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- PDB-7qij: Complex of the Yersinia enterocolitica Type III secretion export ... -

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基本情報

登録情報
データベース: PDB / ID: 7qij
タイトルComplex of the Yersinia enterocolitica Type III secretion export gate YscV with substrate:chaperone complex YscX:YscY
要素
  • Chaperone protein YscY
  • Low calcium response locus protein D
  • Yop proteins translocation protein X
キーワードPROTEIN TRANSPORT / Type III Secretion System / T3SS / SctV / SctXY
機能・相同性
機能・相同性情報


protein secretion / membrane => GO:0016020 / extracellular region / plasma membrane / cytoplasm
類似検索 - 分子機能
Type III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 ...Type III secretion system YscX / Type III secretion system chaperone, YscY / Type III secretion system YscX (type_III_YscX) / Type III secretion protein HrcV / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
Chaperone protein YscY / Yop proteins translocation protein X / Low calcium response locus protein D
類似検索 - 構成要素
生物種Yersinia enterocolitica (腸炎エルシニア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 4.1 Å
データ登録者Gilzer, D. / Niemann, H.H.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Direct interaction of a chaperone-bound type III secretion substrate with the export gate.
著者: Gilzer, D. / Schreiner, M. / Niemann, H.H.
履歴
登録2021年12月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年6月1日Provider: repository / タイプ: Initial release
改定 1.12022年6月15日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AA: Low calcium response locus protein D
BA: Low calcium response locus protein D
CA: Low calcium response locus protein D
DA: Low calcium response locus protein D
EA: Low calcium response locus protein D
FA: Low calcium response locus protein D
GA: Low calcium response locus protein D
HA: Low calcium response locus protein D
IA: Low calcium response locus protein D
JA: Low calcium response locus protein D
KA: Low calcium response locus protein D
LA: Low calcium response locus protein D
MA: Low calcium response locus protein D
NA: Low calcium response locus protein D
OA: Low calcium response locus protein D
PA: Low calcium response locus protein D
QA: Low calcium response locus protein D
RA: Low calcium response locus protein D
CB: Yop proteins translocation protein X
CC: Chaperone protein YscY
JB: Yop proteins translocation protein X
JC: Chaperone protein YscY
KB: Yop proteins translocation protein X
KC: Chaperone protein YscY
RB: Yop proteins translocation protein X
RC: Chaperone protein YscY
GB: Yop proteins translocation protein X
GC: Chaperone protein YscY
LB: Yop proteins translocation protein X
LC: Chaperone protein YscY
NB: Yop proteins translocation protein X
NC: Chaperone protein YscY
OB: Yop proteins translocation protein X
OC: Chaperone protein YscY
PB: Yop proteins translocation protein X
PC: Chaperone protein YscY
EB: Yop proteins translocation protein X
EC: Chaperone protein YscY
FB: Yop proteins translocation protein X
FC: Chaperone protein YscY
HB: Yop proteins translocation protein X
HC: Chaperone protein YscY
IB: Yop proteins translocation protein X
IC: Chaperone protein YscY
AB: Yop proteins translocation protein X
AC: Chaperone protein YscY
BB: Yop proteins translocation protein X
BC: Chaperone protein YscY
DB: Yop proteins translocation protein X
DC: Chaperone protein YscY
MB: Yop proteins translocation protein X
MC: Chaperone protein YscY
QB: Yop proteins translocation protein X
QC: Chaperone protein YscY


分子量 (理論値)分子数
合計 (水以外)1,172,84654
ポリマ－1,172,84654
非ポリマー00
水00
1
AA: Low calcium response locus protein D
BA: Low calcium response locus protein D
CA: Low calcium response locus protein D
DA: Low calcium response locus protein D
EA: Low calcium response locus protein D
FA: Low calcium response locus protein D
GA: Low calcium response locus protein D
HA: Low calcium response locus protein D
IA: Low calcium response locus protein D
CB: Yop proteins translocation protein X
CC: Chaperone protein YscY
GB: Yop proteins translocation protein X
GC: Chaperone protein YscY
EB: Yop proteins translocation protein X
EC: Chaperone protein YscY
FB: Yop proteins translocation protein X
FC: Chaperone protein YscY
HB: Yop proteins translocation protein X
HC: Chaperone protein YscY
IB: Yop proteins translocation protein X
IC: Chaperone protein YscY
AB: Yop proteins translocation protein X
AC: Chaperone protein YscY
BB: Yop proteins translocation protein X
BC: Chaperone protein YscY
DB: Yop proteins translocation protein X
DC: Chaperone protein YscY


  • 登録者が定義した集合体
  • 根拠: gel filtration, Complex confirmed via co-expression, pull-down and gel filtration.
  • 586 kDa, 27 ポリマー
分子量 (理論値)分子数
合計 (水以外)586,42327
ポリマ－586,42327
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
JA: Low calcium response locus protein D
KA: Low calcium response locus protein D
LA: Low calcium response locus protein D
MA: Low calcium response locus protein D
NA: Low calcium response locus protein D
OA: Low calcium response locus protein D
PA: Low calcium response locus protein D
QA: Low calcium response locus protein D
RA: Low calcium response locus protein D
JB: Yop proteins translocation protein X
JC: Chaperone protein YscY
KB: Yop proteins translocation protein X
KC: Chaperone protein YscY
RB: Yop proteins translocation protein X
RC: Chaperone protein YscY
LB: Yop proteins translocation protein X
LC: Chaperone protein YscY
NB: Yop proteins translocation protein X
NC: Chaperone protein YscY
OB: Yop proteins translocation protein X
OC: Chaperone protein YscY
PB: Yop proteins translocation protein X
PC: Chaperone protein YscY
MB: Yop proteins translocation protein X
MC: Chaperone protein YscY
QB: Yop proteins translocation protein X
QC: Chaperone protein YscY


