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- PDB-6s6y: X-ray crystal structure of the formyltransferase/hydrolase comple... -

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基本情報

登録情報
データベース: PDB / ID: 6s6y
タイトルX-ray crystal structure of the formyltransferase/hydrolase complex (FhcABCD) from Methylorubrum extorquens in complex with methylofuran
要素
  • (Formylmethanofuran dehydrogenase subunit ...) x 2
  • Formylmethanofuran--tetrahydromethanopterin formyltransferase
  • Tungsten-containing formylmethanofuran dehydrogenase, subunit B
キーワードHYDROLASE / Methylotrophy / channeling / polyglutamate / prosthetic group / metallo-hydrolase / formate dehydrogenase / formyl-transferase / methylofuran
機能・相同性
機能・相同性情報


formylmethanofuran-tetrahydromethanopterin N-formyltransferase / formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity / formylmethanofuran dehydrogenase activity / formaldehyde catabolic process / methanogenesis / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / transition metal ion binding / one-carbon metabolic process / cytoplasm
類似検索 - 分子機能
Alpha-Beta Plaits - #520 / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, C-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, N-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, ferredoxin-like superfamily / Formylmethanofuran-tetrahydromethanopterin formyltransferase / FTR, proximal lobe / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal ...Alpha-Beta Plaits - #520 / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, C-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, N-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, ferredoxin-like superfamily / Formylmethanofuran-tetrahydromethanopterin formyltransferase / FTR, proximal lobe / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal / GXGXG motif / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Amidohydrolase 3 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Metal-dependent hydrolase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
D-GLUTAMIC ACID / FORMIC ACID / GLUTAMIC ACID / BETA-L-ASPARTIC ACID / : / Chem-L6K / Chem-MFN / AMINO GROUP / Formylmethanofuran dehydrogenase subunit C / Formylmethanofuran--tetrahydromethanopterin formyltransferase ...D-GLUTAMIC ACID / FORMIC ACID / GLUTAMIC ACID / BETA-L-ASPARTIC ACID / : / Chem-L6K / Chem-MFN / AMINO GROUP / Formylmethanofuran dehydrogenase subunit C / Formylmethanofuran--tetrahydromethanopterin formyltransferase / Formylmethanofuran dehydrogenase subunit A / Tungsten-containing formylmethanofuran dehydrogenase, subunit B
類似検索 - 構成要素
生物種Methylobacterium extorquens (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å
データ登録者Wagner, T. / Hemmann, J.L. / Shima, S. / Vorholt, J.
資金援助 ドイツ, スイス, 2件
組織認可番号国
Max Planck Society ドイツ
Swiss National Science Foundation31003A-173094 スイス
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2019
タイトル: Methylofuran is a prosthetic group of the formyltransferase/hydrolase complex and shuttles one-carbon units between two active sites.
著者: Hemmann, J.L. / Wagner, T. / Shima, S. / Vorholt, J.A.
履歴
登録2019年7月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年12月4日Provider: repository / タイプ: Initial release
改定 1.12019年12月11日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
改定 1.22019年12月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32024年1月24日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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

