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- PDB-6ymt: RNASE 3/1 version1 -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6ymt
タイトルRNASE 3/1 version1
要素RNase 3/1 version 1
キーワードHYDROLASE / RNASE 3/1 version1 / PANCREATIC RIBONUCLEASE
生物種synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.58 Å
データ登録者Fernandez-Millan, P. / Prats-Ejarque, G. / Vazquez-Monteagudo, S. / Boix, E.
資金援助 スペイン, 1件
組織認可番号国
Spanish Ministry of Economy and CompetitivenessSAF2015-66007-P スペイン
引用ジャーナル: Front Mol Biosci / 年: 2022
タイトル: Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras.
著者: Fernandez-Millan, P. / Vazquez-Monteagudo, S. / Boix, E. / Prats-Ejarque, G.
履歴
登録2020年4月9日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年7月21日Provider: repository / タイプ: Initial release
改定 1.12023年3月29日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22024年2月7日Group: Data collection / Refinement description
カテゴリ: 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
改定 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
G: RNase 3/1 version 1
J: RNase 3/1 version 1
C: RNase 3/1 version 1
D: RNase 3/1 version 1
E: RNase 3/1 version 1
F: RNase 3/1 version 1
A: RNase 3/1 version 1
H: RNase 3/1 version 1
I: RNase 3/1 version 1
B: RNase 3/1 version 1
L: RNase 3/1 version 1
K: RNase 3/1 version 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)179,39713
ポリマ－179,30512
非ポリマー921
水35,3631963
1
G: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
A: RNase 3/1 version 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)15,0342
ポリマ－14,9421
非ポリマー921
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
10
B: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
11
L: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
12
K: RNase 3/1 version 1


分子量 (理論値)分子数
合計 (水以外)14,9421
ポリマ－14,9421
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.845, 115.676, 284.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDモデル要素
11B-64-

GLU

21A-324-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain 'A' and (resid 2 through 3 or resid 5...AG2 - 33 - 4
12PHEPHETHRTHR(chain 'A' and (resid 2 through 3 or resid 5...AG5 - 66 - 7
13ALAALAPHEPHE(chain 'A' and (resid 2 through 3 or resid 5...AG8 - 119 - 12
14GLNGLNASPASP(chain 'A' and (resid 2 through 3 or resid 5...AG14 - 1715 - 18
15ASPASPASPASP(chain 'A' and (resid 2 through 3 or resid 5...AG1920
16PROPROSERSER(chain 'A' and (resid 2 through 3 or resid 5...AG22 - 2423 - 25
17SERSERSERSER(chain 'A' and (resid 2 through 3 or resid 5...AG2627
18TYRTYRTHRTHR(chain 'A' and (resid 2 through 3 or resid 5...AG28 - 3029 - 31
19ALAALAARGARG(chain 'A' and (resid 2 through 3 or resid 5...AG32 - 3433 - 35
110ASNASNARGARG(chain 'A' and (resid 2 through 3 or resid 5...AG37 - 4038 - 41
111CYSCYSPROPRO(chain 'A' and (resid 2 through 3 or resid 5...AG43 - 4544 - 46
112ASNASNASNASN(chain 'A' and (resid 2 through 3 or resid 5...AG4748
113PHEPHELEULEU(chain 'A' and (resid 2 through 3 or resid 5...AG49 - 5450 - 55
114ASPASPGLNGLN(chain 'A' and (resid 2 through 3 or resid 5...AG56 - 5857 - 59
115CYSCYSPHEPHE(chain 'A' and (resid 2 through 3 or resid 5...AG61 - 6262 - 63
116VALVALVALVAL(chain 'A' and (resid 2 through 3 or resid 5...AG6667
117CYSCYSCYSCYS(chain 'A' and (resid 2 through 3 or resid 5...AG6869
118GLYGLYPHEPHE(chain 'A' and (resid 2 through 3 or resid 5...AG73 - 8074 - 81
119HISHISHISHIS(chain 'A' and (resid 2 through 3 or resid 5...AG8384
120THRTHRCYSCYS(chain 'A' and (resid 2 through 3 or resid 5...AG85 - 8786 - 88
121LEULEULEULEU(chain 'A' and (resid 2 through 3 or resid 5...AG8990
122TYRTYRCYSCYS(chain 'A' and (resid 2 through 3 or resid 5...AG95 - 9896 - 99
123TYRTYRTYRTYR(chain 'A' and (resid 2 through 3 or resid 5...AG100101
124THRTHRTHRTHR(chain 'A' and (resid 2 through 3 or resid 5...AG102103
125PROPROPROPRO(chain 'A' and (resid 2 through 3 or resid 5...AG104105
126ILEILEILEILE(chain 'A' and (resid 2 through 3 or resid 5...AG109 - 110110 - 111
127ALAALACYSCYS(chain 'A' and (resid 2 through 3 or resid 5...AG112 - 113113 - 114
128GLYGLYVALVAL(chain 'A' and (resid 2 through 3 or resid 5...AG115 - 121116 - 122
129PHEPHEPHEPHE(chain 'A' and (resid 2 through 3 or resid 5...AG123124
230PROPROPROPRO(chain 'B' and (resid 2 through 3 or resid 5...BJ2 - 33 - 4
231PHEPHETHRTHR(chain 'B' and (resid 2 through 3 or resid 5...BJ5 - 66 - 7
232ALAALAPHEPHE(chain 'B' and (resid 2 through 3 or resid 5...BJ8 - 119 - 12
233GLNGLNASPASP(chain 'B' and (resid 2 through 3 or resid 5...BJ14 - 1715 - 18
234ASPASPASPASP(chain 'B' and (resid 2 through 3 or resid 5...BJ1920
235PROPROSERSER(chain 'B' and (resid 2 through 3 or resid 5...BJ22 - 2423 - 25
236SERSERSERSER(chain 'B' and (resid 2 through 3 or resid 5...BJ2627