  • 登録者が定義した集合体
  • 586 kDa, 27 ポリマー
分子量 (理論値)分子数
合計 (水以外)586,42327
ポリマ－586,42327
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)143.460, 324.920, 369.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "AA" and (resid 361 through 387 or resid 390...
d_2ens_1(chain "BA" and (resid 361 through 387 or resid 390...
d_3ens_1(chain "CA" and (resid 361 through 387 or resid 390...
d_4ens_1(chain "DA" and (resid 361 through 387 or resid 390...
d_5ens_1(chain "EA" and (resid 361 through 418 or resid 424...
d_6ens_1(chain "FA" and (resid 361 through 387 or resid 390...
d_7ens_1(chain "GA" and (resid 361 through 387 or resid 390...
d_8ens_1(chain "HA" and (resid 361 through 387 or resid 390...
d_9ens_1(chain "IA" and (resid 361 through 387 or resid 390...
d_10ens_1(chain "JA" and (resid 361 through 387 or resid 390...
d_11ens_1(chain "KA" and (resid 361 through 387 or resid 390...
d_12ens_1(chain "LA" and (resid 361 through 387 or resid 390...
d_13ens_1(chain "MA" and (resid 361 through 387 or resid 390...
d_14ens_1(chain "NA" and (resid 361 through 387 or resid 390...
d_15ens_1(chain "OA" and (resid 361 through 387 or resid 390...
d_16ens_1(chain "PA" and (resid 361 through 387 or resid 390...
d_17ens_1(chain "QA" and (resid 361 through 387 or resid 390...
d_18ens_1(chain "RA" and (resid 361 through 387 or resid 390...
d_1ens_2(chain "AB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_2ens_2(chain "BB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_3ens_2(chain "CB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_4ens_2(chain "DB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_5ens_2(chain "EB" and (resid 52 through 89 or resid 94 through 122))
d_6ens_2(chain "FB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_7ens_2(chain "GB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_8ens_2(chain "HB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_9ens_2(chain "IB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_10ens_2(chain "JB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_11ens_2(chain "KB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_12ens_2(chain "LB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_13ens_2(chain "MB" and (resid 52 through 62 or resid 75 through 122))
d_14ens_2(chain "NB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_15ens_2(chain "OB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_16ens_2(chain "PB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_17ens_2(chain "QB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_18ens_2(chain "RB" and (resid 52 through 62 or resid 75 through 89 or resid 94 through 122))
d_1ens_3(chain "AC" and (resid 8 through 58 or resid 62...
d_2ens_3(chain "BC" and (resid 8 through 41 or resid 50...
d_3ens_3(chain "CC" and (resid 8 through 41 or resid 50...
d_4ens_3(chain "DC" and (resid 8 through 41 or resid 50...
d_5ens_3(chain "EC" and (resid 8 through 41 or resid 50...
d_6ens_3(chain "FC" and (resid 8 through 41 or resid 50...
d_7ens_3(chain "GC" and (resid 8 through 41 or resid 50...
d_8ens_3(chain "HC" and (resid 8 through 41 or resid 50...
d_9ens_3(chain "IC" and (resid 8 through 41 or resid 50 through 58 or resid 62 through 107))
d_10ens_3(chain "JC" and (resid 8 through 41 or resid 50...
d_11ens_3(chain "LC" and (resid 8 through 41 or resid 50...
d_12ens_3(chain "MC" and (resid 8 through 41 or resid 50...
d_13ens_3(chain "NC" and (resid 8 through 41 or resid 50...
d_14ens_3(chain "OC" and (resid 8 through 41 or resid 50...
d_15ens_3(chain "PC" and (resid 8 through 41 or resid 50...
d_16ens_3(chain "QC" and (resid 8 through 41 or resid 50...
d_17ens_3(chain "RC" and (resid 8 through 41 or resid 50...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LEUALAA3 - 29
