[English] 日本語
Yorodumi
- PDB-8iq5: Crystal structure of trimeric K2-2 TSP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iq5
TitleCrystal structure of trimeric K2-2 TSP
ComponentsK2-2 TSP
KeywordsHYDROLASE / bacteriophage / tailspike protein / Klebsiella pneumoniae K2
Biological speciesKlebsiella phage VLC6 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsYe, T.J. / Huang, K.F. / Ko, T.P.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Mbio / Year: 2024
Title: Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation.
Authors: Ye, T.J. / Fung, K.M. / Lee, I.M. / Ko, T.P. / Lin, C.Y. / Wong, C.L. / Tu, I.F. / Huang, T.Y. / Yang, F.L. / Chang, Y.P. / Wang, J.T. / Lin, T.L. / Huang, K.F. / Wu, S.H.
History
DepositionMar 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: K2-2 TSP
B: K2-2 TSP
C: K2-2 TSP
D: K2-2 TSP
E: K2-2 TSP
F: K2-2 TSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,94434
Polymers389,2346
Non-polymers2,71028
Water93,0475165
1
A: K2-2 TSP
B: K2-2 TSP
C: K2-2 TSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,84416
Polymers194,6173
Non-polymers1,22713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: K2-2 TSP
E: K2-2 TSP
F: K2-2 TSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,10018
Polymers194,6173
Non-polymers1,48315
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.815, 82.838, 196.140
Angle α, β, γ (deg.)90.000, 98.371, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 15 through 21 or resid 23...
d_2ens_1(chain "B" and (resid 15 through 21 or resid 23...
d_3ens_1(chain "C" and (resid 15 through 21 or resid 23...
d_4ens_1(chain "D" and (resid 15 through 21 or resid 23...
d_5ens_1(chain "E" and (resid 15 through 21 or resid 23...
d_6ens_1(chain "F" and (resid 15 through 21 or resid 23...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUSERSERAA15 - 2146 - 52
d_12ALAALAALAALAAA2354
d_13LEULEULEULEUAA2556
d_14ALAALASERSERAA27 - 3158 - 62
d_15ASPASPGLYGLYAA33 - 3464 - 65
d_16LEULEULEULEUAA3667
d_17LEULEUVALVALAA39 - 5570 - 86
d_18SERSERARGARGAA59 - 7690 - 107
d_19LEULEUVALVALAA78 - 80109 - 111
d_110PROPROALAALAAA84 - 87115 - 118
d_111METMETALAALAAA89 - 123120 - 154
d_112TYRTYRPHEPHEAA125 - 127156 - 158
d_113GLYGLYILEILEAA129 - 133160 - 164
d_114VALVALSERSERAA135 - 138166 - 169
d_115ALAALAILEILEAA140 - 142171 - 173
d_116GLYGLYTYRTYRAA144 - 145175 - 176
d_117GLYGLYVALVALAA147 - 149178 - 180
d_118ILEILEGLYGLYAA151 - 158182 - 189
d_119VALVALTYRTYRAA161 - 168192 - 199
d_120TYRTYRLEULEUAA170 - 183201 - 214
d_121GLYGLYALAALAAA185 - 191216 - 222
d_122THRTHRTHRTHRAA193224
d_123GLYGLYGLYGLYAA195 - 202226 - 233
d_124THRTHRVALVALAA205 - 206236 - 237
d_125LYSLYSARGARGAA210 - 231241 - 262
d_126GLYGLYTYRTYRAA233 - 242264 - 273
d_127VALVALLEULEUAA244 - 262275 - 293
d_128SERSERLEULEUAA265 - 269296 - 300
d_129PHEPHECYSCYSAA271 - 317302 - 348
d_130GLYGLYSERSERAA319 - 367350 - 398
d_131ASPASPGLUGLUAA369 - 388400 - 419
d_132GLUGLUASPASPAA390 - 444421 - 475
d_133GLYGLYTHRTHRAA446 - 449477 - 480
d_134SERSERVALVALAA451 - 453482 - 484
d_135TYRTYRMETMETAA455 - 468486 - 499
d_136VALVALVALVALAA470 - 473501 - 504
d_137VALVALGLNGLNAA475 - 481506 - 512
d_138GLNGLNALAALAAA483 - 484514 - 515
d_139THRTHRGLYGLYAA486 - 489517 - 520
d_140PHEPHESERSERAA491 - 494522 - 525
d_141METMETMETMETAA496527
d_142ASNASNGLYGLYAA498 - 507529 - 538
d_143VALVALVALVALAA509540
d_144GLYGLYPHEPHEAA512 - 513543 - 544
d_145ASPASPLEULEUAA515 - 521546 - 552
d_146VALVALVALVALAA525556
d_147ALAALAASNASNAA527 - 528558 - 559
d_148GLYGLYTHRTHRAA530 - 532561 - 563
d_149GLYGLYASNASNAA534 - 541565 - 572
d_150LEULEUPROPROAA543 - 548574 - 579
d_151GLYGLYILEILEAA550 - 558581 - 589
d_152THRTHRLYSLYSAA560 - 577591 - 608
d_153GOLGOLGOLGOLAH601
d_21GLUGLUSERSERBB15 - 2146 - 52
d_22ALAALAALAALABB2354
d_23LEULEULEULEUBB2556
d_24ALAALASERSERBB27 - 3158 - 62
d_25ASPASPGLYGLYBB33 - 3464 - 65
d_26LEULEULEULEUBB3667
d_27LEULEUVALVALBB39 - 5570 - 86
d_28SERSERARGARGBB59 - 7690 - 107
d_29LEULEUVALVALBB78 - 80109 - 111
d_210PROPROALAALABB84 - 87115 - 118
d_211METMETALAALABB89 - 123120 - 154
d_212TYRTYRPHEPHEBB125 - 127156 - 158
d_213GLYGLYILEILEBB129 - 133160 - 164
d_214VALVALSERSERBB135 - 138166 - 169
d_215ALAALAILEILEBB140 - 142171 - 173
d_216GLYGLYTYRTYRBB144 - 145175 - 176
d_217GLYGLYVALVALBB147 - 149178 - 180
d_218ILEILEGLYGLYBB151 - 158182 - 189
d_219VALVALTYRTYRBB161 - 168192 - 199
d_220TYRTYRLEULEUBB170 - 183201 - 214
d_221GLYGLYALAALABB185 - 191216 - 222