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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
A: Formylmethanofuran dehydrogenase subunit A
B: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
C: Formylmethanofuran dehydrogenase subunit C
D: Formylmethanofuran--tetrahydromethanopterin formyltransferase
E: Formylmethanofuran dehydrogenase subunit A
F: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
G: Formylmethanofuran dehydrogenase subunit C
H: Formylmethanofuran--tetrahydromethanopterin formyltransferase
I: Formylmethanofuran dehydrogenase subunit A
J: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
K: Formylmethanofuran dehydrogenase subunit C
L: Formylmethanofuran--tetrahydromethanopterin formyltransferase
M: Formylmethanofuran dehydrogenase subunit A
N: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
O: Formylmethanofuran dehydrogenase subunit C
P: Formylmethanofuran--tetrahydromethanopterin formyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)628,80074
ポリマ－623,08916
非ポリマー5,71258
水00
1
A: Formylmethanofuran dehydrogenase subunit A
B: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
C: Formylmethanofuran dehydrogenase subunit C
D: Formylmethanofuran--tetrahydromethanopterin formyltransferase
E: Formylmethanofuran dehydrogenase subunit A
F: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
G: Formylmethanofuran dehydrogenase subunit C
H: Formylmethanofuran--tetrahydromethanopterin formyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)314,12134
ポリマ－311,5448
非ポリマー2,57626
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
I: Formylmethanofuran dehydrogenase subunit A
J: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
K: Formylmethanofuran dehydrogenase subunit C
L: Formylmethanofuran--tetrahydromethanopterin formyltransferase
M: Formylmethanofuran dehydrogenase subunit A
N: Tungsten-containing formylmethanofuran dehydrogenase, subunit B
O: Formylmethanofuran dehydrogenase subunit C
P: Formylmethanofuran--tetrahydromethanopterin formyltransferase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)314,68040
ポリマ－311,5448
非ポリマー3,13532
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)84.974, 130.322, 172.689
Angle α, β, γ (deg.)84.970, 75.910, 82.090
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 1 through 269 or resid 275...
21(chain E and (resid 1 through 325 or resid 327 through 544 or resid 546 through 547))
31(chain I and (resid 1 through 267 or (resid 268...
41(chain M and (resid 1 through 269 or resid 275...
12(chain B and (resid 2 through 129 or (resid 130...
22(chain F and (resid 2 through 119 or (resid 120...
32(chain J and (resid 2 through 119 or (resid 120...
42(chain N and (resid 2 through 119 or (resid 120...
13(chain C and (resid 2 through 26 or resid 28 through 266))
23(chain G and (resid 2 through 26 or resid 28 through 266))
33(chain K and (resid 2 through 26 or resid 28 through 266))
43(chain O and (resid 2 through 26 or resid 28 through 266))
14(chain D and (resid 4 through 138 or resid 140 through 309))
24(chain H and (resid 4 through 138 or resid 140 through 309))
34(chain L and (resid 4 through 138 or resid 140 through 309))
44(chain P and (resid 4 through 138 or resid 140 through 309))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPRO(chain A and (resid 1 through 269 or resid 275...AA1 - 2691 - 269
121GLYGLYPROPRO(chain A and (resid 1 through 269 or resid 275...AA275 - 325275 - 325
131LYSLYSLYSLYS(chain A and (resid 1 through 269 or resid 275...AA327327
211METMETPROPRO(chain E and (resid 1 through 325 or resid 327 through 544 or resid 546 through 547))EE1 - 3251 - 325
221LYSLYSVALVAL(chain E and (resid 1 through 325 or resid 327 through 544 or resid 546 through 547))EE327 - 544327 - 544
231CYSCYSARGARG(chain E and (resid 1 through 325 or resid 327 through 544 or resid 546 through 547))EE546 - 547546 - 547
311METMETVALVAL(chain I and (resid 1 through 267 or (resid 268...II1 - 2671 - 267
321ASPASPASPASP(chain I and (resid 1 through 267 or (resid 268...II268268
331METMETALAALA(chain I and (resid 1 through 267 or (resid 268...II1 - 5481 - 548
341METMETALAALA(chain I and (resid 1 through 267 or (resid 268...II1 - 5481 - 548
351METMETALAALA(chain I and (resid 1 through 267 or (resid 268...II1 - 5481 - 548
361METMETALAALA(chain I and (resid 1 through 267 or (resid 268...II1 - 5481 - 548
411METMETPROPRO(chain M and (resid 1 through 269 or resid 275...MM1 - 2691 - 269
421GLYGLYPROPRO(chain M and (resid 1 through 269 or resid 275...MM275 - 325275 - 325
431LYSLYSVALVAL(chain M and (resid 1 through 269 or resid 275...MM327 - 544327 - 544
441CYSCYSARGARG(chain M and (resid 1 through 269 or resid 275...MM546 - 547546 - 547
112ALAALAPROPRO(chain B and (resid 2 through 129 or (resid 130...BB2 - 1291 - 128
122GLNGLNASNASN(chain B and (resid 2 through 129 or (resid 130...BB130 - 131129 - 130
132ALAALASERSER(chain B and (resid 2 through 129 or (resid 130...BB2 - 3611 - 360
142ALAALASERSER(chain B and (resid 2 through 129 or (resid 130...BB2 - 3611 - 360
152ALAALASERSER(chain B and (resid 2 through 129 or (resid 130...BB2 - 3611 - 360
162ALAALASERSER(chain B and (resid 2 through 129 or (resid 130...BB2 - 3611 - 360
212ALAALAALAALA(chain F and (resid 2 through 119 or (resid 120...FF2 - 1191 - 118
222GLUGLUGLUGLU(chain F and (resid 2 through 119 or (resid 120...FF120119
232ALAALASERSER(chain F and (resid 2 through 119 or (resid 120...FF2 - 3611 - 360
242ALAALASERSER(chain F and (resid 2 through 119 or (resid 120...FF2 - 3611 - 360
252ALAALASERSER(chain F and (resid 2 through 119 or (resid 120...FF2 - 3611 - 360
262ALAALASERSER(chain F and (resid 2 through 119 or (resid 120...FF2 - 3611 - 360
312ALAALAALAALA(chain J and (resid 2 through 119 or (resid 120...JJ2 - 1191 - 118
322GLUGLUGLUGLU(chain J and (resid 2 through 119 or (resid 120...JJ120119
332ALAALASERSER(chain J and (resid 2 through 119 or (resid 120...JJ2 - 3611 - 360
342ALAALASERSER(chain J and (resid 2 through 119 or (resid 120...JJ2 - 3611 - 360
352ALAALASERSER(chain J and (resid 2 through 119 or (resid 120...JJ2 - 3611 - 360
362ALAALASERSER(chain J and (resid 2 through 119 or (resid 120...JJ2 - 3611 - 360
412ALAALAALAALA(chain N and (resid 2 through 119 or (resid 120...NN2 - 1191 - 118
422GLUGLUGLUGLU(chain N and (resid 2 through 119 or (resid 120...NN120119
432ALAALASERSER(chain N and (resid 2 through 119 or (resid 120...NN2 - 3611 - 360
113SERSERGLYGLY(chain C and (resid 2 through 26 or resid 28 through 266))CC2 - 261 - 25
123SERSERHISHIS(chain C and (resid 2 through 26 or resid 28 through 266))CC28 - 26627 - 265
213SERSERGLYGLY(chain G and (resid 2 through 26 or resid 28 through 266))GG2 - 261 - 25
223SERSERHISHIS(chain G and (resid 2 through 26 or resid 28 through 266))GG28 - 26627 - 265
313SERSERGLYGLY(chain K and (resid 2 through 26 or resid 28 through 266))KK2 - 261 - 25
323SERSERHISHIS(chain K and (resid 2 through 26 or resid 28 through 266))KK28 - 26627 - 265
413SERSERGLYGLY(chain O and (resid 2 through 26 or resid 28 through 266))OO2 - 261 - 25
423SERSERHISHIS(chain O and (resid 2 through 26 or resid 28 through 266))OO28 - 26627 - 265
114PHEPHEASPASP(chain D and (resid 4 through 138 or resid 140 through 309))DD4 - 1383 - 137
124GLUGLUPROPRO(chain D and (resid 4 through 138 or resid 140 through 309))DD140 - 309139 - 308
214PHEPHEASPASP(chain H and (resid 4 through 138 or resid 140 through 309))HH4 - 1383 - 137
224GLUGLUPROPRO(chain H and (resid 4 through 138 or resid 140 through 309))HH140 - 309139 - 308
314PHEPHEASPASP(chain L and (resid 4 through 138 or resid 140 through 309))LL4 - 1383 - 137
324GLUGLUPROPRO(chain L and (resid 4 through 138 or resid 140 through 309))LL140 - 309139 - 308
414PHEPHEASPASP(chain P and (resid 4 through 138 or resid 140 through 309))PP4 - 1383 - 137
424GLUGLUPROPRO(chain P and (resid 4 through 138 or resid 140 through 309))PP140 - 309139 - 308