d_12ens_1LEUGLUA32 - 60
d_13ens_1GLUARGA66 - 78
d_14ens_1LEULEUA89
d_15ens_1LEULEUA92
d_16ens_1TRPILEA99 - 271
d_17ens_1SERSERA273
d_18ens_1LYSGLUA277 - 308
d_19ens_1THRLEUA310 - 323
d_21ens_1LEUALAB2 - 28
d_22ens_1LEUGLUB31 - 59
d_23ens_1GLUARGB65 - 77
d_24ens_1LEULEUB94
d_25ens_1LEULEUB97
d_26ens_1TRPSERB101 - 113
d_27ens_1PHEILEB117 - 276
d_28ens_1SERSERB280
d_29ens_1LYSGLUB285 - 316
d_210ens_1THRLEUB318 - 331
d_31ens_1LEUALAC3 - 29
d_32ens_1LEUGLUC32 - 60
d_33ens_1GLUARGC66 - 78
d_34ens_1LEULEUC95
d_35ens_1LEULEUC98
d_36ens_1TRPSERC116 - 128
d_37ens_1PHEILEC132 - 291
d_38ens_1SERSERC293
d_39ens_1LYSLEUC298 - 343
d_41ens_1LEUALAD1 - 27
d_42ens_1LEUGLUD30 - 58
d_43ens_1GLUARGD64 - 76
d_44ens_1LEULEUD89 - 90
d_45ens_1TRPSERD97 - 109
d_46ens_1PHEILED113 - 272
d_47ens_1SERSERD275
d_48ens_1LYSGLUD280 - 311
d_49ens_1THRLEUD313 - 326
d_51ens_1LEUGLUE2 - 57
d_52ens_1GLUARGE63 - 75
d_53ens_1LEULEUE89
d_54ens_1LEULEUE92
d_55ens_1TRPSERE102 - 114
d_56ens_1PHEILEE117 - 276
d_57ens_1SERSERE278
d_58ens_1LYSGLUE283 - 314
d_59ens_1THRLEUE316 - 329
d_61ens_1LEUALAF4 - 30
d_62ens_1LEUGLUF33 - 61
d_63ens_1GLUARGF67 - 79
d_64ens_1LEULEUF94
d_65ens_1LEULEUF97
d_66ens_1TRPSERF109 - 121
d_67ens_1PHEILEF123 - 282
d_68ens_1SERSERF286
d_69ens_1LYSGLUF291 - 322
d_610ens_1THRLEUF324 - 337
d_71ens_1LEUALAG3 - 29
d_72ens_1LEUGLUG32 - 60
d_73ens_1GLUARGG66 - 78
d_74ens_1LEULEUG94
d_75ens_1LEULEUG97
d_76ens_1TRPSERG111 - 123
d_77ens_1PHEILEG127 - 286
d_78ens_1SERSERG290
d_79ens_1LYSGLUG295 - 326
d_710ens_1THRLEUG328 - 341
d_81ens_1LEUALAH1 - 27
d_82ens_1LEUGLUH29 - 57
d_83ens_1GLUARGH63 - 75
d_84ens_1LEULEUH92
d_85ens_1LEULEUH95
d_86ens_1TRPSERH107 - 119
d_87ens_1PHEILEH123 - 282
d_88ens_1SERSERH284
d_89ens_1LYSGLUH289 - 320
d_810ens_1THRLEUH322 - 335
d_91ens_1LEUALAI3 - 29
d_92ens_1LEUGLUI32 - 60
d_93ens_1GLUARGI66 - 78
d_94ens_1LEULEUI90
d_95ens_1LEULEUI93
d_96ens_1TRPSERI106 - 118
d_97ens_1PHEILEI122 - 281
d_98ens_1SERSERI285
d_99ens_1LYSGLUI290 - 321
d_910ens_1THRLEUI323 - 336
d_101ens_1LEUALAJ3 - 29
d_102ens_1LEUGLUJ32 - 60
d_103ens_1GLUARGJ66 - 78
d_104ens_1LEULEUJ88
d_105ens_1LEULEUJ91
d_106ens_1TRPSERJ100 - 112
d_107ens_1PHEILEJ116 - 275
d_108ens_1SERSERJ279
d_109ens_1LYSGLUJ284 - 315
d_1010ens_1THRLEUJ317 - 330
d_111ens_1LEUALAK2 - 28
d_112ens_1LEUGLUK31 - 59
d_113ens_1GLUARGK62 - 74
d_114ens_1LEULEUK90
d_115ens_1LEULEUK93
d_116ens_1TRPSERK107 - 119
d_117ens_1PHEILEK123 - 282
d_118ens_1SERSERK284
d_119ens_1LYSGLUK289 - 320
d_1110ens_1THRLEUK322 - 335
d_121ens_1LEUALAL1 - 27
d_122ens_1LEUGLUL30 - 58
d_123ens_1GLUARGL64 - 76
d_124ens_1LEULEUL91
d_125ens_1LEULEUL94
d_126ens_1TRPSERL109 - 121
d_127ens_1PHESERL125 - 285
d_128ens_1LYSGLUL290 - 321
d_129ens_1THRLEUL323 - 336
d_131ens_1LEUALAM4 - 30
d_132ens_1LEUARGM33 - 74
d_133ens_1LEULEUM89
d_134ens_1LEULEUM92
d_135ens_1TRPSERM98 - 110
d_136ens_1PHEILEM114 - 273
d_137ens_1SERGLUM275 - 307
d_138ens_1THRLEUM309 - 322
d_141ens_1LEUALAN2 - 28
d_142ens_1LEUGLUN31 - 59
d_143ens_1GLUARGN65 - 77
d_144ens_1LEULEUN87
d_145ens_1LEULEUN90
d_146ens_1TRPSERN102 - 114
d_147ens_1PHEILEN117 - 276
d_148ens_1SERSERN280
d_149ens_1LYSGLUN285 - 316
d_1410ens_1THRLEUN318 - 331
d_151ens_1LEUALAO3 - 29
d_152ens_1LEUGLUO32 - 60
d_153ens_1GLUARGO66 - 78
d_154ens_1LEULEUO93
d_155ens_1LEULEUO96
d_156ens_1TRPILEO105 - 277
d_157ens_1SERSERO280
d_158ens_1LYSGLUO285 - 316
d_159ens_1THRLEUO318 - 331
d_161ens_1LEUALAP3 - 29
d_162ens_1LEUGLUP32 - 60
d_163ens_1GLUARGP66 - 78
d_164ens_1LEULEUP88
d_165ens_1LEULEUP91
d_166ens_1TRPSERP102 - 114
d_167ens_1PHEILEP118 - 277
d_168ens_1SERSERP279
d_169ens_1LYSGLUP284 - 315
d_1610ens_1THRLEUP317 - 330
d_171ens_1LEUALAQ3 - 29
d_172ens_1LEUGLUQ32 - 60