d_222THRTHRTHRTHRBB193224
d_223GLYGLYGLYGLYBB195 - 202226 - 233
d_224THRTHRVALVALBB205 - 206236 - 237
d_225LYSLYSARGARGBB210 - 231241 - 262
d_226GLYGLYTYRTYRBB233 - 242264 - 273
d_227VALVALLEULEUBB244 - 262275 - 293
d_228SERSERLEULEUBB265 - 269296 - 300
d_229PHEPHECYSCYSBB271 - 317302 - 348
d_230GLYGLYSERSERBB319 - 367350 - 398
d_231ASPASPGLUGLUBB369 - 388400 - 419
d_232GLUGLUASPASPBB390 - 444421 - 475
d_233GLYGLYTHRTHRBB446 - 449477 - 480
d_234SERSERVALVALBB451 - 453482 - 484
d_235TYRTYRMETMETBB455 - 468486 - 499
d_236VALVALVALVALBB470 - 473501 - 504
d_237VALVALGLNGLNBB475 - 481506 - 512
d_238GLNGLNALAALABB483 - 484514 - 515
d_239THRTHRGLYGLYBB486 - 489517 - 520
d_240PHEPHESERSERBB491 - 494522 - 525
d_241METMETMETMETBB496527
d_242ASNASNGLYGLYBB498 - 507529 - 538
d_243VALVALVALVALBB509540
d_244GLYGLYPHEPHEBB512 - 513543 - 544
d_245ASPASPLEULEUBB515 - 521546 - 552
d_246VALVALVALVALBB525556
d_247ALAALAASNASNBB527 - 528558 - 559
d_248GLYGLYTHRTHRBB530 - 532561 - 563
d_249GLYGLYASNASNBB534 - 541565 - 572
d_250LEULEUPROPROBB543 - 548574 - 579
d_251GLYGLYILEILEBB550 - 558581 - 589
d_252THRTHRLYSLYSBB560 - 577591 - 608
d_253GOLGOLGOLGOLBL602
d_31GLUGLUSERSERCC15 - 2146 - 52
d_32ALAALAALAALACC2354
d_33LEULEULEULEUCC2556
d_34ALAALASERSERCC27 - 3158 - 62
d_35ASPASPGLYGLYCC33 - 3464 - 65
d_36LEULEULEULEUCC3667
d_37LEULEUVALVALCC39 - 5570 - 86
d_38SERSERARGARGCC59 - 7690 - 107
d_39LEULEUVALVALCC78 - 80109 - 111
d_310PROPROALAALACC84 - 87115 - 118
d_311METMETALAALACC89 - 123120 - 154
d_312TYRTYRPHEPHECC125 - 127156 - 158
d_313GLYGLYILEILECC129 - 133160 - 164
d_314VALVALSERSERCC135 - 138166 - 169
d_315ALAALAILEILECC140 - 142171 - 173
d_316GLYGLYTYRTYRCC144 - 145175 - 176
d_317GLYGLYVALVALCC147 - 149178 - 180
d_318ILEILEGLYGLYCC151 - 158182 - 189
d_319VALVALTYRTYRCC161 - 168192 - 199
d_320TYRTYRLEULEUCC170 - 183201 - 214
d_321GLYGLYALAALACC185 - 191216 - 222
d_322THRTHRTHRTHRCC193224
d_323GLYGLYGLYGLYCC195 - 202226 - 233
d_324THRTHRVALVALCC205 - 206236 - 237
d_325LYSLYSARGARGCC210 - 231241 - 262
d_326GLYGLYTYRTYRCC233 - 242264 - 273
d_327VALVALLEULEUCC244 - 262275 - 293
d_328SERSERLEULEUCC265 - 269296 - 300
d_329PHEPHECYSCYSCC271 - 317302 - 348
d_330GLYGLYSERSERCC319 - 367350 - 398
d_331ASPASPGLUGLUCC369 - 388400 - 419
d_332GLUGLUASPASPCC390 - 444421 - 475
d_333GLYGLYTHRTHRCC446 - 449477 - 480
d_334SERSERVALVALCC451 - 453482 - 484
d_335TYRTYRMETMETCC455 - 468486 - 499
d_336VALVALVALVALCC470 - 473501 - 504
d_337VALVALGLNGLNCC475 - 481506 - 512
d_338GLNGLNALAALACC483 - 484514 - 515
d_339THRTHRGLYGLYCC486 - 489517 - 520
d_340PHEPHESERSERCC491 - 494522 - 525
d_341METMETMETMETCC496527
d_342ASNASNGLYGLYCC498 - 507529 - 538
d_343VALVALVALVALCC509540
d_344GLYGLYPHEPHECC512 - 513543 - 544
d_345ASPASPLEULEUCC515 - 521546 - 552
d_346VALVALVALVALCC525556
d_347ALAALAASNASNCC527 - 528558 - 559
d_348GLYGLYTHRTHRCC530 - 532561 - 563
d_349GLYGLYASNASNCC534 - 541565 - 572
d_350LEULEUPROPROCC543 - 548574 - 579
d_351GLYGLYILEILECC550 - 558581 - 589
d_352THRTHRLYSLYSCC560 - 577591 - 608
d_353GOLGOLGOLGOLCQ602
d_41GLUGLUSERSERDD15 - 2146 - 52
d_42ALAALAALAALADD2354
d_43LEULEULEULEUDD2556
d_44ALAALASERSERDD27 - 3158 - 62
d_45ASPASPGLYGLYDD33 - 3464 - 65
d_46LEULEULEULEUDD3667
d_47LEULEUVALVALDD39 - 5570 - 86
d_48SERSERARGARGDD59 - 7690 - 107
d_49LEULEUVALVALDD78 - 80109 - 111
d_410PROPROALAALADD84 - 87115 - 118
d_411METMETALAALADD89 - 123120 - 154
d_412TYRTYRPHEPHEDD125 - 127156 - 158
d_413GLYGLYILEILEDD129 - 133160 - 164
d_414VALVALSERSERDD135 - 138166 - 169
d_415ALAALAILEILEDD140 - 142171 - 173
d_416GLYGLYTYRTYRDD144 - 145175 - 176
d_417GLYGLYVALVALDD147 - 149178 - 180
d_418ILEILEGLYGLYDD151 - 158182 - 189
d_419VALVALTYRTYRDD161 - 168192 - 199
d_420TYRTYRLEULEUDD170 - 183201 - 214
d_421GLYGLYALAALADD185 - 191216 - 222
d_422THRTHRTHRTHRDD193224
d_423GLYGLYGLYGLYDD195 - 202226 - 233
d_424THRTHRVALVALDD205 - 206236 - 237
d_425LYSLYSARGARGDD210 - 231241 - 262
d_426GLYGLYTYRTYRDD233 - 242264 - 273
d_427VALVALLEULEUDD244 - 262275 - 293
d_428SERSERLEULEUDD265 - 269296 - 300
d_429PHEPHECYSCYSDD271 - 317302 - 348
d_430GLYGLYSERSERDD319 - 367350 - 398
d_431ASPASPGLUGLUDD369 - 388400 - 419
d_432GLUGLUASPASPDD390 - 444421 - 475
d_433GLYGLYTHRTHRDD446 - 449477 - 480
d_434SERSERVALVALDD451 - 453482 - 484
d_435TYRTYRMETMETDD455 - 468486 - 499
d_436VALVALVALVALDD470 - 473501 - 504
d_437VALVALGLNGLNDD475 - 481506 - 512
d_438GLNGLNALAALADD483 - 484514 - 515
d_439THRTHRGLYGLYDD486 - 489517 - 520