NCSアンサンブル:
ID
1
2
3
4

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要素

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Formylmethanofuran dehydrogenase subunit ... , 2種, 8分子 AEIMCGKO

#1: タンパク質
Formylmethanofuran dehydrogenase subunit A


分子量: 58562.992 Da / 分子数: 4 / 変異: wild type / 由来タイプ: 天然 / 詳細: Lys178 is a carboxy-lysine.
由来: (天然) Methylobacterium extorquens (strain PA1) (バクテリア)
Plasmid details: / / 参照: UniProt: A9W3R9
#3: タンパク質
Formylmethanofuran dehydrogenase subunit C


分子量: 27896.566 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: a Strep-tag II sequence (HGSAWSHPQFEK) was added in the C-terminal
由来: (組換発現) Methylobacterium extorquens (strain PA1) (バクテリア)
組織: / / 細胞株: / / 遺伝子: Mext_1824 / 器官: / / Variant: / / Plasmid details: /
発現宿主: Methylobacterium extorquens (strain PA1) (バクテリア)
参照: UniProt: A9W3R7

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タンパク質 , 2種, 8分子 BFJNDHLP

#2: タンパク質
Tungsten-containing formylmethanofuran dehydrogenase, subunit B


分子量: 37032.543 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Methylobacterium extorquens (strain PA1) (バクテリア)
Plasmid details: / / 参照: UniProt: A9W3S0
#4: タンパク質
Formylmethanofuran--tetrahydromethanopterin formyltransferase / H4MPT formyltransferase


分子量: 32280.045 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Methylobacterium extorquens (strain PA1) (バクテリア)
Plasmid details: /
参照: UniProt: A9W3R8, formylmethanofuran-tetrahydromethanopterin N-formyltransferase

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非ポリマー , 14種, 58分子

#5: 化合物 ChemComp-FMT / FORMIC ACID / ギ酸


分子量: 46.025 Da / 分子数: 3 / 由来タイプ: 合成 / 式: CH2O2
#6: 化合物 ChemComp-MFN / N-[4,5,7-TRICARBOXYHEPTANOYL]-L-GAMMA-GLUTAMYL-N-{2-[4-({5-[(FORMYLAMINO)METHYL]-3-FURYL}METHOXY)PHENYL]ETHYL}-D-GLUTAMINE


分子量: 776.741 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C35H44N4O16 / タイプ: SUBJECT OF INVESTIGATION
#7: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#9: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Ca
#10: 化合物
ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 9 / 由来タイプ: 合成 / 式: K
#11: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Cl
#12: 化合物
ChemComp-DGL / D-GLUTAMIC ACID / D-グルタミン酸


タイプ: D-peptide linking / 分子量: 147.129 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C5H9NO4
#13: 化合物 ChemComp-NH2 / AMINO GROUP / アンモニア


分子量: 16.023 Da / 分子数: 1 / 由来タイプ: 合成 / 式: NH2
#14: 化合物
ChemComp-GLU / GLUTAMIC ACID / グルタミン酸


タイプ: L-peptide linking / 分子量: 147.129 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C5H9NO4
#15: 化合物 ChemComp-IAS / BETA-L-ASPARTIC ACID / L-aspartic acid / アスパラギン酸


タイプ: L-beta-peptide, C-gamma linking / 分子量: 133.103 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H7NO4
#16: 化合物 ChemComp-L6K / (2~{S})-3-[4-[[5-(aminomethyl)furan-3-yl]methoxy]phenyl]-2-(methylamino)propanoic acid


分子量: 304.341 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C16H20N2O4
#17: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6O2
#18: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.99 Å3/Da / 溶媒含有率: 58.82 % / 解説: Transparent square plate
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.7
詳細: The best hit was obtained in a CombiClover Junior Plate by using the sitting drop vapor diffusion method. 2 ul protein was mixed with 1 ul of the crystallization solution containing 0.2 M ...詳細: The best hit was obtained in a CombiClover Junior Plate by using the sitting drop vapor diffusion method. 2 ul protein was mixed with 1 ul of the crystallization solution containing 0.2 M CaCl2 and 20% (w/v) PEG 3350. The protein buffer contained 25 mM Tris pH 7.7, 10% (v/v) glycerol, 2 mM DTT, 6 mM KCl and 200 mM NaCl.
Temp details: The temperature was oscillating between 291 - 295