d_173ens_1GLUARGQ66 - 78
d_174ens_1LEULEUQ89
d_175ens_1LEULEUQ92
d_176ens_1TRPSERQ104 - 116
d_177ens_1PHEILEQ120 - 279
d_178ens_1SERSERQ283
d_179ens_1LYSGLUQ288 - 319
d_1710ens_1THRLEUQ321 - 334
d_181ens_1LEUALAR3 - 29
d_182ens_1LEUGLUR32 - 60
d_183ens_1GLUARGR66 - 78
d_184ens_1LEULEUR93
d_185ens_1LEULEUR96
d_186ens_1TRPSERR114 - 126
d_187ens_1PHEILER130 - 289
d_188ens_1SERSERR293
d_189ens_1LYSGLUR298 - 329
d_1810ens_1THRLEUR331 - 344
d_11ens_2GLNSERSA2 - 12
d_12ens_2ASPTHRSA23 - 37
d_13ens_2GLUVALSA42 - 70
d_21ens_2GLNSERUA2 - 12
d_22ens_2ASPTHRUA18 - 32
d_23ens_2GLUVALUA37 - 65
d_31ens_2GLNSERS2 - 12
d_32ens_2ASPTHRS21 - 35
d_33ens_2GLUVALS40 - 68
d_41ens_2GLNSERWA1 - 11
d_42ens_2ASPTHRWA14 - 28
d_43ens_2GLUVALWA33 - 61
d_51ens_2GLNTHRKA2 - 27
d_52ens_2GLUVALKA32 - 60
d_61ens_2GLNSERMA9 - 19
d_62ens_2ASPTHRMA24 - 38
d_63ens_2GLUVALMA43 - 71
d_71ens_2GLNSERAA10 - 20
d_72ens_2ASPTHRAA26 - 40
d_73ens_2GLUVALAA45 - 73
d_81ens_2GLNSEROA2 - 12
d_82ens_2ASPTHROA18 - 32
d_83ens_2GLUVALOA37 - 65
d_91ens_2GLNSERQA2 - 12
d_92ens_2ASPTHRQA16 - 30
d_93ens_2GLUVALQA35 - 63
d_101ens_2GLNSERU3 - 13
d_102ens_2ASPTHRU22 - 36
d_103ens_2GLUVALU41 - 69
d_111ens_2GLNSERW10 - 20
d_112ens_2ASPTHRW30 - 44
d_113ens_2GLUVALW49 - 77
d_121ens_2GLNSERCA8 - 18
d_122ens_2ASPTHRCA23 - 37
d_123ens_2GLUVALCA42 - 70
d_131ens_2GLNSERYA2 - 12
d_132ens_2ASPVALYA21 - 64
d_141ens_2GLNSEREA2 - 12
d_142ens_2ASPTHREA15 - 29
d_143ens_2GLUVALEA33 - 61
d_151ens_2GLNSERGA2 - 12
d_152ens_2ASPTHRGA23 - 37
d_153ens_2GLUVALGA42 - 70
d_161ens_2GLNSERIA3 - 13
d_162ens_2ASPTHRIA18 - 32
d_163ens_2GLUVALIA37 - 65
d_171ens_2GLNSERAB2 - 12
d_172ens_2ASPTHRAB21 - 35
d_173ens_2GLUVALAB38 - 66
d_181ens_2GLNSERY3 - 13
d_182ens_2ASPTHRY23 - 37
d_183ens_2GLUVALY42 - 70
d_11ens_3ARGASNTA2 - 44
d_12ens_3ARGHISTA48 - 59
d_13ens_3ASNASNTA64 - 75
d_14ens_3ASPLEUTA79 - 91
d_21ens_3ARGPROVA3 - 36
d_22ens_3ARGASNVA39 - 47
d_23ens_3ARGHISVA51 - 62
d_24ens_3ASNASNVA66 - 77
d_25ens_3ASPLEUVA81 - 93
d_31ens_3ARGPROT6 - 39
d_32ens_3ARGASNT48 - 56
d_33ens_3ARGHIST59 - 70
d_34ens_3ASNASNT77 - 88
d_35ens_3ASPLEUT92 - 104
d_41ens_3ARGPROXA6 - 39
d_42ens_3ARGHISXA46 - 66
d_43ens_3ASNASNXA73 - 84
d_44ens_3ASPLEUXA88 - 100
d_51ens_3ARGPROLA3 - 36
d_52ens_3ARGASNLA43 - 51
d_53ens_3ARGHISLA55 - 66
d_54ens_3ASNLEULA71 - 95
d_61ens_3ARGPRONA6 - 39
d_62ens_3ARGASNNA48 - 56
d_63ens_3ARGHISNA60 - 71
d_64ens_3ASNASNNA76 - 87
d_65ens_3ASPLEUNA91 - 103
d_71ens_3ARGPROBA6 - 39
d_72ens_3ARGASNBA48 - 56
d_73ens_3ARGHISBA60 - 71
d_74ens_3ASNASNBA78 - 89
d_75ens_3ASPLEUBA93 - 105
d_81ens_3ARGPROPA3 - 36
d_82ens_3ARGASNPA45 - 53
d_83ens_3ARGHISPA57 - 68
d_84ens_3ASNASNPA75 - 86
d_85ens_3ASPLEUPA89 - 101
d_91ens_3ARGPRORA3 - 36
d_92ens_3ARGASNRA43 - 51
d_93ens_3ARGLEURA53 - 89
d_101ens_3ARGPROV3 - 36
d_102ens_3ARGASNV45 - 53
d_103ens_3ARGHISV57 - 68
d_104ens_3ASNASNV75 - 86
d_105ens_3ASPLEUV90 - 102
d_111ens_3ARGPRODA6 - 39
d_112ens_3ARGASNDA48 - 56
d_113ens_3ARGHISDA60 - 71
d_114ens_3ASNASNDA76 - 87
d_115ens_3ASPLEUDA91 - 103
d_121ens_3ARGPROZA3 - 36
d_122ens_3ARGHISZA42 - 62
d_123ens_3ASNASNZA67 - 78
d_124ens_3ASPLEUZA81 - 93
d_131ens_3ARGPROFA1 - 34
d_132ens_3ARGASNFA43 - 51
d_133ens_3ARGHISFA55 - 66
d_134ens_3ASNASNFA73 - 84
d_135ens_3ASPLEUFA88 - 100
d_141ens_3ARGPROHA3 - 36
d_142ens_3ARGASNHA45 - 53
d_143ens_3ARGHISHA57 - 68
d_144ens_3ASNASNHA75 - 86
d_145ens_3ASPLEUHA90 - 102
d_151ens_3ARGPROJA6 - 39
d_152ens_3ARGASNJA48 - 56
d_153ens_3ARGHISJA60 - 71
d_154ens_3ASNASNJA78 - 89
d_155ens_3ASPLEUJA93 - 105
d_161ens_3ARGPROBB2 - 35
d_162ens_3ARGHISBB42 - 62
d_163ens_3ASNASNBB66 - 77
d_164ens_3ASPLEUBB80 - 92
d_171ens_3ARGPROZ6 - 39
d_172ens_3ARGASNZ48 - 56
d_173ens_3ARGHISZ60 - 71
d_174ens_3ASNASNZ78 - 89
d_175ens_3ASPLEUZ93 - 105