237TYRTYRTHRTHR(chain 'B' and (resid 2 through 3 or resid 5...BJ28 - 3029 - 31
238ALAALAARGARG(chain 'B' and (resid 2 through 3 or resid 5...BJ32 - 3433 - 35
239ASNASNARGARG(chain 'B' and (resid 2 through 3 or resid 5...BJ37 - 4038 - 41
240CYSCYSPROPRO(chain 'B' and (resid 2 through 3 or resid 5...BJ43 - 4544 - 46
241ASNASNASNASN(chain 'B' and (resid 2 through 3 or resid 5...BJ4748
242PHEPHELEULEU(chain 'B' and (resid 2 through 3 or resid 5...BJ49 - 5450 - 55
243ASPASPGLNGLN(chain 'B' and (resid 2 through 3 or resid 5...BJ56 - 5857 - 59
244CYSCYSPHEPHE(chain 'B' and (resid 2 through 3 or resid 5...BJ61 - 6262 - 63
245VALVALVALVAL(chain 'B' and (resid 2 through 3 or resid 5...BJ6667
246CYSCYSCYSCYS(chain 'B' and (resid 2 through 3 or resid 5...BJ6869
247GLYGLYPHEPHE(chain 'B' and (resid 2 through 3 or resid 5...BJ73 - 8074 - 81
248HISHISHISHIS(chain 'B' and (resid 2 through 3 or resid 5...BJ8384
249THRTHRCYSCYS(chain 'B' and (resid 2 through 3 or resid 5...BJ85 - 8786 - 88
250LEULEULEULEU(chain 'B' and (resid 2 through 3 or resid 5...BJ8990
251TYRTYRCYSCYS(chain 'B' and (resid 2 through 3 or resid 5...BJ95 - 9896 - 99
252TYRTYRTYRTYR(chain 'B' and (resid 2 through 3 or resid 5...BJ100101
253THRTHRTHRTHR(chain 'B' and (resid 2 through 3 or resid 5...BJ102103
254PROPROPROPRO(chain 'B' and (resid 2 through 3 or resid 5...BJ104105
255ILEILEILEILE(chain 'B' and (resid 2 through 3 or resid 5...BJ109 - 110110 - 111
256ALAALACYSCYS(chain 'B' and (resid 2 through 3 or resid 5...BJ112 - 113113 - 114
257GLYGLYVALVAL(chain 'B' and (resid 2 through 3 or resid 5...BJ115 - 121116 - 122
258PHEPHEPHEPHE(chain 'B' and (resid 2 through 3 or resid 5...BJ123124
359PROPROPROPRO(chain 'C' and (resid 2 through 3 or resid 5...CC2 - 33 - 4
360PHEPHETHRTHR(chain 'C' and (resid 2 through 3 or resid 5...CC5 - 66 - 7
361ALAALAPHEPHE(chain 'C' and (resid 2 through 3 or resid 5...CC8 - 119 - 12
362GLNGLNASPASP(chain 'C' and (resid 2 through 3 or resid 5...CC14 - 1715 - 18
363ASPASPASPASP(chain 'C' and (resid 2 through 3 or resid 5...CC1920
364PROPROSERSER(chain 'C' and (resid 2 through 3 or resid 5...CC22 - 2423 - 25
365SERSERSERSER(chain 'C' and (resid 2 through 3 or resid 5...CC2627
366TYRTYRTHRTHR(chain 'C' and (resid 2 through 3 or resid 5...CC28 - 3029 - 31
367ALAALAARGARG(chain 'C' and (resid 2 through 3 or resid 5...CC32 - 3433 - 35
368ASNASNARGARG(chain 'C' and (resid 2 through 3 or resid 5...CC37 - 4038 - 41
369CYSCYSPROPRO(chain 'C' and (resid 2 through 3 or resid 5...CC43 - 4544 - 46
370ASNASNASNASN(chain 'C' and (resid 2 through 3 or resid 5...CC4748
371PHEPHELEULEU(chain 'C' and (resid 2 through 3 or resid 5...CC49 - 5450 - 55
372ASPASPGLNGLN(chain 'C' and (resid 2 through 3 or resid 5...CC56 - 5857 - 59
373CYSCYSPHEPHE(chain 'C' and (resid 2 through 3 or resid 5...CC61 - 6262 - 63
374VALVALVALVAL(chain 'C' and (resid 2 through 3 or resid 5...CC6667
375CYSCYSCYSCYS(chain 'C' and (resid 2 through 3 or resid 5...CC6869
376GLYGLYPHEPHE(chain 'C' and (resid 2 through 3 or resid 5...CC73 - 8074 - 81
377HISHISHISHIS(chain 'C' and (resid 2 through 3 or resid 5...CC8384
378THRTHRCYSCYS(chain 'C' and (resid 2 through 3 or resid 5...CC85 - 8786 - 88
379LEULEULEULEU(chain 'C' and (resid 2 through 3 or resid 5...CC8990
380TYRTYRCYSCYS(chain 'C' and (resid 2 through 3 or resid 5...CC95 - 9896 - 99
381TYRTYRTYRTYR(chain 'C' and (resid 2 through 3 or resid 5...CC100101
382THRTHRTHRTHR(chain 'C' and (resid 2 through 3 or resid 5...CC102103
383PROPROPROPRO(chain 'C' and (resid 2 through 3 or resid 5...CC104105
384ILEILEILEILE(chain 'C' and (resid 2 through 3 or resid 5...CC109 - 110110 - 111
385ALAALACYSCYS(chain 'C' and (resid 2 through 3 or resid 5...CC112 - 113113 - 114
386GLYGLYVALVAL(chain 'C' and (resid 2 through 3 or resid 5...CC115 - 121116 - 122
387PHEPHEPHEPHE(chain 'C' and (resid 2 through 3 or resid 5...CC123124
488PROPROPROPRO(chain 'D' and (resid 2 through 3 or resid 5...DD2 - 33 - 4
489PHEPHETHRTHR(chain 'D' and (resid 2 through 3 or resid 5...DD5 - 66 - 7
490ALAALAPHEPHE(chain 'D' and (resid 2 through 3 or resid 5...DD8 - 119 - 12
491GLNGLNASPASP(chain 'D' and (resid 2 through 3 or resid 5...DD14 - 1715 - 18
492ASPASPASPASP(chain 'D' and (resid 2 through 3 or resid 5...DD1920
493PROPROSERSER(chain 'D' and (resid 2 through 3 or resid 5...DD22 - 2423 - 25
494SERSERSERSER(chain 'D' and (resid 2 through 3 or resid 5...DD2627
495TYRTYRTHRTHR(chain 'D' and (resid 2 through 3 or resid 5...DD28 - 3029 - 31
496ALAALAARGARG(chain 'D' and (resid 2 through 3 or resid 5...DD32 - 3433 - 35
497ASNASNARGARG(chain 'D' and (resid 2 through 3 or resid 5...DD37 - 4038 - 41
498CYSCYSPROPRO(chain 'D' and (resid 2 through 3 or resid 5...DD43 - 4544 - 46