d_440PHEPHESERSERDD491 - 494522 - 525
d_441METMETMETMETDD496527
d_442ASNASNGLYGLYDD498 - 507529 - 538
d_443VALVALVALVALDD509540
d_444GLYGLYPHEPHEDD512 - 513543 - 544
d_445ASPASPLEULEUDD515 - 521546 - 552
d_446VALVALVALVALDD525556
d_447ALAALAASNASNDD527 - 528558 - 559
d_448GLYGLYTHRTHRDD530 - 532561 - 563
d_449GLYGLYASNASNDD534 - 541565 - 572
d_450LEULEUPROPRODD543 - 548574 - 579
d_451GLYGLYILEILEDD550 - 558581 - 589
d_452THRTHRLYSLYSDD560 - 577591 - 608
d_453GOLGOLGOLGOLDU601
d_51GLUGLUSERSEREE15 - 2146 - 52
d_52ALAALAALAALAEE2354
d_53LEULEULEULEUEE2556
d_54ALAALASERSEREE27 - 3158 - 62
d_55ASPASPGLYGLYEE33 - 3464 - 65
d_56LEULEULEULEUEE3667
d_57LEULEUVALVALEE39 - 5570 - 86
d_58SERSERARGARGEE59 - 7690 - 107
d_59LEULEUVALVALEE78 - 80109 - 111
d_510PROPROALAALAEE84 - 87115 - 118
d_511METMETALAALAEE89 - 123120 - 154
d_512TYRTYRPHEPHEEE125 - 127156 - 158
d_513GLYGLYILEILEEE129 - 133160 - 164
d_514VALVALSERSEREE135 - 138166 - 169
d_515ALAALAILEILEEE140 - 142171 - 173
d_516GLYGLYTYRTYREE144 - 145175 - 176
d_517GLYGLYVALVALEE147 - 149178 - 180
d_518ILEILEGLYGLYEE151 - 158182 - 189
d_519VALVALTYRTYREE161 - 168192 - 199
d_520TYRTYRLEULEUEE170 - 183201 - 214
d_521GLYGLYALAALAEE185 - 191216 - 222
d_522THRTHRTHRTHREE193224
d_523GLYGLYGLYGLYEE195 - 202226 - 233
d_524THRTHRVALVALEE205 - 206236 - 237
d_525LYSLYSARGARGEE210 - 231241 - 262
d_526GLYGLYTYRTYREE233 - 242264 - 273
d_527VALVALLEULEUEE244 - 262275 - 293
d_528SERSERLEULEUEE265 - 269296 - 300
d_529PHEPHECYSCYSEE271 - 317302 - 348
d_530GLYGLYSERSEREE319 - 367350 - 398
d_531ASPASPGLUGLUEE369 - 388400 - 419
d_532GLUGLUASPASPEE390 - 444421 - 475
d_533GLYGLYTHRTHREE446 - 449477 - 480
d_534SERSERVALVALEE451 - 453482 - 484
d_535TYRTYRMETMETEE455 - 468486 - 499
d_536VALVALVALVALEE470 - 473501 - 504
d_537VALVALGLNGLNEE475 - 481506 - 512
d_538GLNGLNALAALAEE483 - 484514 - 515
d_539THRTHRGLYGLYEE486 - 489517 - 520
d_540PHEPHESERSEREE491 - 494522 - 525
d_541METMETMETMETEE496527
d_542ASNASNGLYGLYEE498 - 507529 - 538
d_543VALVALVALVALEE509540
d_544GLYGLYPHEPHEEE512 - 513543 - 544
d_545ASPASPLEULEUEE515 - 521546 - 552
d_546VALVALVALVALEE525556
d_547ALAALAASNASNEE527 - 528558 - 559
d_548GLYGLYTHRTHREE530 - 532561 - 563
d_549GLYGLYASNASNEE534 - 541565 - 572
d_550LEULEUPROPROEE543 - 548574 - 579
d_551GLYGLYILEILEEE550 - 558581 - 589
d_552THRTHRLYSLYSEE560 - 577591 - 608
d_553GOLGOLGOLGOLEBA601
d_61GLUGLUSERSERFF15 - 2146 - 52
d_62ALAALAALAALAFF2354
d_63LEULEULEULEUFF2556
d_64ALAALASERSERFF27 - 3158 - 62
d_65ASPASPGLYGLYFF33 - 3464 - 65
d_66LEULEULEULEUFF3667
d_67LEULEUVALVALFF39 - 5570 - 86
d_68SERSERARGARGFF59 - 7690 - 107
d_69LEULEUVALVALFF78 - 80109 - 111
d_610PROPROALAALAFF84 - 87115 - 118
d_611METMETALAALAFF89 - 123120 - 154
d_612TYRTYRPHEPHEFF125 - 127156 - 158
d_613GLYGLYILEILEFF129 - 133160 - 164
d_614VALVALSERSERFF135 - 138166 - 169
d_615ALAALAILEILEFF140 - 142171 - 173
d_616GLYGLYTYRTYRFF144 - 145175 - 176
d_617GLYGLYVALVALFF147 - 149178 - 180
d_618ILEILEGLYGLYFF151 - 158182 - 189
d_619VALVALTYRTYRFF161 - 168192 - 199
d_620TYRTYRLEULEUFF170 - 183201 - 214
d_621GLYGLYALAALAFF185 - 191216 - 222
d_622THRTHRTHRTHRFF193224
d_623GLYGLYGLYGLYFF195 - 202226 - 233
d_624THRTHRVALVALFF205 - 206236 - 237
d_625LYSLYSARGARGFF210 - 231241 - 262
d_626GLYGLYTYRTYRFF233 - 242264 - 273
d_627VALVALLEULEUFF244 - 262275 - 293
d_628SERSERLEULEUFF265 - 269296 - 300
d_629PHEPHECYSCYSFF271 - 317302 - 348
d_630GLYGLYSERSERFF319 - 367350 - 398
d_631ASPASPGLUGLUFF369 - 388400 - 419
d_632GLUGLUASPASPFF390 - 444421 - 475
d_633GLYGLYTHRTHRFF446 - 449477 - 480
d_634SERSERVALVALFF451 - 453482 - 484
d_635TYRTYRMETMETFF455 - 468486 - 499
d_636VALVALVALVALFF470 - 473501 - 504
d_637VALVALGLNGLNFF475 - 481506 - 512
d_638GLNGLNALAALAFF483 - 484514 - 515
d_639THRTHRGLYGLYFF486 - 489517 - 520
d_640PHEPHESERSERFF491 - 494522 - 525
d_641METMETMETMETFF496527
d_642ASNASNGLYGLYFF498 - 507529 - 538
d_643VALVALVALVALFF509540
d_644GLYGLYPHEPHEFF512 - 513543 - 544
d_645ASPASPLEULEUFF515 - 521546 - 552
d_646VALVALVALVALFF525556
d_647ALAALAASNASNFF527 - 528558 - 559
d_648GLYGLYTHRTHRFF530 - 532561 - 563
d_649GLYGLYASNASNFF534 - 541565 - 572
d_650LEULEUPROPROFF543 - 548574 - 579
d_651GLYGLYILEILEFF550 - 558581 - 589
d_652THRTHRLYSLYSFF560 - 577591 - 608
d_653GOLGOLGOLGOLFGA602

NCS oper:
IDCodeMatrixVector
1given(0.304197422478, 0.582850053821, 0.753491700631), (-0.59182585905, -0.504176076659, 0.628926574637), (0.746462377296, -0.637253715945, 0.191576670805)-104.244117433, -56.0608770555, 112.082215255