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.996624921177, 0.0446865536795, -0.0688612983376), (-0.0780657728197, 0.775349716344, -0.626688560993), (0.025387036112, 0.629949148175, 0.776221340284)3.50158140853, 30.9338484556, 10.8359263957
2given(0.989362416566, 0.0217733385447, -0.14383299488), (-0.145298564736, 0.196127107337, -0.969753826934), (0.00709477084667, 0.980336717407, 0.197204423709)6.84819324409, 48.2523127889, 39.9536763243
3given(0.981642410393, -0.030887307884, -0.188213050372), (-0.180037467344, -0.475828351488, -0.860914566187), (-0.0629657722194, 0.878995650804, -0.472654162572)8.92559848373, 42.6873827103, 73.369359697
4given(0.975564123706, -0.0931159473772, -0.199007690507), (-0.158708108403, -0.925014994505, -0.345194142865), (-0.151942018099, 0.368343155611, -0.9171896984)10.1048125901, 16.8422150252, 94.5671364811
5given(0.97742373765, -0.142443113442, -0.156053825684), (-0.0841757697547, -0.939956538557, 0.330750881193), (-0.19379699911, -0.310147811627, -0.930726091866)8.16561451765, -16.5354304379, 95.532048755
6given(0.980573206676, -0.168603536508, -0.100244869324), (-0.00105386815928, -0.515574222266, 0.856844274473), (-0.19615064545, -0.840092892966, -0.505735954305)5.58532206091, -42.6787968885, 74.14201135
7given(0.988384625025, -0.149024353589, -0.0297921978133), (0.0525656955747, 0.151301265881, 0.987089040863), (-0.142592709007, -0.977189679121, 0.157377413747)1.69057254625, -49.4503200416, 41.1605501635
8given(0.995317124661, -0.0921876378608, 0.0290733689496), (0.0497968821546, 0.746791108689, 0.663191759984), (-0.0828498152328, -0.658638352519, 0.747884635962)-2.22898445226, -33.8868020446, 11.2500597153
9given(-0.999978430929, 0.0038454609813, -0.00532448172622), (0.00654438200472, 0.514796112027, -0.857287661235), (-0.000555643759817, -0.85730401578, -0.514810174519)-1.67238654976, 42.2556474253, 74.8947987621
10given(-0.997591346157, -0.0405769713627, 0.0562584701862), (-0.0500049862119, -0.141399877917, -0.988688816503), (0.04807293861, -0.989120611412, 0.139030243664)-4.6795913316, 49.1894950998, 42.2836985986
11given(-0.992331194727, -0.0289509859223, 0.120169215631), (-0.060547169178, -0.733717588509, -0.676751461481), (0.10776288914, -0.678837492134, 0.726337950955)-7.2546921887, 34.263619863, 12.3804716535
12given(-0.983475258209, 0.00108791186629, 0.181039313238), (-0.00573270286363, -0.999667628987, -0.0251349890349), (0.180951796365, -0.0257574844206, 0.983154616217)-10.6643323961, 1.24241553719, 0.355374937994
13given(-0.976424353838, 0.0650173060373, 0.205835446772), (0.0812187878565, -0.772831097107, 0.629393044006), (0.199997474312, 0.631272401788, 0.749330477833)-12.0299927754, -31.0845673582, 12.7096817161
14given(-0.974284817046, 0.132624562712, 0.18215328885), (0.152659253296, -0.206057167179, 0.966558635695), (0.165723407088, 0.969510788604, 0.180512002714)-11.0184038269, -48.3649180936, 40.2280103591
15given(-0.976351923451, 0.18566904306, 0.110742620621), (0.186288921767, 0.462633113274, 0.866756621047), (0.109696669046, 0.866889617513, -0.486280815835)-6.70261410354, -43.55427913, 73.8246794812
16given(-0.985258868639, 0.167899274069, 0.032784074424), (0.16853538664, 0.919802436463, 0.354343479306), (0.0293391414142, 0.354645332189, -0.934540476993)-2.84382415547, -17.7412137271, 95.7436722723
17given(-0.993863784959, 0.107673848531, -0.025320333524), (0.109901159402, 0.935374509229, -0.336149167256), (-0.0125104799754, -0.336869217691, -0.941468330887)0.421003328378, 17.154714675, 95.6473583302
18given(0.997711460017, 0.0527987629718, -0.0422390006919), (-0.0676126443349, 0.784691694487, -0.61618785685), (0.000610636426402, 0.617633576834, 0.786465760152)1.27429501126, 30.8489403224, 9.1389789184
19given(0.984049559021, 0.0495718191788, -0.170848178611), (-0.177638450712, 0.222306096795, -0.958657697072), (-0.00954181428212, 0.973715889811, 0.227566077677)10.8318102618, 47.665368979, 36.3395847876
20given(0.977426847303, 0.0147851852773, -0.210756154042), (-0.183062129503, -0.438742295895, -0.879768977934), (-0.105475186238, 0.898491288822, -0.426131891553)13.0930028026, 45.8315584499, 69.0028617903
21given(0.974605418277, -0.0297010340351, -0.221950731567), (-0.120662243554, -0.904619323236, -0.408784176563), (-0.188639607841, 0.425184346613, -0.885230687306)15.0513066693, 24.3975481105, 93.4740889028
22given(0.983404774042, -0.0935501836629, -0.155445854005), (-0.039620029109, -0.946862467251, 0.319189162419), (-0.177046049615, -0.307733376885, -0.934855531656)10.1730124717, -15.4730394359, 96.2611433709
23given(0.986481141886, -0.0960951048975, -0.132742937733), (0.0557754388058, -0.564782590321, 0.823352734918), (-0.154091067649, -0.819625741717, -0.551787627974)11.7521751819, -40.7546471042, 79.9420588538
24given(0.992553532668, -0.114085052052, -0.0426858956454), (0.0573557994, 0.128570215422, 0.990040409267), (-0.107460676826, -0.98511638937, 0.134156260873)4.5869655904, -50.7925673004, 43.4414698163
25given(0.998316069412, -0.0497009076876, 0.0299139654623), (0.0150830763986, 0.720342206256, 0.693454833924), (-0.0560136265654, -0.691835909491, 0.719878842568)-0.704365695188, -38.2249282792, 12.8864743522