499ASNASNASNASN(chain 'D' and (resid 2 through 3 or resid 5...DD4748
4100PHEPHELEULEU(chain 'D' and (resid 2 through 3 or resid 5...DD49 - 5450 - 55
4101ASPASPGLNGLN(chain 'D' and (resid 2 through 3 or resid 5...DD56 - 5857 - 59
4102CYSCYSPHEPHE(chain 'D' and (resid 2 through 3 or resid 5...DD61 - 6262 - 63
4103VALVALVALVAL(chain 'D' and (resid 2 through 3 or resid 5...DD6667
4104CYSCYSCYSCYS(chain 'D' and (resid 2 through 3 or resid 5...DD6869
4105GLYGLYPHEPHE(chain 'D' and (resid 2 through 3 or resid 5...DD73 - 8074 - 81
4106HISHISHISHIS(chain 'D' and (resid 2 through 3 or resid 5...DD8384
4107THRTHRCYSCYS(chain 'D' and (resid 2 through 3 or resid 5...DD85 - 8786 - 88
4108LEULEULEULEU(chain 'D' and (resid 2 through 3 or resid 5...DD8990
4109TYRTYRCYSCYS(chain 'D' and (resid 2 through 3 or resid 5...DD95 - 9896 - 99
4110TYRTYRTYRTYR(chain 'D' and (resid 2 through 3 or resid 5...DD100101
4111THRTHRTHRTHR(chain 'D' and (resid 2 through 3 or resid 5...DD102103
4112PROPROPROPRO(chain 'D' and (resid 2 through 3 or resid 5...DD104105
4113ILEILEILEILE(chain 'D' and (resid 2 through 3 or resid 5...DD109 - 110110 - 111
4114ALAALACYSCYS(chain 'D' and (resid 2 through 3 or resid 5...DD112 - 113113 - 114
4115GLYGLYVALVAL(chain 'D' and (resid 2 through 3 or resid 5...DD115 - 121116 - 122
4116PHEPHEPHEPHE(chain 'D' and (resid 2 through 3 or resid 5...DD123124
5117PROPROPROPRO(chain 'E' and (resid 2 through 3 or resid 5...EE2 - 33 - 4
5118PHEPHETHRTHR(chain 'E' and (resid 2 through 3 or resid 5...EE5 - 66 - 7
5119ALAALAPHEPHE(chain 'E' and (resid 2 through 3 or resid 5...EE8 - 119 - 12
5120GLNGLNASPASP(chain 'E' and (resid 2 through 3 or resid 5...EE14 - 1715 - 18
5121ASPASPASPASP(chain 'E' and (resid 2 through 3 or resid 5...EE1920
5122PROPROSERSER(chain 'E' and (resid 2 through 3 or resid 5...EE22 - 2423 - 25
5123SERSERSERSER(chain 'E' and (resid 2 through 3 or resid 5...EE2627
5124TYRTYRTHRTHR(chain 'E' and (resid 2 through 3 or resid 5...EE28 - 3029 - 31
5125ALAALAARGARG(chain 'E' and (resid 2 through 3 or resid 5...EE32 - 3433 - 35
5126ASNASNARGARG(chain 'E' and (resid 2 through 3 or resid 5...EE37 - 4038 - 41
5127CYSCYSPROPRO(chain 'E' and (resid 2 through 3 or resid 5...EE43 - 4544 - 46
5128ASNASNASNASN(chain 'E' and (resid 2 through 3 or resid 5...EE4748
5129PHEPHELEULEU(chain 'E' and (resid 2 through 3 or resid 5...EE49 - 5450 - 55
5130ASPASPGLNGLN(chain 'E' and (resid 2 through 3 or resid 5...EE56 - 5857 - 59
5131CYSCYSPHEPHE(chain 'E' and (resid 2 through 3 or resid 5...EE61 - 6262 - 63
5132VALVALVALVAL(chain 'E' and (resid 2 through 3 or resid 5...EE6667
5133CYSCYSCYSCYS(chain 'E' and (resid 2 through 3 or resid 5...EE6869
5134GLYGLYPHEPHE(chain 'E' and (resid 2 through 3 or resid 5...EE73 - 8074 - 81
5135HISHISHISHIS(chain 'E' and (resid 2 through 3 or resid 5...EE8384
5136THRTHRCYSCYS(chain 'E' and (resid 2 through 3 or resid 5...EE85 - 8786 - 88
5137LEULEULEULEU(chain 'E' and (resid 2 through 3 or resid 5...EE8990
5138TYRTYRCYSCYS(chain 'E' and (resid 2 through 3 or resid 5...EE95 - 9896 - 99
5139TYRTYRTYRTYR(chain 'E' and (resid 2 through 3 or resid 5...EE100101
5140THRTHRTHRTHR(chain 'E' and (resid 2 through 3 or resid 5...EE102103
5141PROPROPROPRO(chain 'E' and (resid 2 through 3 or resid 5...EE104105
5142ILEILEILEILE(chain 'E' and (resid 2 through 3 or resid 5...EE109 - 110110 - 111
5143ALAALACYSCYS(chain 'E' and (resid 2 through 3 or resid 5...EE112 - 113113 - 114
5144GLYGLYVALVAL(chain 'E' and (resid 2 through 3 or resid 5...EE115 - 121116 - 122
5145PHEPHEPHEPHE(chain 'E' and (resid 2 through 3 or resid 5...EE123124
6146PROPROPROPRO(chain 'F' and (resid 2 through 3 or resid 5...FF2 - 33 - 4
6147PHEPHETHRTHR(chain 'F' and (resid 2 through 3 or resid 5...FF5 - 66 - 7
6148ALAALAPHEPHE(chain 'F' and (resid 2 through 3 or resid 5...FF8 - 119 - 12
6149GLNGLNASPASP(chain 'F' and (resid 2 through 3 or resid 5...FF14 - 1715 - 18
6150ASPASPASPASP(chain 'F' and (resid 2 through 3 or resid 5...FF1920
6151PROPROSERSER(chain 'F' and (resid 2 through 3 or resid 5...FF22 - 2423 - 25
6152SERSERSERSER(chain 'F' and (resid 2 through 3 or resid 5...FF2627
6153TYRTYRTHRTHR(chain 'F' and (resid 2 through 3 or resid 5...FF28 - 3029 - 31
6154ALAALAARGARG(chain 'F' and (resid 2 through 3 or resid 5...FF32 - 3433 - 35
6155ASNASNARGARG(chain 'F' and (resid 2 through 3 or resid 5...FF37 - 4038 - 41
6156CYSCYSPROPRO(chain 'F' and (resid 2 through 3 or resid 5...FF43 - 4544 - 46
6157ASNASNASNASN(chain 'F' and (resid 2 through 3 or resid 5...FF4748
6158PHEPHELEULEU(chain 'F' and (resid 2 through 3 or resid 5...FF49 - 5450 - 55
6159ASPASPGLNGLN(chain 'F' and (resid 2 through 3 or resid 5...FF56 - 5857 - 59
6160CYSCYSPHEPHE(chain 'F' and (resid 2 through 3 or resid 5...FF61 - 6262 - 63