2given(0.304274410875, -0.5946810811, 0.744158245716), (0.584285297373, -0.500477542729, -0.638852815989), (0.752348173494, 0.629187286112, 0.195180902843)-84.7897702263, 104.122481138, 92.0912836307
3given(-0.388414384001, -0.626476142234, -0.675767644618), (-0.622858987052, -0.361961754374, 0.693563530341), (-0.679103047078, 0.690298002012, -0.249615143507)28.8885850941, -63.8334451513, -7.58769279207
4given(-0.252742443312, 0.519848652869, -0.816013869649), (0.544132668372, -0.621008810614, -0.564152192542), (-0.800025559941, -0.586605007864, -0.125911350522)28.7720545116, 99.0207793159, -3.13018662129
5given(-0.993741307451, 0.109658963832, -0.0212867450881), (0.111145690761, 0.989700067929, -0.0902242260464), (0.0111735979189, -0.092025470342, -0.995693960772)-65.3217379923, 13.9087140151, 98.9501106478

-
Components

#1: Protein
K2-2 TSP


Mass: 64872.395 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella phage VLC6 (virus) / Gene: VLC6_58 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5165 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine pH 9.0, 22% PEG-6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. obs: 651990 / % possible obs: 98.1 % / Redundancy: 4 % / Biso Wilson estimate: 12.95 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Rsym value: 0.058 / Χ2: 1.259 / Net I/σ(I): 24.1
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.56 / Num. unique obs: 63676 / CC1/2: 0.653 / Rpim(I) all: 0.402 / Rrim(I) all: 0.693 / Rsym value: 0.6 / Χ2: 0.556

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8IQE
Resolution: 1.38→25.42 Å / SU ML: 0.105 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.7109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1578 2000 0.31 %
Rwork0.1341 649918 -
obs0.1341 651918 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.42 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25074 0 177 5167 30418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012326278
X-RAY DIFFRACTIONf_angle_d1.243635743
X-RAY DIFFRACTIONf_chiral_restr0.11354011
X-RAY DIFFRACTIONf_plane_restr0.01094649
X-RAY DIFFRACTIONf_dihedral_angle_d12.34589240
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.570009709563
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.55314647223
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.53898178637
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS2.06466388732
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS1.52455294079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.23021380.213244711X-RAY DIFFRACTION95.15
1.42-1.450.2121410.192345748X-RAY DIFFRACTION96.74
1.45-1.50.20321400.173745724X-RAY DIFFRACTION97.02
1.5-1.550.20381410.156545930X-RAY DIFFRACTION97.27
1.55-1.60.16271420.143546021X-RAY DIFFRACTION97.56
1.6-1.660.17771430.137646214X-RAY DIFFRACTION97.81
1.66-1.740.16411420.13346301X-RAY DIFFRACTION98.08
1.74-1.830.15371430.129146530X-RAY DIFFRACTION98.34
1.83-1.950.16661430.12646580X-RAY DIFFRACTION98.61
1.95-2.10.11551440.120846808X-RAY DIFFRACTION98.88
2.1-2.310.1441440.123546955X-RAY DIFFRACTION99.11
2.31-2.640.1451450.132347157X-RAY DIFFRACTION99.36
2.64-3.330.16391460.131747360X-RAY DIFFRACTION99.51
3.33-25.420.1511480.126347879X-RAY DIFFRACTION99.51
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0575490933225-0.0318110609769-0.05549046887080.1802143770010.01091945271550.250131638606-0.00406964323185-0.03885530282890.08761115561930.2520524978770.0219747876493-0.294671609064-0.1667432282380.3612834335740.009996879692220.205630846856-0.0150309785227-0.06056539126310.2237653875180.02175783019690.17510958796-19.1837732326.67477766448120.054012798
20.3539554037310.1382355693970.1648824974570.343274647038-0.06308091698320.3753433821680.0360184650799-0.0105573334385-0.04853935369620.0893508481311-0.0232023249069-0.05518281285390.05935222503070.0593284351401-8.19747895295E-50.1110097726890.00657807372637-0.02087159595010.1116911905660.0122322220470.104183715671-31.99205323933.11892705534108.84167426
30.557033105434-0.240773934342-0.06748915964360.4809044344290.23960352080.498783226455-0.00349493361013-0.0873447621642-0.09559639881380.09053019726590.0001290472295940.03148999804140.107971473077-0.0114713743046-0.03697081380620.0949649200606-0.00335230567232-0.00446250939160.09715360737660.01566637315420.0980128661421-46.93667870020.30495512609599.1236025307