26given(-0.999195943567, -0.0224448122507, 0.0332219319539), (-0.0400910224745, 0.568012065305, -0.822043188394), (-0.000419853157092, -0.822714120501, -0.568455187022)-6.73403387607, 40.6504913136, 81.3207393758
27given(-0.991043011783, -0.114137494632, 0.0693280687413), (-0.0587564721618, -0.093516676116, -0.993882441875), (0.119922582424, -0.989053721295, 0.085972731824)-8.8774622535, 51.6285826442, 48.4661468989
28given(-0.98509059951, -0.116297222899, 0.126773288605), (-0.0122366115644, -0.68766584343, -0.725924206179), (0.171600629647, -0.716652386953, 0.675990074024)-11.6798550284, 41.6709604145, 16.7735746209
29given(-0.986330492052, -0.012921777337, 0.164271689949), (0.00802217403144, -0.999503953539, -0.0304547465046), (0.164583733012, -0.0287206290199, 0.985944887048)-9.82004803526, 1.84620311867, -0.296268533259
30given(-0.98361332914, 0.0450657658877, 0.174567738955), (0.0784190834619, -0.76492516955, 0.639327719044), (0.16234305063, 0.642540708231, 0.748856576507)-9.91864868607, -32.0028391281, 12.6169733599
31given(-0.981772718356, 0.0740705683606, 0.175031084084), (0.154730883313, -0.223280238238, 0.962395079456), (0.110366132676, 0.971935947537, 0.20774944198)-12.7110786137, -48.8386125303, 37.1497424606
32given(-0.97307668051, 0.187098595524, 0.134595280011), (0.209026875795, 0.470347931322, 0.857368408968), (0.097105813646, 0.86241923625, -0.496793238584)-9.24741653365, -42.270640646, 74.3419020653
33given(-0.989164764686, 0.139898535562, 0.0445136838612), (0.146311369661, 0.914440895948, 0.377347096088), (0.0120851731891, 0.379771309561, -0.925001460011)-5.29098083391, -20.5589280725, 95.3589903525
34given(-0.997679116313, 0.0670357220248, -0.0119412246027), (0.0674219474221, 0.948043139488, -0.310915561971), (-0.00952165312386, -0.310999063733, -0.950362520557)-2.6200265298, 14.4828230615, 97.5219452245
35given(0.997544560629, 0.0252932897587, -0.0653077258229), (-0.0589833780744, 0.806188676989, -0.588711116089), (0.0377599082349, 0.59111764192, 0.805701013243)2.49212012592, 29.0451561259, 5.94107699868
36given(0.98086767203, 0.0203432759498, -0.193609816617), (-0.192038833562, 0.264242831931, -0.945143805025), (0.0319326849946, 0.964241607118, 0.263093950391)11.67899653, 48.3902177083, 33.2677918762
37given(0.96481986651, -0.0169214577202, -0.26236670798), (-0.24774681604, -0.392537656454, -0.885740200853), (-0.0880007973222, 0.919580258887, -0.382920366573)17.1388029974, 47.7483298405, 65.8824918152
38given(0.956799073432, -0.124207787277, -0.262883926209), (-0.230206359668, -0.875909317739, -0.424014031685), (-0.1775966358, 0.466213784307, -0.866662646175)14.7210826398, 25.9431066093, 94.142222539
39given(0.974381731502, -0.143137386982, -0.173470256133), (-0.0903766545161, -0.955506837752, 0.280782377166), (-0.20594247166, -0.257911557431, -0.943964685203)10.1889657637, -12.4860273572, 99.5725763817
40given(0.968082797227, -0.103088610277, -0.228447884965), (0.106901711426, -0.654580348149, 0.748396012757), (-0.226688600966, -0.748930775338, -0.622667625579)21.6517106986, -36.7953864866, 89.9473919808
41given(0.980307249324, -0.162883078547, -0.11165482366), (0.121160576218, 0.0496113606414, 0.99139236817), (-0.155941693251, -0.985397288213, 0.0683693841384)9.13571292757, -53.7235188781, 49.4128698067
42given(0.994446373503, -0.0804092727002, -0.067902570572), (0.10400074875, 0.651903438778, 0.751136306385), (-0.0161324048374, -0.754026694072, 0.656645635134)8.6059237909, -46.8533704754, 16.6605256171
43given(-0.991279097212, 0.054404775397, 0.120024463528), (-0.0599717243429, 0.624770884114, -0.778501595787), (-0.117341994658, -0.778910433091, -0.616059569776)-11.7136932359, 38.8849071651, 86.8140734311
44given(-0.97566780432, -0.0774685279325, 0.205112073741), (-0.111269012156, -0.63113404277, -0.76765163127), (0.18892205416, -0.771795599389, 0.607157319165)-18.1629988939, 47.3542921548, 20.9845531371
45given(-0.982394362893, 0.0148649147659, 0.186226609443), (-0.0269917972944, -0.997663982667, -0.0627536498351), (0.1848587532, -0.0666754227418, 0.9805007034)-10.6706728506, 4.74259507086, -1.49023417875
46given(-0.976344019999, 0.0555384679053, 0.208968498094), (0.0834568565967, -0.794762486807, 0.601155173521), (0.19946756052, 0.604374112737, 0.771326535362)-13.2063932677, -29.0927832886, 9.02061809965
47given(-0.962550664967, 0.103652738094, 0.250504146189), (0.208908454804, -0.305314958926, 0.92905329953), (0.172781581436, 0.946593305354, 0.272227183387)-19.388290635, -48.582329329, 30.0208811751
48given(-0.952349681124, 0.235520786349, 0.193804138398), (0.281757166795, 0.435995190902, 0.854705266434), (0.116803184129, 0.868583992892, -0.48157955051)-12.7287213088, -42.4262622627, 73.3438387949
49given(-0.978667475764, 0.19900086572, 0.0510747229522), (0.202579877983, 0.893285072806, 0.401252005276), (0.0342252088106, 0.403038998292, -0.914542618437)-2.66894015336, -22.9795128131, 96.1864400325
50given(-0.989208559113, 0.130651925749, 0.0663061149203), (0.106208689058, 0.951190550149, -0.289752052066), (-0.100926413521, -0.279582924382, -0.954802203311)-8.05210147885, 13.4390815783, 98.4512865492