6161VALVALVALVAL(chain 'F' and (resid 2 through 3 or resid 5...FF6667
6162CYSCYSCYSCYS(chain 'F' and (resid 2 through 3 or resid 5...FF6869
6163GLYGLYPHEPHE(chain 'F' and (resid 2 through 3 or resid 5...FF73 - 8074 - 81
6164HISHISHISHIS(chain 'F' and (resid 2 through 3 or resid 5...FF8384
6165THRTHRCYSCYS(chain 'F' and (resid 2 through 3 or resid 5...FF85 - 8786 - 88
6166LEULEULEULEU(chain 'F' and (resid 2 through 3 or resid 5...FF8990
6167TYRTYRCYSCYS(chain 'F' and (resid 2 through 3 or resid 5...FF95 - 9896 - 99
6168TYRTYRTYRTYR(chain 'F' and (resid 2 through 3 or resid 5...FF100101
6169THRTHRTHRTHR(chain 'F' and (resid 2 through 3 or resid 5...FF102103
6170PROPROPROPRO(chain 'F' and (resid 2 through 3 or resid 5...FF104105
6171ILEILEILEILE(chain 'F' and (resid 2 through 3 or resid 5...FF109 - 110110 - 111
6172ALAALACYSCYS(chain 'F' and (resid 2 through 3 or resid 5...FF112 - 113113 - 114
6173GLYGLYVALVAL(chain 'F' and (resid 2 through 3 or resid 5...FF115 - 121116 - 122
6174PHEPHEPHEPHE(chain 'F' and (resid 2 through 3 or resid 5...FF123124
7175PROPROPROPRO(chain 'G' and (resid 2 through 3 or resid 5...GA2 - 33 - 4
7176PHEPHETHRTHR(chain 'G' and (resid 2 through 3 or resid 5...GA5 - 66 - 7
7177ALAALAPHEPHE(chain 'G' and (resid 2 through 3 or resid 5...GA8 - 119 - 12
7178GLNGLNASPASP(chain 'G' and (resid 2 through 3 or resid 5...GA14 - 1715 - 18
7179ASPASPASPASP(chain 'G' and (resid 2 through 3 or resid 5...GA1920
7180PROPROSERSER(chain 'G' and (resid 2 through 3 or resid 5...GA22 - 2423 - 25
7181SERSERSERSER(chain 'G' and (resid 2 through 3 or resid 5...GA2627
7182TYRTYRTHRTHR(chain 'G' and (resid 2 through 3 or resid 5...GA28 - 3029 - 31
7183ALAALAARGARG(chain 'G' and (resid 2 through 3 or resid 5...GA32 - 3433 - 35
7184ASNASNARGARG(chain 'G' and (resid 2 through 3 or resid 5...GA37 - 4038 - 41
7185CYSCYSPROPRO(chain 'G' and (resid 2 through 3 or resid 5...GA43 - 4544 - 46
7186ASNASNASNASN(chain 'G' and (resid 2 through 3 or resid 5...GA4748
7187PHEPHELEULEU(chain 'G' and (resid 2 through 3 or resid 5...GA49 - 5450 - 55
7188ASPASPGLNGLN(chain 'G' and (resid 2 through 3 or resid 5...GA56 - 5857 - 59
7189CYSCYSPHEPHE(chain 'G' and (resid 2 through 3 or resid 5...GA61 - 6262 - 63
7190VALVALVALVAL(chain 'G' and (resid 2 through 3 or resid 5...GA6667
7191CYSCYSCYSCYS(chain 'G' and (resid 2 through 3 or resid 5...GA6869
7192GLYGLYPHEPHE(chain 'G' and (resid 2 through 3 or resid 5...GA73 - 8074 - 81
7193HISHISHISHIS(chain 'G' and (resid 2 through 3 or resid 5...GA8384
7194THRTHRCYSCYS(chain 'G' and (resid 2 through 3 or resid 5...GA85 - 8786 - 88
7195LEULEULEULEU(chain 'G' and (resid 2 through 3 or resid 5...GA8990
7196TYRTYRCYSCYS(chain 'G' and (resid 2 through 3 or resid 5...GA95 - 9896 - 99
7197TYRTYRTYRTYR(chain 'G' and (resid 2 through 3 or resid 5...GA100101
7198THRTHRTHRTHR(chain 'G' and (resid 2 through 3 or resid 5...GA102103
7199PROPROPROPRO(chain 'G' and (resid 2 through 3 or resid 5...GA104105
7200ILEILEILEILE(chain 'G' and (resid 2 through 3 or resid 5...GA109 - 110110 - 111
7201ALAALACYSCYS(chain 'G' and (resid 2 through 3 or resid 5...GA112 - 113113 - 114
7202GLYGLYVALVAL(chain 'G' and (resid 2 through 3 or resid 5...GA115 - 121116 - 122
7203PHEPHEPHEPHE(chain 'G' and (resid 2 through 3 or resid 5...GA123124
8204PROPROPROPRO(chain 'H' and (resid 2 through 3 or resid 5...HH2 - 33 - 4
8205PHEPHETHRTHR(chain 'H' and (resid 2 through 3 or resid 5...HH5 - 66 - 7
8206ALAALAPHEPHE(chain 'H' and (resid 2 through 3 or resid 5...HH8 - 119 - 12
8207GLNGLNASPASP(chain 'H' and (resid 2 through 3 or resid 5...HH14 - 1715 - 18
8208ASPASPASPASP(chain 'H' and (resid 2 through 3 or resid 5...HH1920
8209PROPROSERSER(chain 'H' and (resid 2 through 3 or resid 5...HH22 - 2423 - 25
8210SERSERSERSER(chain 'H' and (resid 2 through 3 or resid 5...HH2627
8211TYRTYRTHRTHR(chain 'H' and (resid 2 through 3 or resid 5...HH28 - 3029 - 31
8212ALAALAARGARG(chain 'H' and (resid 2 through 3 or resid 5...HH32 - 3433 - 35
8213ASNASNARGARG(chain 'H' and (resid 2 through 3 or resid 5...HH37 - 4038 - 41
8214CYSCYSPROPRO(chain 'H' and (resid 2 through 3 or resid 5...HH43 - 4544 - 46
8215ASNASNASNASN(chain 'H' and (resid 2 through 3 or resid 5...HH4748
8216PHEPHELEULEU(chain 'H' and (resid 2 through 3 or resid 5...HH49 - 5450 - 55
8217ASPASPGLNGLN(chain 'H' and (resid 2 through 3 or resid 5...HH56 - 5857 - 59
8218CYSCYSPHEPHE(chain 'H' and (resid 2 through 3 or resid 5...HH61 - 6262 - 63
8219VALVALVALVAL(chain 'H' and (resid 2 through 3 or resid 5...HH6667
8220CYSCYSCYSCYS(chain 'H' and (resid 2 through 3 or resid 5...HH6869
8221GLYGLYPHEPHE(chain 'H' and (resid 2 through 3 or resid 5...HH73 - 8074 - 81