40.31116954718-9.45283617635E-50.2055190781660.147683026938-0.003826238067510.2955147388170.0288824094070.0432388258991-0.0385300050507-0.0419787350617-0.00226037720112-0.003260528057990.05328376226050.01491095233120.0001626154629840.07677614158580.001256662744650.001927341529680.0789352734859-0.005333962090510.0859370627148-52.9746342325-0.43513222001374.9303935974
50.4221801839670.00172210902174-0.04411406262370.300165383596-0.0730664261030.2521225438790.04288369043370.013963399334-0.04844071886160.00769442396193-0.029060501359-0.00301748232920.0862921937168-0.03432915247032.06420301116E-60.1601562053120.00107239145661-0.01471510837540.12440503575-0.007033420468560.120711886983-74.6168481742-5.4098467601946.2947983524
60.2345064198250.02808632196990.005227892161650.03359423745060.04457244047250.1137167172290.03562296712540.1012772659840.026840596849-0.0816917009461-0.0432794855241-0.1007463839360.01475297223990.0141289252365-3.77706543208E-60.1607651623740.0225446480016-0.006615381556470.142981026293-0.02325080305210.135327869253-63.59417067710.52958714199142.6085643788
70.2087127707410.07088299183060.005818028003790.105629071591-0.0844850050060.09740715047880.03525763212240.07196518429240.0299098616239-0.010305551418-0.0389828942726-0.01959286886970.01859791433380.02720356064322.37207194327E-50.14049195950.00978806711106-0.00954993959310.123536485541-0.01300284666070.122131303715-64.65059194220.47925795533846.8730796769
80.3410645267530.197347102370.1376159340630.1669248855140.1778915928610.2935168816690.0769205758796-0.01750861337930.003419355754670.0167380616101-0.0195935799244-0.0596963943662-0.02796370203680.1326214143353.16701582923E-50.109835749709-0.0357838559279-0.0125639218440.137902919357-0.007069254215970.143041221866-16.846964739829.907786929112.392341339
90.2800580034060.06717793532350.1017076427140.242530530344-0.01973312461290.139102134661-0.0124937861227-0.07337241081670.01581865188580.0733756396269-0.0241756993106-0.0316346060756-0.04615700636050.0267969282889-0.005455070504750.0954838031223-0.00948301311087-0.01826512327680.107226998732-0.006891156137250.117686284477-36.516935243328.1860310117106.485169492
100.4574427008150.17624938958-0.3613570503440.284988366705-0.2593589102150.8773044088350.00886207565625-0.03941026546490.1207006171680.04539962693430.00681687979999-0.00130538882769-0.1324042731730.01318144766020.03703421668830.0791071777954-0.00135432200369-0.01744430279140.0758085088133-0.01408970748790.112607037136-43.614717388533.918206500795.9416596669
110.3531996232630.05042756809690.3095621823930.1369293170110.06271758503180.391932173212-0.0221644557175-0.04555883527470.026651560467-0.0166222433758-0.00439202488750.0171378897373-0.0185819744337-0.092606835323-0.002505172187910.05556169612910.0112513277823-0.0007086475992560.0811019847882-0.006618704929290.0814028269181-64.147020257822.82169930587.0421498092
120.2652005819580.04194473916270.02496255686390.381937928575-0.05555244115260.347684674764-0.00288448326063-0.07677169156360.0900350725888-0.0142842195666-0.006573084351520.0314640545255-0.0136001994001-0.03668314112482.14641830667E-50.0955082248670.008279774797290.001821016321920.143022051282-0.01644263710370.125840646424-95.175704433819.764101383368.8679195313
130.183858905968-0.08476499856630.2094098852510.461774920194-0.08223620673450.308765422344-0.00621291121073-0.0431513930417-0.002390745645220.01207709846990.02126610212450.01606763055450.0935614006317-0.03473310127829.93935401329E-50.0872232144232-0.002242073911280.001870799504590.1472954064880.0005490545906590.0965399111414-89.45843860259.7326218213572.5601283766
140.383599267807-0.07113507034020.1445554973620.219842692849-0.1454778543960.125363765182-0.0102728093291-0.0177281281615-0.01608998314390.0728581606656-0.0116301507682-0.107854291240.04194163688990.0332483517941-7.70994403507E-50.0972648462810.022598823888-0.01326227382410.1410697392980.005464885454140.159131596551-7.671940817119.79591286967102.448191869
150.149058887906-0.02398558368660.0527280739650.222843790326-0.1256485432040.326741274507-0.002711472017850.05158147043440.02559184087190.03892322823240.00111908981983-0.0720611314848-0.06290898662750.0886073604188-0.001374099814620.07701960256340.000612300694125-0.000870048547280.1478084672490.005523428671840.139366839883-18.614743835818.527497047887.3542212385
