_03735, EHB55_11200, EHC98_03055, EIE48_09660, EIW53_18530, EJI18_05890, EJO08_11670, EJO98_09225, EKA25_06365, EL822_04920, ELO47_13715, ELR28_07270, ELS01_06375, EM832_11915, EM840_10400, EMN66_05265, EMY79_13580, EO190_14565, EP115_07705, EP446_06155, EPB30_06160, EPH81_07280, EQG93_08445, EQG94_09870, ERM04_03720, EU306_03750, EU349_08360, EU873_00795, EUB95_13460, EUQ56_00860, EUQ65_11050, EUQ74_00860, EUS13_03060, EVY71_04545, EW905_00790, EWB18_11520, EWC77_19870, EWE52_19105, EWJ47_08400, EWZ09_02835, EXA47_09580, EXB31_15725, EXB41_07345, EYA29_03770, EYJ91_09420, F0D96_17675, F2O93_12650, F2P00_07215, F3Q46_04935, F3Q58_03020, F3Q59_06955, F3Q88_01670, F3Q97_08560, F3R12_09955, F3R61_02840, F3R63_05705, F9G02_14055, F9O44_13860, FE758_17770, FEM52_12105, FGZ46_08045, FJM64_04970, FL833_04735, FQC24_05140, FQD13_14905, GCH31_10620, GCQ81_09345, GCZ80_15175, GEZ01_02980, GW08_10915, JO10_11580, KP44_05620, LZ63_12340, NG02_13495, NG06_06920, NG18_10515, NU83_16840, QA89_06420, QB40_06310, QD15_00880, R035_07945, RJ78_12550, Y934_03050, YG50_18310, YR17_08350, Z700_03565, ZB89_00915, ZC54_06305, ZT09_03790, ZT28_04760, ZT74_03190, ZT89_19225, ZU86_18125, ZU92_03995, ZV06_08505, ZV17_16945, ZV33_03590, ZV34_03955, ZV38_11975, ZV58_14395, ZV70_03800, ZV78_07765, ZW74_17220, ZX03_04645, ZY23_00845, ZY27_09200, ZY40_05085, ZY51_16640, ZZ18_05055, ZZ43_02670, ZZ77_08755, ZZ79_12430
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2J0RDY6
#3: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0 M Ammonium tartrate dibasic, 0.1 M Sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→48.85 Å / Num. obs: 43178 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 61.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.05 / Rrim(I) all: 0.138 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 7.4 % / % possible all: 100

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.5-2.541.61587321490.3520.97
6.78-48.86231614321810.0230.063

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FVJ

5fvj


Resolution: 2.5→48.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.466 / SU ML: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.888 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 2094 4.9 %RANDOM
Rwork0.2139 ---
obs0.2164 41056 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.16 Å2 / Biso mean: 73.782 Å2 / Biso min: 39.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20.9 Å2-0 Å2
2--1.8 Å20 Å2
3----5.83 Å2
Refinement stepCycle: final / Resolution: 2.5→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8859 0 317 213 9389
Biso mean--95.55 70.22 -
Num. residues----1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0139373
X-RAY DIFFRACTIONr_bond_other_d0.0040.0178887
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.64712740
X-RAY DIFFRACTIONr_angle_other_deg1.1741.58320396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06751109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6722.274497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.584151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5051554
X-RAY DIFFRACTIONr_chiral_restr0.0570.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022158
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41190.12
12B41190.12
21A41690.12
22C41690.12
31A41660.11
32D41660.11
41A42050.12
42E42050.12
51A42000.11
52F42000.11
61B41940.12
62C41940.12
71B41150.12
72D41150.12
81B40810.14
82E40810.14
91B40960.12
92F40960.12
101C41640.13
102D41640.13
111C41340.13
112E41340.13
121C41720.12
122F41720.12
131D41170.13
132E41170.13
141D41620.11
142F41620.11
151E41700.12
152F41700.12
161G9760.15
162H9760.15
171G10100.15
172I10100.15
181G9890.14
182J9890.14
191G9870.12
192K9870.12
201G9770.16
202L9770.16
211H10200.17
212I10200.17
221H9730.18
222J9730.18
231H9520.14
232K9520.14
241H9580.19
242L9580.19
251I10040.16
252J10040.16
261I9780.14
262K9780.14
271I9930.18
272L9930.18
281J9690.17
282K9690.17
291J10020.19
292L10020.19
301K9660.17
302L9660.17
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 134 -
Rwork0.372 3063 -
all-3197 -
obs--100 %

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more