8222HISHISHISHIS(chain 'H' and (resid 2 through 3 or resid 5...HH8384
8223THRTHRCYSCYS(chain 'H' and (resid 2 through 3 or resid 5...HH85 - 8786 - 88
8224LEULEULEULEU(chain 'H' and (resid 2 through 3 or resid 5...HH8990
8225TYRTYRCYSCYS(chain 'H' and (resid 2 through 3 or resid 5...HH95 - 9896 - 99
8226TYRTYRTYRTYR(chain 'H' and (resid 2 through 3 or resid 5...HH100101
8227THRTHRTHRTHR(chain 'H' and (resid 2 through 3 or resid 5...HH102103
8228PROPROPROPRO(chain 'H' and (resid 2 through 3 or resid 5...HH104105
8229ILEILEILEILE(chain 'H' and (resid 2 through 3 or resid 5...HH109 - 110110 - 111
8230ALAALACYSCYS(chain 'H' and (resid 2 through 3 or resid 5...HH112 - 113113 - 114
8231GLYGLYVALVAL(chain 'H' and (resid 2 through 3 or resid 5...HH115 - 121116 - 122
8232PHEPHEPHEPHE(chain 'H' and (resid 2 through 3 or resid 5...HH123124
9233PROPROPROPRO(chain 'I' and (resid 2 through 3 or resid 5...II2 - 33 - 4
9234PHEPHETHRTHR(chain 'I' and (resid 2 through 3 or resid 5...II5 - 66 - 7
9235ALAALAPHEPHE(chain 'I' and (resid 2 through 3 or resid 5...II8 - 119 - 12
9236GLNGLNASPASP(chain 'I' and (resid 2 through 3 or resid 5...II14 - 1715 - 18
9237ASPASPASPASP(chain 'I' and (resid 2 through 3 or resid 5...II1920
9238PROPROSERSER(chain 'I' and (resid 2 through 3 or resid 5...II22 - 2423 - 25
9239SERSERSERSER(chain 'I' and (resid 2 through 3 or resid 5...II2627
9240TYRTYRTHRTHR(chain 'I' and (resid 2 through 3 or resid 5...II28 - 3029 - 31
9241ALAALAARGARG(chain 'I' and (resid 2 through 3 or resid 5...II32 - 3433 - 35
9242ASNASNARGARG(chain 'I' and (resid 2 through 3 or resid 5...II37 - 4038 - 41
9243CYSCYSPROPRO(chain 'I' and (resid 2 through 3 or resid 5...II43 - 4544 - 46
9244ASNASNASNASN(chain 'I' and (resid 2 through 3 or resid 5...II4748
9245PHEPHELEULEU(chain 'I' and (resid 2 through 3 or resid 5...II49 - 5450 - 55
9246ASPASPGLNGLN(chain 'I' and (resid 2 through 3 or resid 5...II56 - 5857 - 59
9247CYSCYSPHEPHE(chain 'I' and (resid 2 through 3 or resid 5...II61 - 6262 - 63
9248VALVALVALVAL(chain 'I' and (resid 2 through 3 or resid 5...II6667
9249CYSCYSCYSCYS(chain 'I' and (resid 2 through 3 or resid 5...II6869
9250GLYGLYPHEPHE(chain 'I' and (resid 2 through 3 or resid 5...II73 - 8074 - 81
9251HISHISHISHIS(chain 'I' and (resid 2 through 3 or resid 5...II8384
9252THRTHRCYSCYS(chain 'I' and (resid 2 through 3 or resid 5...II85 - 8786 - 88
9253LEULEULEULEU(chain 'I' and (resid 2 through 3 or resid 5...II8990
9254TYRTYRCYSCYS(chain 'I' and (resid 2 through 3 or resid 5...II95 - 9896 - 99
9255TYRTYRTYRTYR(chain 'I' and (resid 2 through 3 or resid 5...II100101
9256THRTHRTHRTHR(chain 'I' and (resid 2 through 3 or resid 5...II102103
9257PROPROPROPRO(chain 'I' and (resid 2 through 3 or resid 5...II104105
9258ILEILEILEILE(chain 'I' and (resid 2 through 3 or resid 5...II109 - 110110 - 111
9259ALAALACYSCYS(chain 'I' and (resid 2 through 3 or resid 5...II112 - 113113 - 114
9260GLYGLYVALVAL(chain 'I' and (resid 2 through 3 or resid 5...II115 - 121116 - 122
9261PHEPHEPHEPHE(chain 'I' and (resid 2 through 3 or resid 5...II123124
10262PROPROPROPRO(chain 'J' and (resid 2 through 3 or resid 5...JB2 - 33 - 4
10263PHEPHETHRTHR(chain 'J' and (resid 2 through 3 or resid 5...JB5 - 66 - 7
10264ALAALAPHEPHE(chain 'J' and (resid 2 through 3 or resid 5...JB8 - 119 - 12
10265GLNGLNASPASP(chain 'J' and (resid 2 through 3 or resid 5...JB14 - 1715 - 18
10266ASPASPASPASP(chain 'J' and (resid 2 through 3 or resid 5...JB1920
10267PROPROSERSER(chain 'J' and (resid 2 through 3 or resid 5...JB22 - 2423 - 25
10268SERSERSERSER(chain 'J' and (resid 2 through 3 or resid 5...JB2627
10269TYRTYRTHRTHR(chain 'J' and (resid 2 through 3 or resid 5...JB28 - 3029 - 31
10270ALAALAARGARG(chain 'J' and (resid 2 through 3 or resid 5...JB32 - 3433 - 35
10271ASNASNARGARG(chain 'J' and (resid 2 through 3 or resid 5...JB37 - 4038 - 41
10272CYSCYSPROPRO(chain 'J' and (resid 2 through 3 or resid 5...JB43 - 4544 - 46
10273ASNASNASNASN(chain 'J' and (resid 2 through 3 or resid 5...JB4748
10274PHEPHELEULEU(chain 'J' and (resid 2 through 3 or resid 5...JB49 - 5450 - 55
10275ASPASPGLNGLN(chain 'J' and (resid 2 through 3 or resid 5...JB56 - 5857 - 59
10276CYSCYSPHEPHE(chain 'J' and (resid 2 through 3 or resid 5...JB61 - 6262 - 63
10277VALVALVALVAL(chain 'J' and (resid 2 through 3 or resid 5...JB6667
10278CYSCYSCYSCYS(chain 'J' and (resid 2 through 3 or resid 5...JB6869
10279GLYGLYPHEPHE(chain 'J' and (resid 2 through 3 or resid 5...JB73 - 8074 - 81
10280HISHISHISHIS(chain 'J' and (resid 2 through 3 or resid 5...JB8384
10281THRTHRCYSCYS(chain 'J' and (resid 2 through 3 or resid 5...JB85 - 8786 - 88
10282LEULEULEULEU(chain 'J' and (resid 2 through 3 or resid 5...JB8990
10283TYRTYRCYSCYS(chain 'J' and (resid 2 through 3 or resid 5...JB95 - 9896 - 99