160.2752566558980.1713618719480.1209540291740.9600351907150.06763752373440.201452578604-0.005094172979620.0757608725565-0.0104176688138-0.0786539118882-0.00646442819193-0.1158867295040.008956370119910.1106601587420.0005950613581830.07198590964160.0122644081440.01077128580010.143466232640.005998584666640.115912649015-25.359147288113.398093034776.2946609324
170.438733383175-0.06338781286630.2446188024150.0908321899008-0.07105888497640.32597198095-0.02676422772230.0793826848440.0540169564511-0.0353755376629-0.00370500531251-0.00339696277496-0.03878396509040.0455184348064-0.001079994853310.0823228986824-0.007150300906620.003180080561330.09173385401710.01324808546230.0869290834089-44.837492567225.353546816966.3644601821
180.36267542670.0494273872133-0.02238717531680.3416143328960.1479482932910.271711564483-0.005689067520050.1001462580140.038070459943-0.0454179444176-0.0292547030211-0.0327093630542-0.04447030178140.0199021990474-1.9073550341E-50.1401098421850.00221805123789-0.004356605159450.1490662657270.03092622345410.121272150919-69.935906778834.025653013841.5478688417
190.3746944574080.008301256096810.08869132155920.2189832413220.2660774263710.375822188255-0.0131620904005-0.008626508251790.0860606360793-0.0143364045036-0.03843562383290.0255620536684-0.0759111170189-0.000426037204021-1.72273346042E-50.114183145847-0.00312941643818-0.01847384004080.09043523408450.02489438685170.106644237493-71.57906805937.686850080753.3157758804
200.109843730018-0.1018673860580.03830126226740.113674448197-0.0111115159270.139769053466-0.009439763961340.0665713724462-0.05769909449910.003797655061580.001773660070590.1432850969820.0274161330372-0.1476508279120.0001311745699950.1160105165370.0105315391906-0.005312754737860.1194448519290.003605078322580.123548071062-49.230680708228.8029414633-19.598965507
210.3861367938520.0417757767970.2355166228870.216341516568-0.05218183850130.207797216082-0.01987914110610.02528718762720.028086985359-0.02092118586610.007623852653080.0192295131965-0.0231040207565-0.008264921721964.97961716968E-50.1166246561690.009572186620750.000130240642960.1028305485170.006898442509950.0938071267971-34.025110823430.5196082286-11.0026237622
220.2228823577160.008807493811370.106119679030.184254004855-0.004220263287170.2369711769650.009807069204460.03264331494590.0670061959695-0.04661073962770.00243547449993-0.0183057785087-0.09941558612060.02128506160970.002514584183070.1081883990630.0007900132080930.00631569554270.08630959160590.00955032460140.0960131261907-20.252042106933.8513541369-0.183277101385
230.4027592969-0.06937421682390.1642028189410.0560143789002-0.07246321866280.2194488698-0.00294479789950.01955721301-0.00322466712592-0.00281680706257-0.00731490706849-0.02618444496490.008474116837090.04677845740381.45295745432E-50.1000760994210.001754404418610.007566834396630.09323203318540.004594661040120.0977467845753-0.8798354367121.46422949499.51270779661
240.192352818729-0.02216020202360.09101534167120.3336393038550.06755133019950.346851990622-0.009669194958430.01103448629580.1017138546050.003238482903590.00800303380754-0.0439790309996-0.00226221732730.0587268494738-8.42330685694E-50.1040473178940.004004802054090.009853546059130.1407095643910.01493543131370.13394653511130.002261271516.515698300327.7206673161
250.1093467326370.03391135592490.07987205657940.2431631693760.08904362215480.112009399827-0.01121875220620.03672485201640.02357562599470.001410829310620.0194261470420.0006862328331330.1004236376178.0520118599E-51.15058121767E-50.1107152377290.01439034669770.01398071756140.1576484860130.001011133022270.11100718819424.22218132284.8251222909825.6708200328
260.1004527713990.02377072879510.08286236031490.155213930607-0.01466922673820.1390886157140.01438707572570.00181957962606-0.000710701805246-0.002158160482680.001651543069750.001115896995610.07944598052620.02179725744699.45546705109E-70.1083313188220.008545386233980.01264655386540.1391321250320.00556839972790.11601151541821.76517108488.7401820008525.0581711733
270.155771856650.1046892631870.009875945885750.369047812448-0.07269925730650.0727698382625-0.0009097328818680.143707509727-0.0446154930729-0.296267782820.003127521601790.1594748494420.054975333793-0.15108516024-0.0008146189040990.145822866763-0.00735261001724-0.01663707990070.145440598983-0.002481663763210.172092295903-60.799196084316.9585612894-6.30091152947