-
要素

#1: タンパク質
Low calcium response locus protein D


分子量: 40404.172 Da / 分子数: 18 / 由来タイプ: 組換発現 / 詳細: Cytosolic domain of YscV
由来: (組換発現) Yersinia enterocolitica (腸炎エルシニア)
遺伝子: lcrD / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0C2V3
#2: タンパク質
Yop proteins translocation protein X


分子量: 10676.037 Da / 分子数: 18 / 由来タイプ: 組換発現 / 詳細: N-terminally truncated YscX
由来: (組換発現) Yersinia enterocolitica (腸炎エルシニア)
遺伝子: yscX / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0C2N4
#3: タンパク質
Chaperone protein YscY / Yop proteins translocation protein Y


分子量: 14077.914 Da / 分子数: 18 / 由来タイプ: 組換発現 / 詳細: YscY with N-terminal hexahistidine tag
由来: (組換発現) Yersinia enterocolitica (腸炎エルシニア)
遺伝子: yscY / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0C2N2

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.75 Å3/Da / 溶媒含有率: 67.2 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: Protein Concentration: 3-5 mg/ml; Protein Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP; Reservoir Solution: 0.1 M Hepes pH 6.8-8.0, 1 % PEG 2'000 MME, 0.8-1.2 M sodium succinate; Drop ...詳細: Protein Concentration: 3-5 mg/ml; Protein Buffer: 20 mM Tris pH 8.0, 150 mM NaCl, 5 mM TCEP; Reservoir Solution: 0.1 M Hepes pH 6.8-8.0, 1 % PEG 2'000 MME, 0.8-1.2 M sodium succinate; Drop Ratio: 0.33 uL Reservoir + 0.66 uL Protein
PH範囲: 6.8 - 8.0

-
データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 0.9762 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年9月18日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9762 Å / 相対比: 1
反射解像度: 3.7→49.83 Å / Num. obs: 135378 / % possible obs: 99.5 % / 冗長度: 5.2 % / Biso Wilson estimate: 162.98 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.17 / Net I/σ(I): 7.1
反射 シェル解像度: 3.7→3.92 Å / 冗長度: 5.23 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 28922 / CC1/2: 0.395 / Rrim(I) all: 2.893 / % possible all: 98.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
PHASER位相決定
XDSデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 7ALW