10284TYRTYRTYRTYR(chain 'J' and (resid 2 through 3 or resid 5...JB100101
10285THRTHRTHRTHR(chain 'J' and (resid 2 through 3 or resid 5...JB102103
10286PROPROPROPRO(chain 'J' and (resid 2 through 3 or resid 5...JB104105
10287ILEILEILEILE(chain 'J' and (resid 2 through 3 or resid 5...JB109 - 110110 - 111
10288ALAALACYSCYS(chain 'J' and (resid 2 through 3 or resid 5...JB112 - 113113 - 114
10289GLYGLYVALVAL(chain 'J' and (resid 2 through 3 or resid 5...JB115 - 121116 - 122
10290PHEPHEPHEPHE(chain 'J' and (resid 2 through 3 or resid 5...JB123124
11291PROPROPROPRO(chain 'K' and (resid 2 through 3 or resid 5...KL2 - 33 - 4
11292PHEPHETHRTHR(chain 'K' and (resid 2 through 3 or resid 5...KL5 - 66 - 7
11293ALAALAPHEPHE(chain 'K' and (resid 2 through 3 or resid 5...KL8 - 119 - 12
11294GLNGLNASPASP(chain 'K' and (resid 2 through 3 or resid 5...KL14 - 1715 - 18
11295ASPASPASPASP(chain 'K' and (resid 2 through 3 or resid 5...KL1920
11296PROPROSERSER(chain 'K' and (resid 2 through 3 or resid 5...KL22 - 2423 - 25
11297SERSERSERSER(chain 'K' and (resid 2 through 3 or resid 5...KL2627
11298TYRTYRTHRTHR(chain 'K' and (resid 2 through 3 or resid 5...KL28 - 3029 - 31
11299ALAALAARGARG(chain 'K' and (resid 2 through 3 or resid 5...KL32 - 3433 - 35
11300ASNASNARGARG(chain 'K' and (resid 2 through 3 or resid 5...KL37 - 4038 - 41
11301CYSCYSPROPRO(chain 'K' and (resid 2 through 3 or resid 5...KL43 - 4544 - 46
11302ASNASNASNASN(chain 'K' and (resid 2 through 3 or resid 5...KL4748
11303PHEPHELEULEU(chain 'K' and (resid 2 through 3 or resid 5...KL49 - 5450 - 55
11304ASPASPGLNGLN(chain 'K' and (resid 2 through 3 or resid 5...KL56 - 5857 - 59
11305CYSCYSPHEPHE(chain 'K' and (resid 2 through 3 or resid 5...KL61 - 6262 - 63
11306VALVALVALVAL(chain 'K' and (resid 2 through 3 or resid 5...KL6667
11307CYSCYSCYSCYS(chain 'K' and (resid 2 through 3 or resid 5...KL6869
11308GLYGLYPHEPHE(chain 'K' and (resid 2 through 3 or resid 5...KL73 - 8074 - 81
11309HISHISHISHIS(chain 'K' and (resid 2 through 3 or resid 5...KL8384
11310THRTHRCYSCYS(chain 'K' and (resid 2 through 3 or resid 5...KL85 - 8786 - 88
11311LEULEULEULEU(chain 'K' and (resid 2 through 3 or resid 5...KL8990
11312TYRTYRCYSCYS(chain 'K' and (resid 2 through 3 or resid 5...KL95 - 9896 - 99
11313TYRTYRTYRTYR(chain 'K' and (resid 2 through 3 or resid 5...KL100101
11314THRTHRTHRTHR(chain 'K' and (resid 2 through 3 or resid 5...KL102103
11315PROPROPROPRO(chain 'K' and (resid 2 through 3 or resid 5...KL104105
11316ILEILEILEILE(chain 'K' and (resid 2 through 3 or resid 5...KL109 - 110110 - 111
11317ALAALACYSCYS(chain 'K' and (resid 2 through 3 or resid 5...KL112 - 113113 - 114
11318GLYGLYVALVAL(chain 'K' and (resid 2 through 3 or resid 5...KL115 - 121116 - 122
11319PHEPHEPHEPHE(chain 'K' and (resid 2 through 3 or resid 5...KL123124
12320PROPROPROPRO(chain 'L' and (resid 2 through 3 or resid 5...LK2 - 33 - 4
12321PHEPHETHRTHR(chain 'L' and (resid 2 through 3 or resid 5...LK5 - 66 - 7
12322ALAALAPHEPHE(chain 'L' and (resid 2 through 3 or resid 5...LK8 - 119 - 12
12323GLNGLNASPASP(chain 'L' and (resid 2 through 3 or resid 5...LK14 - 1715 - 18
12324ASPASPASPASP(chain 'L' and (resid 2 through 3 or resid 5...LK1920
12325PROPROSERSER(chain 'L' and (resid 2 through 3 or resid 5...LK22 - 2423 - 25
12326SERSERSERSER(chain 'L' and (resid 2 through 3 or resid 5...LK2627
12327TYRTYRTHRTHR(chain 'L' and (resid 2 through 3 or resid 5...LK28 - 3029 - 31
12328ALAALAARGARG(chain 'L' and (resid 2 through 3 or resid 5...LK32 - 3433 - 35
12329ASNASNARGARG(chain 'L' and (resid 2 through 3 or resid 5...LK37 - 4038 - 41
12330CYSCYSPROPRO(chain 'L' and (resid 2 through 3 or resid 5...LK43 - 4544 - 46
12331ASNASNASNASN(chain 'L' and (resid 2 through 3 or resid 5...LK4748
12332PHEPHELEULEU(chain 'L' and (resid 2 through 3 or resid 5...LK49 - 5450 - 55
12333ASPASPGLNGLN(chain 'L' and (resid 2 through 3 or resid 5...LK56 - 5857 - 59
12334CYSCYSPHEPHE(chain 'L' and (resid 2 through 3 or resid 5...LK61 - 6262 - 63
12335VALVALVALVAL(chain 'L' and (resid 2 through 3 or resid 5...LK6667
12336CYSCYSCYSCYS(chain 'L' and (resid 2 through 3 or resid 5...LK6869
12337GLYGLYPHEPHE(chain 'L' and (resid 2 through 3 or resid 5...LK73 - 8074 - 81
12338HISHISHISHIS(chain 'L' and (resid 2 through 3 or resid 5...LK8384
12339THRTHRCYSCYS(chain 'L' and (resid 2 through 3 or resid 5...LK85 - 8786 - 88
12340LEULEULEULEU(chain 'L' and (resid 2 through 3 or resid 5...LK8990
12341TYRTYRCYSCYS(chain 'L' and (resid 2 through 3 or resid 5...LK95 - 9896 - 99
12342TYRTYRTYRTYR(chain 'L' and (resid 2 through 3 or resid 5...LK100101
12343THRTHRTHRTHR(chain 'L' and (resid 2 through 3 or resid 5...LK102103
12344PROPROPROPRO(chain 'L' and (resid 2 through 3 or resid 5...LK104105