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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: SLS / ビームライン: X10SA / 波長: 1.00005 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年11月16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: 1.00005 Å / 相対比: 1
反射解像度: 3.1→48.5 Å / Num. obs: 124496 / % possible obs: 96.6 % / 冗長度: 1.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.147 / Rrim(I) all: 0.209 / Rsym value: 0.149 / Net I/av σ(I): 4.9 / Net I/σ(I): 5.2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
3.1-3.271.81.2860.6182850.3081.2751.8111.28696.9
3.27-3.471.80.7791170360.7721.0970.77995.8
3.47-3.711.80.4671.6161060.4640.6590.46796
3.71-41.90.2842.6149840.2810.3990.28496.4
4-4.381.80.1674.3138740.1660.2360.16796.6
4.38-4.91.70.1036.9125990.1020.1450.10397.4
4.9-5.661.90.1096.7112230.1080.1530.10997.7
5.66-6.931.80.0878.593730.0860.1230.08797.2
6.93-9.81.80.03619.471470.0350.050.03696.1
9.8-48.5021.80.02128.838690.0210.030.02194.7

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
SCALA3.3.22データスケーリング
PDB_EXTRACT3.25データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5T5I

5t5i


解像度: 3.1→24.949 Å / SU ML: 0.55 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 31.26
Rfactor反射数%反射
Rfree0.2513 5953 4.81 %
Rwork0.2212 --
obs0.2227 123826 96.22 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 325.8 Å2 / Biso mean: 108.4772 Å2 / Biso min: 20.11 Å2
精密化ステップサイクル: final / 解像度: 3.1→24.949 Å
タンパク質核酸リガンド溶媒全体
原子数43018 0 270 0 43288
Biso mean--75.13 --
残基数----5894
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6572X-RAY DIFFRACTION5.234TORSIONAL
12E6572X-RAY DIFFRACTION5.234TORSIONAL
13I6572X-RAY DIFFRACTION5.234TORSIONAL
14M6572X-RAY DIFFRACTION5.234TORSIONAL
21B4276X-RAY DIFFRACTION5.234TORSIONAL
22F4276X-RAY DIFFRACTION5.234TORSIONAL
23J4276X-RAY DIFFRACTION5.234TORSIONAL
24N4276X-RAY DIFFRACTION5.234TORSIONAL
31C3220X-RAY DIFFRACTION5.234TORSIONAL
32G3220X-RAY DIFFRACTION5.234TORSIONAL
33K3220X-RAY DIFFRACTION5.234TORSIONAL
34O3220X-RAY DIFFRACTION5.234TORSIONAL
41D3700X-RAY DIFFRACTION5.234TORSIONAL
42H3700X-RAY DIFFRACTION5.234TORSIONAL
43L3700X-RAY DIFFRACTION5.234TORSIONAL
44P3700X-RAY DIFFRACTION5.234TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.13520.45241880.4068381492
3.1352-3.1720.39641880.3884382895
3.172-3.21060.37541990.3832386695
3.2106-3.25110.40432000.3695398296
3.2511-3.29380.38221800.3633392696
3.2938-3.33880.3781900.3447391796
3.3388-3.38640.40082070.3395395695
3.3864-3.43690.3472160.3321380195
3.4369-3.49040.35952000.3209382595
3.4904-3.54750.35361840.3077401096
3.5475-3.60850.341590.2974393696
3.6085-3.67390.31012000.2831390896
3.6739-3.74430.28782020.2732393596
3.7443-3.82050.2741850.253398496
3.8205-3.90330.30261920.2456389796
3.9033-3.99370.24511720.2327395897
3.9937-4.09320.23932130.2326394497
4.0932-4.20330.25961890.2166398897
4.2033-4.32640.23711950.1997392796
4.3264-4.46530.21892290.1894393997
4.4653-4.62390.21071800.1751390997
4.6239-4.80780.2051930.1671405298
4.8078-5.02490.21941990.1717402398
5.0249-5.28750.23362170.1923392698
5.2875-5.61520.22462250.1906399098
5.6152-6.0430.24131990.1915395197
6.043-6.64080.2282150.1902396697
6.6408-7.5780.21272290.1765395198
7.578-9.46020.15932080.1397389295
9.4602-24.9490.19392000.1613387295
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)
10.6203-1.74260.78324.0385-1.57441.91380.02630.08470.14080.41480.30450.72-0.4488-0.2205-0.29110.58830.0734-0.01540.51340.12281.1308-22.998661.292-43.8285
21.7068-0.6141.12091.9901-0.10011.8553-0.09280.00880.04970.35830.0546-0.1503-0.29380.15270.02640.5483-0.0334-0.07870.3621-0.10030.72723.32354.8207-32.938
33.0347-0.1510.19571.6104-0.32842.1939-0.4689-1.27940.59710.96840.01330.5648-0.5702-0.2218-0.24431.15250.21580.29230.7428-0.22770.6363-6.553456.1182-10.8235
41.76260.1525-0.93483.539-0.08832.4839-0.051-0.1430.17460.50360.050.6784-0.3633-0.2067-0.09080.69570.0598-0.05720.426-0.08030.722-14.503551.179-25.0159