7alw


解像度: 4.1→49.83 Å / SU ML: 0.6977 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 38.9605
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3248 6766 5 %
Rwork0.3054 128472 -
obs0.3064 135238 99.62 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 193.98 Å2
精密化ステップサイクル: LAST / 解像度: 4.1→49.83 Å
タンパク質核酸リガンド溶媒全体
原子数73476 0 0 0 73476
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002374609
X-RAY DIFFRACTIONf_angle_d0.6037100741
X-RAY DIFFRACTIONf_chiral_restr0.038811382
X-RAY DIFFRACTIONf_plane_restr0.003913006
X-RAY DIFFRACTIONf_dihedral_angle_d12.484328457
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS0.85256737185
ens_1d_3CAX-RAY DIFFRACTIONTorsion NCS0.786804979295
ens_1d_4DAX-RAY DIFFRACTIONTorsion NCS1.75691841774
ens_1d_5EAX-RAY DIFFRACTIONTorsion NCS0.847026473966
ens_1d_6FAX-RAY DIFFRACTIONTorsion NCS0.77171431547
ens_1d_7GAX-RAY DIFFRACTIONTorsion NCS0.873096666079
ens_1d_8HAX-RAY DIFFRACTIONTorsion NCS0.893490288339
ens_1d_9IAX-RAY DIFFRACTIONTorsion NCS0.887906325323
ens_1d_10JAX-RAY DIFFRACTIONTorsion NCS0.888329132175
ens_1d_11KAX-RAY DIFFRACTIONTorsion NCS0.854055248031
ens_1d_12LAX-RAY DIFFRACTIONTorsion NCS0.896312451958
ens_1d_13MAX-RAY DIFFRACTIONTorsion NCS1.04779624547
ens_1d_14NAX-RAY DIFFRACTIONTorsion NCS0.848481719203
ens_1d_15OAX-RAY DIFFRACTIONTorsion NCS0.911561458901
ens_1d_16PAX-RAY DIFFRACTIONTorsion NCS1.11041859029
ens_1d_17QAX-RAY DIFFRACTIONTorsion NCS0.850617892816
ens_1d_18RAX-RAY DIFFRACTIONTorsion NCS0.795770916612
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS2.13432362709
ens_2d_3CBX-RAY DIFFRACTIONTorsion NCS1.5625695554
ens_2d_4DBX-RAY DIFFRACTIONTorsion NCS1.63497488409
ens_2d_5EBX-RAY DIFFRACTIONTorsion NCS1.74904456737
ens_2d_6FBX-RAY DIFFRACTIONTorsion NCS1.77979406395
ens_2d_7GBX-RAY DIFFRACTIONTorsion NCS1.42731382195
ens_2d_8HBX-RAY DIFFRACTIONTorsion NCS1.98909259929
ens_2d_9IBX-RAY DIFFRACTIONTorsion NCS1.40980063366
ens_2d_10JBX-RAY DIFFRACTIONTorsion NCS1.57284551804
ens_2d_11KBX-RAY DIFFRACTIONTorsion NCS1.62918534799
ens_2d_12LBX-RAY DIFFRACTIONTorsion NCS1.9027996074
ens_2d_13MBX-RAY DIFFRACTIONTorsion NCS1.66412364231
ens_2d_14NBX-RAY DIFFRACTIONTorsion NCS1.46833049734
ens_2d_15OBX-RAY DIFFRACTIONTorsion NCS1.49706681536
ens_2d_16PBX-RAY DIFFRACTIONTorsion NCS1.47576411423
ens_2d_17QBX-RAY DIFFRACTIONTorsion NCS1.22329848564
ens_2d_18RBX-RAY DIFFRACTIONTorsion NCS1.56560971822
ens_3d_2BCX-RAY DIFFRACTIONTorsion NCS1.65098292735
ens_3d_3CCX-RAY DIFFRACTIONTorsion NCS1.66556871665
ens_3d_4DCX-RAY DIFFRACTIONTorsion NCS1.82125074089
ens_3d_5ECX-RAY DIFFRACTIONTorsion NCS1.80953092227
ens_3d_6FCX-RAY DIFFRACTIONTorsion NCS1.46235198647
ens_3d_7GCX-RAY DIFFRACTIONTorsion NCS1.68861038254
ens_3d_8HCX-RAY DIFFRACTIONTorsion NCS1.57146152388
ens_3d_9ICX-RAY DIFFRACTIONTorsion NCS1.81860198237
ens_3d_10JCX-RAY DIFFRACTIONTorsion NCS1.95950653626
ens_3d_11LCX-RAY DIFFRACTIONTorsion NCS1.757468435
ens_3d_12MCX-RAY DIFFRACTIONTorsion NCS1.73758755732
ens_3d_13NCX-RAY DIFFRACTIONTorsion NCS2.15015580321
ens_3d_14OCX-RAY DIFFRACTIONTorsion NCS1.76719717792
ens_3d_15PCX-RAY DIFFRACTIONTorsion NCS1.68471985359
ens_3d_16QCX-RAY DIFFRACTIONTorsion NCS1.54506260777
ens_3d_17RCX-RAY DIFFRACTIONTorsion NCS1.48200451372
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.150.47252200.42624197X-RAY DIFFRACTION99.84
4.15-4.20.43882240.40864244X-RAY DIFFRACTION99.69
4.2-4.250.3422250.38514275X-RAY DIFFRACTION99.8
4.25-4.30.42332200.38264198X-RAY DIFFRACTION99.75
4.3-4.360.43722250.39274267X-RAY DIFFRACTION99.76
4.36-4.420.40372230.3694231X-RAY DIFFRACTION99.8
4.42-4.480.3732230.35424252X-RAY DIFFRACTION99.56
4.48-4.550.33852230.34234219X-RAY DIFFRACTION99.78
4.55-4.620.35092260.34384310X-RAY DIFFRACTION99.71
4.62-4.690.34022210.34224201X-RAY DIFFRACTION99.8
4.69-4.770.36012280.34164311X-RAY DIFFRACTION99.87
4.77-4.860.36772210.34784214X-RAY DIFFRACTION99.78
4.86-4.950.34332250.34294262X-RAY DIFFRACTION99.51
4.95-5.050.34962230.33244222X-RAY DIFFRACTION99.71
5.05-5.160.37052250.34324289X-RAY DIFFRACTION99.87
5.16-5.280.36352260.33794297X-RAY DIFFRACTION99.85
5.28-5.420.32842230.33784253X-RAY DIFFRACTION99.75
5.42-5.560.40962260.34724292X-RAY DIFFRACTION99.87
5.56-5.730.37362250.3564275X-RAY DIFFRACTION99.84
5.73-5.910.36422250.35084271X-RAY DIFFRACTION99.71
5.91-6.120.34992270.35524281X-RAY DIFFRACTION99.82
6.12-6.370.40282250.37294283X-RAY DIFFRACTION99.78
6.37-6.660.3562270.34614314X-RAY DIFFRACTION99.82
6.66-7.010.36412270.35174307X-RAY DIFFRACTION99.71
7.01-7.440.36592260.33364301X-RAY DIFFRACTION99.6
7.44-8.020.32152290.30584339X-RAY DIFFRACTION99.43
8.02-8.820.28972270.25874324X-RAY DIFFRACTION99.56
8.82-10.080.22072320.21284367X-RAY DIFFRACTION99.42
10.09-12.670.22972310.20364374X-RAY DIFFRACTION98.63
12.67-49.830.3052380.27974502X-RAY DIFFRACTION97.83
精密化 TLS手法: refined / Origin x: -0.559282444825 Å / Origin y: -0.381279521562 Å / Origin z: 49.0060995248 Å
111213212223313233
T1.22680172558 Å2-0.0043028257945 Å20.0255294422946 Å2-1.8788103684 Å2-0.0149952628419 Å2--1.63552584985 Å2
L0.212180156607 °2-0.0382807867561 °20.0244954551441 °2-0.530070383376 °20.00395968759811 °2--0.307189744759 °2
S0.033174818466 Å °0.0156532227823 Å °-0.00372616475773 Å °-0.0088685826065 Å °-0.0373260409788 Å °0.0371221780881 Å °-0.0728520747668 Å °0.00367131326267 Å °0.00149213424099 Å °
精密化 TLSグループSelection details: all

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る