12345ILEILEILEILE(chain 'L' and (resid 2 through 3 or resid 5...LK109 - 110110 - 111
12346ALAALACYSCYS(chain 'L' and (resid 2 through 3 or resid 5...LK112 - 113113 - 114
12347GLYGLYVALVAL(chain 'L' and (resid 2 through 3 or resid 5...LK115 - 121116 - 122
12348PHEPHEPHEPHE(chain 'L' and (resid 2 through 3 or resid 5...LK123124

-
要素

#1: タンパク質
RNase 3/1 version 1


分子量: 14942.065 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli (大腸菌)
#2: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1963 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN
Has protein modificationY

-
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: 2.48 Å3/Da / 溶媒含有率: 50.43 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: sodium acetate 100 mM pH 4.0 , NaCl 1.5 M

-
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: ALBA / ビームライン: XALOC / 波長: 0.97918 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年11月24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: 0.97918 Å / 相対比: 1
反射解像度: 1.58→142.371 Å / Num. obs: 239337 / % possible obs: 99.94 % / 冗長度: 2 % / Biso Wilson estimate: 21.24 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.04
反射 シェル解像度: 1.58→1.636 Å / 冗長度: 2 % / Mean I/σ(I) obs: 1.83 / Num. unique obs: 23748 / CC1/2: 0.611 / % possible all: 99.95

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHENIX1.17.1_3660精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 開始モデル: 1.0E+21 / 解像度: 1.58→71.19 Å / SU ML: 0.1725 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.6529
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2033 11869 4.96 %
Rwork0.1784 227442 -
obs0.1797 239311 99.93 %
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: 31.14 Å2
精密化ステップサイクル: LAST / 解像度: 1.58→71.19 Å
タンパク質核酸リガンド溶媒全体
原子数12391 0 6 1963 14360
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.009413265
X-RAY DIFFRACTIONf_angle_d1.062818038
X-RAY DIFFRACTIONf_chiral_restr0.07031833
X-RAY DIFFRACTIONf_plane_restr0.00792414
X-RAY DIFFRACTIONf_dihedral_angle_d22.60925055
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.60.29793610.27437510X-RAY DIFFRACTION99.99
1.6-1.620.31284010.27327513X-RAY DIFFRACTION99.92
1.62-1.640.28223900.26597568X-RAY DIFFRACTION99.95
1.64-1.660.2933780.25177484X-RAY DIFFRACTION99.96
1.66-1.680.26984100.24127572X-RAY DIFFRACTION99.96
1.68-1.70.2344000.22767497X-RAY DIFFRACTION99.95
1.7-1.730.24383430.2257569X-RAY DIFFRACTION99.94
1.73-1.750.27413710.21857626X-RAY DIFFRACTION99.96
1.75-1.780.24183930.22027508X-RAY DIFFRACTION99.9
1.78-1.810.23033960.21727491X-RAY DIFFRACTION99.92
1.81-1.840.25143980.21587553X-RAY DIFFRACTION99.99
1.84-1.870.21764230.19967580X-RAY DIFFRACTION99.94
1.87-1.910.21754060.19147472X-RAY DIFFRACTION99.92
1.91-1.950.23414210.19197506X-RAY DIFFRACTION99.94
1.95-1.990.2213680.1927561X-RAY DIFFRACTION99.95
1.99-2.040.22884000.1927556X-RAY DIFFRACTION100
2.04-2.090.19873920.18157581X-RAY DIFFRACTION99.95
2.09-2.140.20123890.17327563X-RAY DIFFRACTION99.95
2.14-2.210.20094060.18027543X-RAY DIFFRACTION99.96
2.21-2.280.21153780.18637603X-RAY DIFFRACTION99.96
2.28-2.360.22213870.1867602X-RAY DIFFRACTION99.94
2.36-2.450.19713860.18537615X-RAY DIFFRACTION99.96
2.45-2.570.19634180.17937546X-RAY DIFFRACTION99.95
2.57-2.70.21223980.17847614X-RAY DIFFRACTION99.98
2.7-2.870.20964180.17667572X-RAY DIFFRACTION99.94
2.87-3.090.19554130.17157617X-RAY DIFFRACTION99.89
3.09-3.40.18314160.16347663X-RAY DIFFRACTION99.84
3.4-3.90.17474060.14647660X-RAY DIFFRACTION99.96
3.9-4.910.16794040.14217751X-RAY DIFFRACTION99.95
4.91-71.190.1943990.18087946X-RAY DIFFRACTION99.56
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.61671094738-1.77624727349-0.02179666449234.44750673990.611210112026.281426949750.3423971116230.552281249287-0.129410738999-0.411517372231-0.3687303176390.459343927552-0.115348038023-0.361554247444-0.05249007184960.3038363070430.0898238757268-0.0458971729750.3222398264990.004643108618990.238513582751.4809418469313.9795056975-30.0830974037
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'G' and (resid 0 through 6 )
2X-RAY DIFFRACTION2chain 'G' and (resid 7 through 39 )
3X-RAY DIFFRACTION3chain 'G' and (resid 40 through 62 )
4X-RAY DIFFRACTION4chain 'G' and (resid 63 through 81 )
5X-RAY DIFFRACTION5chain 'G' and (resid 82 through 89 )
6X-RAY DIFFRACTION6chain 'G' and (resid 90 through 99 )
7X-RAY DIFFRACTION7chain 'G' and (resid 100 through 114 )
8X-RAY DIFFRACTION8chain 'G' and (resid 115 through 124 )
9X-RAY DIFFRACTION9chain 'J' and (resid 0 through 15 )
10X-RAY DIFFRACTION10chain 'J' and (resid 16 through 27 )
11X-RAY DIFFRACTION11chain 'J' and (resid 28 through 62 )
12X-RAY DIFFRACTION12chain 'J' and (resid 63 through 74 )