50.5694-0.04680.16411.642-0.72430.80920.05870.07950.27310.11880.19180.4012-0.4061-0.139-0.27660.64790.02020.0110.4856-0.05590.942-12.336360.5114-40.8862
61.848-1.582-0.00971.6947-0.23594.5130.09870.4148-0.1109-0.84880.37440.04910.1684-0.0257-0.40140.778-0.2402-0.16630.5818-0.01050.7901-16.617433.3089-61.0398
73.1804-0.39880.62954.3568-1.82091.84570.0973-0.0353-0.2941-0.3041-0.0383-0.26260.2709-0.01420.02970.47580.0821-0.0980.3915-0.13760.87137.913122.1468-35.5783
81.3668-0.2130.69180.2622-0.67632.54440.2530.1777-0.2641-0.22750.1396-0.10830.6349-0.1408-0.25210.66340.0274-0.09740.3461-0.17820.7899-13.174229.2623-56.4954
92.83320.97250.3683.07011.73425.20570.11140.3380.4509-0.4760.2287-0.1043-0.12060.0162-0.00530.75080.00060.00410.31550.02471.0242-7.735541.8619-63.7026
108.13991.0955-1.73811.96920.8966.82360.13840.9059-0.1758-0.28520.45480.41560.2557-1.01750.0140.5643-0.1169-0.45320.80750.16610.9416-40.260421.587-48.9933
113.06091.19780.41762.2637-2.40825.47560.1550.35850.415-0.01570.66251.0187-0.4897-0.9776-0.91410.7999-0.0434-0.38530.81120.18311.1175-43.621929.8676-47.9235
126.2156-0.8798-0.73215.5748-1.84614.8294-0.57460.72690.967-0.06740.38780.2963-0.0811-0.59650.68890.6103-0.1551-0.38561.07880.29031.4204-48.274620.4661-45.0601
132.79920.3587-1.36593.7730.51887.2108-0.0419-0.4711-0.5072-0.22140.09880.17420.008-0.57530.14950.536-0.0382-0.20040.67610.11860.8736-37.951918.7758-41.4198
142.88592.08540.56692.80410.30762.1005-0.21260.2967-0.03090.20590.0888-0.13520.0154-0.17250.11040.4008-0.0219-0.16540.5725-0.02120.8515-29.654916.4518-38.0338
156.77051.15280.90211.1468-0.53771.8933-0.07490.08370.09990.24120.1259-0.42140.0613-0.00520.11990.50530.0056-0.09980.44410.01530.7675-20.020211.7937-31.5447
161.29750.18810.79391.00141.57044.77230.38740.0071-0.260.7545-0.2951-0.89261.2612-0.8022-0.09530.57450.0639-0.19490.45250.12850.9468-18.38113.3876-21.7867
173.8144-0.66880.94923.14752.95033.67480.208-0.1392-0.58340.7764-0.2316-0.2290.3961-0.0317-0.2050.8104-0.1349-0.28070.59990.14480.7753-15.99122.6173-23.1098
182.5344-0.4805-2.09122.50980.66344.36430.38810.16770.52280.6182-0.15070.12030.1491-1.5022-0.25780.6792-0.2616-0.16271.41080.02420.7565-45.403412.885920.0101
191.5652-0.1922-2.16942.3035-0.53083.8189-0.06410.0114-0.0666-0.0964-0.07980.36430.0371-0.37820.06810.6733-0.177-0.25270.82280.09850.79-26.063810.98343.415
207.3133-0.5672-0.52773.71381.49058.0826-0.25110.02830.4209-0.2519-0.1504-0.196-0.3714-1.39460.08430.55620.157-0.12840.81180.01970.722-24.436113.0367-13.3508
211.28870.3462-1.98010.2127-0.10184.5325-0.0502-0.02260.0254-0.0493-0.02790.34920.998-0.68010.16440.7349-0.2475-0.08180.9201-0.10580.8045-34.26957.735615.1193
223.90751.0446-3.02394.2552-1.69545.85480.46830.4471.11190.278-0.6591-0.0649-1.6968-0.1120.23181.129-0.2625-0.18231.13280.03171.2737-33.102421.137534.966
231.8371-1.2278-0.68911.1534-0.74286.33180.3195-0.3396-0.52420.2174-0.57420.50680.1182-0.9449-0.00530.8207-0.3727-0.0071.3685-0.03410.9334-45.953410.91724.9556
243.99382.23711.26413.10111.85951.41330.0207-0.05570.1161-0.30960.0509-0.6859-0.49440.5775-0.03671.2986-0.3291-0.16791.31580.12091.2925.316252.669771.6498
252.66861.97310.04861.702-0.85331.93410.5711-0.10790.68660.3682-0.5386-0.2206-1.1661-0.57830.10261.820.2367-0.21811.33520.02441.1822-21.82657.013369.4003
263.338-1.172-0.11991.02090.00822.20680.06070.02720.7791-0.1933-0.1401-0.3049-1.31650.1046-0.00011.8726-0.0685-0.0591.20590.16651.2619-17.999260.156152.3444
272.33460.53870.06451.90630.53971.5028-0.13250.3810.0782-0.31340.193-0.3659-0.69840.22170.06861.5023-0.169-0.05971.27780.09821.0685-4.763950.526754.5755
281.64550.5041-0.46822.04251.09962.9758-0.2391-0.0159-0.4920.5579-0.4220.4832-0.95480.28420.15821.8269-0.2466-0.15741.30890.17891.34145.154653.136872.2767
293.13091.9087-0.07581.3840.22830.48410.021-0.1170.74820.3239-0.16990.5934-0.9882-0.43640.08761.71110.1120.0811.69040.0071.364-24.044657.937581.0441