280.300825149301-0.01192465920830.1118872763650.255631096291-0.01239435038460.459363805051-0.00894054182587-0.00965044793553-0.0189852846064-0.005338343417360.01332339552270.03573403036510.00360177436829-0.0798839342111-6.89499178181E-60.0999847697814-0.003422664964970.004794829912560.1091095040930.003526429837720.106891881215-50.304734095418.32717614947.08007196211
290.19690054637-0.07229624891710.09148020855320.171665043313-0.03911426488580.240049999104-0.0176032798748-0.0485122755507-0.04009199769390.07157656720990.02513682166620.0703715447360.00554746001541-0.0881620531952-0.0002102091702460.09665611990860.0005880899398470.01291615670090.1096113464770.009250424141710.0988270219008-40.124759544317.273473060521.4429565157
300.4125211493120.0441011785890.2435208203580.08441723746390.04177315736420.289647453896-0.0212435441022-0.0449332024970.01955461395790.02171178671730.00775112377745-0.0176755296806-0.0367533803416-0.01011064366770.0001032662153530.1049462143040.007247313019730.00304383825250.08759904029230.000792446864070.0753640303787-19.312701894128.071400839330.0312372063
310.341471750862-0.0934273707496-0.04203235483520.326028972333-0.1131318369680.311123500977-0.00224933783419-0.03279631278280.02988403356050.0398903150502-0.00587343664466-0.0155567575416-0.013647240399-0.0171596434938-1.79650623469E-50.1367697086340.000905857439046-0.0108045514390.121871435636-0.01444561249060.1090323324566.7884877243835.827949386853.7454446475
320.114737445926-0.0512206658218-0.03906564455110.154597075254-0.1396026398270.201634092690.02518951123310.05999392859650.0514126123548-0.0209558995155-0.0375684359303-0.0668569374608-0.05914039924870.002973574595952.77866608558E-50.1696647982890.0017536268693-0.0202759386940.112425637861-0.004173661799250.13090360902410.657939424239.700476725141.5315039904
330.193795348875-0.032193810577-0.01264375315990.0899292509566-0.1031115811360.158108019319-0.02015352807930.03293778215280.0309945825480.00109800250224-0.0149920500144-0.0425059047597-0.03407408026630.02922460866993.11426110459E-60.148263266651-8.06226744998E-5-0.01381468503020.116710235787-0.01009532283560.1123172483166.8858920006637.080026470542.1405231176
340.1010636671160.0467468067864-0.003087921319310.07156015701120.01935179379550.09833071098290.01116035808680.07892100830350.100980263715-0.1842083139970.00825464851760.169879024768-0.135686468133-0.06310943331730.0007701785383010.206697817116-0.0247209920158-0.02045932150870.143244838266-0.006857197694880.134703373765-48.31730206467.58763423853-21.0250833247
350.116879276373-0.05142731763470.05606602967270.0736419565884-0.04224492235550.03838036856960.007134001344770.14946939735-0.0493376018011-0.216426781448-0.04204705929850.0201908486254-0.02104842979570.1524890710597.88316584673E-50.2113208465650.00226159382367-0.01221174512720.152804081443-0.02213300868930.122410739198-38.04083912067.02240779797-21.8381583704
360.179409512196-0.0671794088510.06625469341140.0827310551645-0.02529751576170.209795413441-0.009356012778570.0426046414916-0.05474684163510.01374437970770.01839552777280.0461007664890.0780096189037-0.0659136129646-3.06385230112E-60.134031502241-0.01022325787390.000162336485930.108199694746-0.007879884163430.112883051-34.01150168841.6552966676-3.97378759805
370.1788525712560.07926817026810.1014410127320.251020384468-0.01355161769250.222480763976-0.01541302731160.0590391437233-0.134959052091-0.0625435402242-0.0103214842744-0.06209160523090.103306293670.0129989543243-0.0003066441076640.1295634971410.009868888576650.008796226494340.0911024456016-0.008215419992730.124589997312-20.74642634480.295953397391-0.32332719805
380.140333111860.101871889514-0.01681863814310.07499939116980.0002172075358010.1654673017260.01789963729580.0262165613329-0.0656505654265-0.0210556691944-0.00507484395182-0.004328052588460.0530398112376-0.002824769830688.68022041918E-60.1075919042460.009176633973930.0003446030178560.07706289891350.002133545981640.110626347845-21.5532163791-0.5834552658579.91721023063
390.08481121254270.00358430038980.08576544739430.115005368944-0.01408123408820.09327398684910.0241578047196-0.00479876131124-0.0564062736452-0.0596342822887-0.0109679867959-0.02615080005030.05653945031840.045052411088-7.640659698E-60.1167449260930.009377817678340.005539282011980.09872939395490.00864868378990.115443957036-15.47687020181.0855619887915.3053431823
400.1522087196710.02517195326430.1757121929870.178682529710.04322324043030.2020735478810.0331097598983-0.0227699069333-0.06172428204140.0220250931405-0.0132727207465-0.006576538194980.0472475922149-0.0212818619139-8.72421811968E-60.1141747850250.004559953738450.0005985319788720.1116091069740.02265403136960.118296887881-12.72040769990.54387883308328.9416210729