13X-RAY DIFFRACTION13chain 'J' and (resid 75 through 89 )
14X-RAY DIFFRACTION14chain 'J' and (resid 90 through 99 )
15X-RAY DIFFRACTION15chain 'J' and (resid 100 through 107 )
16X-RAY DIFFRACTION16chain 'J' and (resid 108 through 125 )
17X-RAY DIFFRACTION17chain 'C' and (resid 0 through 15 )
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 27 )
19X-RAY DIFFRACTION19chain 'C' and (resid 28 through 62 )
20X-RAY DIFFRACTION20chain 'C' and (resid 63 through 74 )
21X-RAY DIFFRACTION21chain 'C' and (resid 75 through 89 )
22X-RAY DIFFRACTION22chain 'C' and (resid 90 through 99 )
23X-RAY DIFFRACTION23chain 'C' and (resid 100 through 114 )
24X-RAY DIFFRACTION24chain 'C' and (resid 115 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 0 through 15 )
26X-RAY DIFFRACTION26chain 'D' and (resid 16 through 39 )
27X-RAY DIFFRACTION27chain 'D' and (resid 40 through 62 )
28X-RAY DIFFRACTION28chain 'D' and (resid 63 through 81 )
29X-RAY DIFFRACTION29chain 'D' and (resid 82 through 89 )
30X-RAY DIFFRACTION30chain 'D' and (resid 90 through 99 )
31X-RAY DIFFRACTION31chain 'D' and (resid 100 through 114 )
32X-RAY DIFFRACTION32chain 'D' and (resid 115 through 125 )
33X-RAY DIFFRACTION33chain 'E' and (resid 0 through 15 )
34X-RAY DIFFRACTION34chain 'E' and (resid 16 through 27 )
35X-RAY DIFFRACTION35chain 'E' and (resid 28 through 62 )
36X-RAY DIFFRACTION36chain 'E' and (resid 63 through 74 )
37X-RAY DIFFRACTION37chain 'E' and (resid 75 through 89 )
38X-RAY DIFFRACTION38chain 'E' and (resid 90 through 99 )
39X-RAY DIFFRACTION39chain 'E' and (resid 100 through 114 )
40X-RAY DIFFRACTION40chain 'E' and (resid 115 through 125 )
41X-RAY DIFFRACTION41chain 'F' and (resid 0 through 15 )
42X-RAY DIFFRACTION42chain 'F' and (resid 16 through 39 )
43X-RAY DIFFRACTION43chain 'F' and (resid 40 through 62 )
44X-RAY DIFFRACTION44chain 'F' and (resid 63 through 81 )
45X-RAY DIFFRACTION45chain 'F' and (resid 82 through 99 )
46X-RAY DIFFRACTION46chain 'F' and (resid 100 through 107 )
47X-RAY DIFFRACTION47chain 'F' and (resid 108 through 114 )
48X-RAY DIFFRACTION48chain 'F' and (resid 115 through 124 )
49X-RAY DIFFRACTION49chain 'A' and (resid 0 through 27 )
50X-RAY DIFFRACTION50chain 'A' and (resid 28 through 81 )
51X-RAY DIFFRACTION51chain 'A' and (resid 82 through 99 )
52X-RAY DIFFRACTION52chain 'A' and (resid 100 through 127 )
53X-RAY DIFFRACTION53chain 'H' and (resid 0 through 15 )
54X-RAY DIFFRACTION54chain 'H' and (resid 16 through 39 )
55X-RAY DIFFRACTION55chain 'H' and (resid 40 through 81 )
56X-RAY DIFFRACTION56chain 'H' and (resid 82 through 89 )
57X-RAY DIFFRACTION57chain 'H' and (resid 90 through 99 )
58X-RAY DIFFRACTION58chain 'H' and (resid 100 through 114 )
59X-RAY DIFFRACTION59chain 'H' and (resid 115 through 124 )
60X-RAY DIFFRACTION60chain 'I' and (resid 0 through 15 )
61X-RAY DIFFRACTION61chain 'I' and (resid 16 through 62 )
62X-RAY DIFFRACTION62chain 'I' and (resid 63 through 74 )
63X-RAY DIFFRACTION63chain 'I' and (resid 75 through 89 )
64X-RAY DIFFRACTION64chain 'I' and (resid 90 through 99 )
65X-RAY DIFFRACTION65chain 'I' and (resid 100 through 107 )
66X-RAY DIFFRACTION66chain 'I' and (resid 108 through 114 )
67X-RAY DIFFRACTION67chain 'I' and (resid 115 through 127 )
68X-RAY DIFFRACTION68chain 'B' and (resid 0 through 15 )
69X-RAY DIFFRACTION69chain 'B' and (resid 16 through 62 )
70X-RAY DIFFRACTION70chain 'B' and (resid 63 through 81 )
71X-RAY DIFFRACTION71chain 'B' and (resid 82 through 89 )
72X-RAY DIFFRACTION72chain 'B' and (resid 90 through 99 )
73X-RAY DIFFRACTION73chain 'B' and (resid 100 through 107 )
74X-RAY DIFFRACTION74chain 'B' and (resid 108 through 127 )
75X-RAY DIFFRACTION75chain 'L' and (resid 0 through 15 )
76X-RAY DIFFRACTION76chain 'L' and (resid 16 through 39 )
77X-RAY DIFFRACTION77chain 'L' and (resid 40 through 62 )
78X-RAY DIFFRACTION78chain 'L' and (resid 63 through 73 )
79X-RAY DIFFRACTION79chain 'L' and (resid 74 through 89 )
80X-RAY DIFFRACTION80chain 'L' and (resid 90 through 99 )
81X-RAY DIFFRACTION81chain 'L' and (resid 100 through 107 )
82X-RAY DIFFRACTION82chain 'L' and (resid 108 through 124 )
83X-RAY DIFFRACTION83chain 'K' and (resid 0 through 15 )
84X-RAY DIFFRACTION84chain 'K' and (resid 16 through 27 )
85X-RAY DIFFRACTION85chain 'K' and (resid 28 through 62 )
86X-RAY DIFFRACTION86chain 'K' and (resid 63 through 81 )
87X-RAY DIFFRACTION87chain 'K' and (resid 82 through 89 )
88X-RAY DIFFRACTION88chain 'K' and (resid 90 through 99 )
89X-RAY DIFFRACTION89chain 'K' and (resid 100 through 114 )
90X-RAY DIFFRACTION90chain 'K' and (resid 115 through 125 )

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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://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