300.55130.21851.49370.33150.50483.4979-0.1005-0.54970.15210.50460.1362-0.08060.5338-0.3742-0.03241.63560.1645-0.15421.45190.01770.8862-19.872932.563384.2543
310.92870.60050.40830.39350.26820.3031-0.6147-1.24710.71430.13770.2062-0.3294-2.0454-1.28670.95331.80120.5595-0.3171.95550.141.5869-45.143444.963669.6954
325.5175-1.7888-0.87453.6270.88662.7923-0.17740.13510.0820.47670.03090.57940.2394-0.72020.13291.0603-0.0236-0.11231.42620.1060.9991-40.240327.656863.3391
333.6564-0.89851.11910.2508-0.54213.57-0.1946-0.6189-0.07860.23280.25160.1606-0.09060.2888-0.19121.4610.0552-0.28261.27460.15480.9007-17.462228.62885.5774
345.94731.2068-4.67954.4966-0.84753.6842-0.3608-0.69670.58560.0556-0.7975-0.1251-1.3847-0.00130.25371.91130.2889-0.00431.3192-0.10850.9703-26.643943.697587.2028
351.10690.94381.93141.37320.55956.6370.01-1.07220.524-0.2111-0.0981-0.0513-0.09431.0039-0.1961.35540.26890.11081.9716-0.05481.201-10.374741.292295.6823
363.7046-2.3272-0.99453.589-0.08475.72280.1506-1.0999-0.40760.55370.5755-0.30670.52460.5497-0.46661.69980.2707-0.41231.4125-0.00411.11851.83458.68377.1799
372.9275-0.27172.2192.3556-0.94292.77520.7085-1.222-0.121-0.29360.7852-0.39170.35790.1533-0.2531.10350.2055-0.40151.5785-0.04290.99848.832714.407675.9067
385.209-3.06572.46383.5872-1.9791.34410.06120.3097-0.7470.38690.2351-0.9409-0.66081.17670.20121.7560.5401-0.4611.8398-0.27661.27838.21643.838473.0314
392.7314-0.62480.24691.03071.16333.3888-0.6099-0.120.10040.42490.53610.1540.8901-0.08770.00791.3409-0.0571-0.24391.10830.10460.8076-16.86629.135462.5189
402.2635-3.2927-0.22885.62670.56876.41540.24030.63480.1892-0.2404-0.16310.2110.9581-0.86080.13421.4876-0.3912-0.18810.9770.13630.8907-25.69452.698150.1283
412.8630.2122-1.23131.56181.17144.65970.0814-0.0910.40830.11220.4072-0.80320.4010.7811-0.2870.8480.0506-0.2120.68520.18660.94781.38010.39758.9677
420.847-0.2388-1.53423.2787-0.80736.65250.0354-0.395-0.1580.1459-0.1706-0.18520.3490.09890.17721.0036-0.2914-0.24380.89590.07170.9435-18.27811.988923.0297
432.90460.4875-2.72114.3545-0.1186.67150.108-0.10650.21780.6983-0.0471-0.2704-0.66610.4567-0.0470.7851-0.2147-0.16330.84890.17460.6146-13.024712.843722.7139
443.4684-0.9283-1.69011.29620.55125.60860.6507-0.9587-0.37150.6163-0.255-0.3633-0.2289-0.1239-0.30051.0082-0.2778-0.24970.91690.01430.7091-16.964811.955632.0147
452.0121-0.4514-1.55511.79691.18645.99410.5718-0.9462-0.0890.16190.02360.18670.31420.3273-0.23681.2336-0.3429-0.28191.17740.09160.7891-16.93699.885938.8459
461.48451.3813-0.46912.161.2036.58860.3509-0.4483-0.2920.38320.3959-0.57211.1673-0.6726-0.38470.83210.0127-0.37610.75680.21771.0476-8.395-2.14795.5482
473.53760.3214-0.71056.49242.81037.8255-0.3589-0.62290.4794-0.4696-0.2321-0.1135-1.0237-0.0065-0.13750.7805-0.015-0.27890.75390.04930.9256-4.912814.3346-5.6798
481.00460.1264-1.71791.16930.29573.02530.5524-0.09850.22740.16010.1245-0.42550.2650.18190.04930.77070.0138-0.22980.76360.04170.832-3.48111.9963-2.9188
491.62251.4808-0.29233.07542.0515.32620.3517-0.4695-0.10830.5886-0.1508-1.11620.67130.8069-0.03830.70510.0961-0.32140.97270.1161.1362.9236-2.96546.9398
503.13580.84750.40056.84230.00155.63780.1710.32320.6732-0.95270.10321.26211.1598-0.69-0.11641.0633-0.2283-0.29960.66-0.04891.1818-17.2417-63.0125-71.2132
512.36593.24970.61536.1481.1781.7742-0.04150.1422-0.5218-0.88420.2421-0.04870.23670.0448-0.09570.65680.05260.03410.4568-0.15770.6295-3.8471-44.7054-70.4421
523.61710.1157-0.39134.7403-0.4093.0266-0.28720.8949-0.1816-0.24980.47311.36020.234-0.6001-0.16210.4754-0.107-0.11510.59240.11840.9501-11.2667-32.5801-71.4641
532.40830.0981-0.7574.34521.60962.02410.05540.6360.88410.2052-0.04831.4762-0.1745-0.5801-0.01230.575-0.0407-0.16780.70860.21721.4669-21.7828-21.0531-61.4815
541.68710.0607-0.11526.16621.63615.4325-0.0261-0.31251.03260.4694-0.37951.49670.6033-0.4909-0.02330.74470.0370.13570.42760.04271.4889-23.1166-22.4411-52.1197