410.1414173266660.03366287964560.06609458994760.0259818399528-0.02452971632050.1193205320610.0141904548463-0.0273248762290.01677179309860.00209743090095-0.003529460337370.04506085528910.00235802188508-0.04799580318881.75444585417E-50.1234290002540.00361410278378-0.001779708579440.1251363235150.02017475777490.116602839388-7.09515237952.3181413600439.6737005008
420.422434786440.0547598434219-0.0118433360280.3075993574170.1172699993670.2695558082890.03906219597460.00578455697137-0.03600562267610.0166943459402-0.0101836320413-0.01727932134340.09587085819050.0314545860269-6.97830444036E-50.1588121917040.00766484563016-0.009418607642020.1219935694390.01282838110070.1212670489717.03526741742-3.9336411818752.4544457578
430.188434096694-0.0870576824826-0.05579872187140.09942436117280.08404600621680.1360934211240.00809638065068-0.05058443485070.03420437965130.0419648531969-0.01510939474090.08511805139520.0262634464054-0.00647281791981-4.12345497151E-50.154269882174-0.0104968855634-0.002662565333330.1356908564160.02828813876680.13614995087-3.127116506244.0401384812555.7601904006
440.228952249575-0.02069670537520.006908821320340.1423962360470.1292714058350.1321455042520.00769744867424-0.05736776525650.0509831747090.00375181596163-0.01711459926190.03091977674820.0171802933556-0.0131970211422.82762847338E-50.1279009643140.00073167066221-0.005136371961590.1170499924560.02365994105740.113376568399-2.237185941352.9664843514851.3601168148
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 15 through 50 )AA15 - 501 - 36
22chain 'A' and (resid 51 through 152 )AA51 - 15237 - 138
33chain 'A' and (resid 153 through 216 )AA153 - 216139 - 202
44chain 'A' and (resid 217 through 430 )AA217 - 430203 - 416
55chain 'A' and (resid 431 through 489 )AA431 - 489417 - 475
66chain 'A' and (resid 490 through 533 )AA490 - 533476 - 519
77chain 'A' and (resid 534 through 577 )AA534 - 577520 - 563
88chain 'B' and (resid 15 through 86 )BB15 - 861 - 72
99chain 'B' and (resid 87 through 152 )BB87 - 15273 - 138
1010chain 'B' and (resid 153 through 216 )BB153 - 216139 - 202
1111chain 'B' and (resid 217 through 430 )BB217 - 430203 - 416
1212chain 'B' and (resid 431 through 489 )BB431 - 489417 - 475
1313chain 'B' and (resid 490 through 577 )BB490 - 577476 - 563
1414chain 'C' and (resid 15 through 86 )CC15 - 861 - 72
1515chain 'C' and (resid 87 through 152 )CC87 - 15273 - 138
1616chain 'C' and (resid 153 through 216 )CC153 - 216139 - 202
1717chain 'C' and (resid 217 through 430 )CC217 - 430203 - 416
1818chain 'C' and (resid 431 through 489 )CC431 - 489417 - 475
1919chain 'C' and (resid 490 through 577 )CC490 - 577476 - 563
2020chain 'D' and (resid 14 through 50 )DD14 - 501 - 37
2121chain 'D' and (resid 51 through 152 )DD51 - 15238 - 139
2222chain 'D' and (resid 153 through 216 )DD153 - 216140 - 203
2323chain 'D' and (resid 217 through 430 )DD217 - 430204 - 417
2424chain 'D' and (resid 431 through 489 )DD431 - 489418 - 476
2525chain 'D' and (resid 490 through 534 )DD490 - 534477 - 521
2626chain 'D' and (resid 535 through 577 )DD535 - 577522 - 564
2727chain 'E' and (resid 15 through 50 )EE15 - 501 - 36
2828chain 'E' and (resid 51 through 152 )EE51 - 15237 - 138
2929chain 'E' and (resid 153 through 216 )EE153 - 216139 - 202
3030chain 'E' and (resid 217 through 430 )EE217 - 430203 - 416
3131chain 'E' and (resid 431 through 489 )EE431 - 489417 - 475
3232chain 'E' and (resid 490 through 533 )EE490 - 533476 - 519
3333chain 'E' and (resid 534 through 577 )EE534 - 577520 - 563
3434chain 'F' and (resid 15 through 50 )FF15 - 501 - 36
3535chain 'F' and (resid 51 through 86 )FF51 - 8637 - 72
3636chain 'F' and (resid 87 through 152 )FF87 - 15273 - 138
3737chain 'F' and (resid 153 through 216 )FF153 - 216139 - 202
3838chain 'F' and (resid 217 through 258 )FF217 - 258203 - 244
3939chain 'F' and (resid 259 through 307 )FF259 - 307245 - 293
4040chain 'F' and (resid 308 through 386 )FF308 - 386294 - 372
4141chain 'F' and (resid 387 through 430 )FF387 - 430373 - 416
4242chain 'F' and (resid 431 through 489 )FF431 - 489417 - 475
4343chain 'F' and (resid 490 through 533 )FF490 - 533476 - 519
4444chain 'F' and (resid 534 through 577 )FF534 - 577520 - 563

+
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://pdbjlvh1.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