551.98461.2212-0.06482.84770.30971.65910.4475-0.18560.22490.6677-0.12340.36950.6291-0.4404-0.35370.7381-0.03410.04230.4848-0.14110.9796-16.8417-33.6326-49.2829
561.9806-0.2298-0.07682.33020.50131.10470.0091-0.21440.25080.39360.0180.465-0.03280.03140.07240.53290.0206-0.06490.3721-0.08960.7992-8.7969-35.5237-46.5632
572.05411.20510.88033.1253-0.53372.3243-0.13310.0565-0.08480.1160.17530.18910.1599-0.1191-0.03030.47320.09490.14250.359-0.21830.6585-5.4935-44.4344-53.0004
582.49051.53751.18233.4911-1.95243.2505-0.26810.54050.2772-0.8670.2637-0.09440.54180.23140.12980.71320.0106-0.02120.5595-0.27540.8078-7.4699-51.3864-71.5998
592.22191.60260.2714.48961.01541.773-0.00630.29350.7264-0.6247-0.13421.3821-0.2805-0.50770.37870.8372-0.0623-0.42460.89910.25431.7683-20.2925-23.8405-76.2681
607.70531.91430.79136.3494-0.8384.2987-0.29571.31550.6795-1.24910.31220.49210.341-0.2053-0.05520.9977-0.01990.29941.2142-0.45370.23477.2285-30.0166-104.1172
611.3731-0.5766-0.27032.55121.05790.9967-0.09680.3380.6812-0.32940.05440.5368-0.2306-0.1306-0.02090.5784-0.0483-0.18320.52920.18981.09593.0233-10.0128-70.9038
622.38320.54850.05341.3395-1.01973.58460.1959-0.1646-0.02720.1381-0.04460.3235-0.384-0.0659-0.03720.5792-0.0214-0.09040.41150.0031.28657.1533-5.1442-57.9616
632.12610.0565-1.21441.03580.52133.6318-0.23120.56160.5592-0.47260.2360.2248-0.42620.0993-0.02390.6903-0.2585-0.17420.71530.19230.90019.2128-22.3723-84.5571
644.4365-1.1045-1.0955.1312.04695.0828-0.11421.1703-0.0645-0.56160.33680.73050.1151-0.38140.03190.8663-0.3574-0.39440.90120.19531.0888-4.4143-26.2951-90.2879
654.6848-1.04370.65914.2957-0.93885.7367-0.09850.68050.480.1702-0.0708-0.4010.550.4356-0.00470.73880.00660.04080.6715-0.29620.805233.7446-37.2881-80.4102
660.7761-0.1567-1.06133.35493.15224.5862-0.00960.3874-0.8559-0.7030.3142-0.610.47880.3419-0.2380.8146-0.1988-0.06350.5317-0.12470.848930.1526-45.4719-79.3059
674.104-0.3294-0.52023.84091.74292.16760.72610.8014-1.4953-0.11690.0901-1.90231.72110.8945-0.0810.79860.16480.23470.6946-0.17860.965540.3567-42.6524-77.4671
681.50390.98990.33343.29330.1544.7375-0.2098-0.1428-0.2431-0.54070.4582-0.39920.46430.12680.01950.45530.13470.09950.5397-0.1630.833633.5383-31.0719-70.4592
691.3342-0.8467-0.71872.0853-0.13521.64230.33090.4821-0.1885-0.9211-0.81030.1604-0.00990.4673-0.1923-0.42430.59450.55130.46-0.16160.688729.4931-22.1064-64.5453
700.0267-0.3344-0.29842.67731.26233.36-0.06310.03190.26880.0484-0.0580.4647-0.52660.31620.1540.5163-0.0485-0.06250.5196-0.02410.918229.749-10.0199-57.6443
711.66480.21181.57672.63341.09165.1896-0.61650.1463-0.09220.0216-0.0917-0.4398-0.15460.61780.36560.4320.0059-0.05360.49330.0190.942241.0542-13.4895-50.807
722.0378-1.2772-2.45582.0628-1.15358.66580.0486-0.44850.25220.215-0.4427-0.1768-1.10510.29590.10070.5066-0.0403-0.03440.3624-0.14580.896328.0341-7.4365-52.04
737.33454.03950.89753.08721.61412.11011.561-1.9253-2.94691.21320.09180.04721.6257-0.04491.94570.50530.96610.4120.4246-0.29110.760449.3742-41.3224-13.8774
743.8711-1.3981.09292.6949-1.79346.1152-0.726-0.02160.3509-0.23070.4924-0.21790.51810.05590.33240.51640.2450.07520.4207-0.16470.646938.691-24.1404-25.1326
752.68980.45991.292.5084-1.96263.7992-0.19880.2126-0.0657-0.26850.1282-0.28420.62660.05340.04310.6092-0.0201-0.08720.4295-0.0680.782432.8707-23.7406-37.0663
764.71470.36112.93524.5973-1.49596.5896-0.4577-0.4205-0.55080.24580.867-0.97230.53781.04280.10690.61590.41350.03460.7636-0.06130.770554.3211-31.2704-6.897
772.44460.46050.10012.7899-0.42066.4820.1198-0.5579-0.51450.2006-0.4273-0.14930.83421.43570.37720.82130.4763-0.00760.81010.21650.885547.6463-37.1694-5.4008
786.81620.24021.3152.3995-0.51234.0815-0.2509-0.4041-1.44630.4374-0.0414-0.74111.4312-0.02490.0351.34710.3869-0.04360.76410.19311.182248.6615-47.6648-14.0316
792.1765-0.67710.5991.98310.30232.5630.20910.00160.44610.21350.1256-0.33490.2846-1.93730.10221.1429-0.26080.07521.89790.43491.5246-23.5332-36.759551.4191
802.4074-2.1822-0.95552.1260.90174.1274-0.24740.28540.0901-0.21130.3699-0.159-0.1131-0.0374-0.10391.3495-0.3608-0.05161.23390.19921.18744.72-42.374843.4277
810.2768-0.7244-0.37881.95120.3692.3685-0.059-0.0185-0.77670.6566-0.69590.12991.56540.08280.13982.1976-0.43340.02091.36950.06821.2845.4405-66.606431.7728
822.3541-0.8713-1.12692.86-0.22262.8712-0.38950.6526-0.2036-0.1077-0.23480.40610.3748-1.22120.03021.8064-0.4377-0.37121.44660.15041.2697-2.5342-55.317324.2057
830.7764-1.13480.39181.6564-0.15082.2896-0.1092-0.055-0.6521-0.81660.14620.0307-0.1488-0.7294-0.01711.5947-0.3572-0.18241.60060.29421.358-0.021-47.69121.1827
841.1567-0.7673-0.06670.83330.55251.41710.32280.14950.1688-0.0578-0.43570.64060.8105-0.3022-0.08891.5832-0.42620.00971.33040.0831.18438.2043-41.556124.1406
851.82520.2226-0.010.6326-0.2951.2389-0.09570.1684-0.3795-0.04870.05610.4288-0.0679-0.4166-0.4271.3091-0.332-0.21121.70670.26131.4935-10.6353-38.93429.9953
860.53910.5635-0.20561.8463-1.27521.1612-0.2236-0.1262-0.49040.32580.4790.51110.3251-1.16870.06241.3766-0.1817-0.01061.3840.19021.4016-8.2139-37.261147.4525
872.15380.23820.00740.4081-0.50690.63590.1350.4273-0.32580.3508-0.342-0.25720.8594-0.37510.19761.7127-0.19620.04771.3040.19861.39227.6395-63.415149.9932
880.38291.1564-1.52135.748-4.37648.02730.1708-0.7458-0.02181.54550.568-0.0897-0.03-0.4353-0.31252.14990.24490.12511.42610.28451.137322.2162-36.543375.7329
891.7398-0.0954-2.10272.1206-0.07694.8848-0.0703-0.26720.10680.35160.1528-0.35171.27390.11690.18071.3668-0.097-0.08171.2640.3150.994625.6889-46.069746.9928
901.4591-0.8329-0.71720.69310.42490.3761-0.6701-0.556-0.5440.65880.65110.11341.13320.25020.73922.36050.1346-0.12591.35090.31971.921629.3453-68.732334.3815
912.2456-0.40321.2420.13-0.01281.3303-0.9265-0.86910.051.02020.7955-0.18950.78360.27940.25911.64190.3054-0.06441.59140.46781.166543.5097-54.997431.7344
923.1271-0.0459-0.93695.39911.30052.10610.0848-0.2543-0.55830.80950.19330.90611.1643-0.3236-0.30731.59150.07160.19730.94580.22840.864235.328-51.667227.2102
930.4840.52530.191.370.84265.59870.1104-0.2607-0.07880.5191-0.0656-0.18170.320.19660.03981.4076-0.07870.06211.2770.30591.123725.9566-41.261755.5916
942.6773-0.1212-0.38862.91330.17878.457-0.0701-0.02350.07231.05140.57880.37570.7144-0.6786-0.4881.1972-0.12610.261.24440.22871.126215.2478-46.428763.8006
951.5025-1.41691.20034.8167-2.18516.48830.4287-0.345-0.11481.17510.27470.28130.10020.6068-0.37061.3068-0.2187-0.08111.26260.0090.934627.394-11.042450.2275
963.62420.1967-0.92771.21212.06317.31980.0059-0.6860.4490.3423-0.84030.42830.9023-0.21841.10880.7266-0.20530.08060.9877-0.03021.070918.3796-9.437150.3412
970.27630.76750.44013.12521.94091.21590.3289-0.01790.32650.104-0.131.348-0.83940.30820.10591.828-0.1802-0.0911.07560.03651.17426.3969-2.62347.302
980.2162-0.3372-0.44924.0278-2.44035.7738-0.1811-0.10590.05820.6386-0.0681-0.26290.48750.38260.09250.9665-0.1515-0.13490.82380.11230.990931.0384-14.916939.7171
993.57370.0496-0.10943.74121.13125.397-0.1986-0.74640.39660.3992-0.6626-0.2070.45430.2920.35450.8421-0.1067-0.11550.99050.23920.918135.3063-23.430733.3932
1000.52240.1944-1.20122.65950.73973.27360.20950.189-0.16060.4092-0.08090.14070.53930.9651-0.12380.94450.1447-0.26591.06320.20550.734344.4167-30.353225.5286
1014.21770.2496-1.97130.1571-1.02536.3894-0.2187-0.13571.10150.2612-0.2017-0.38750.16841.28010.17820.65620.1216-0.22350.9530.17340.882747.3986-19.120118.1534
1024.05293.66411.39935.54071.06036.07-0.47680.23970.17110.23680.2825-0.66160.62340.4403-0.05820.99380.3898-0.11460.98830.13671.110944.8506-33.347319.9091
1032.419-0.66190.26363.2125-2.08473.7751-0.10460.06410.324-0.17850.43860.8392-0.33-0.5258-0.32060.5683-0.0538-0.23510.3975-0.13390.810927.06182.4954-18.0453
1043.1576-0.15061.77533.038-2.79356.108-0.0567-0.17660.35710.147-0.4649-0.34230.18840.41970.31190.4190.10510.02770.5132-0.18520.590735.4589-15.8651-6.7772
1052.27520.13771.02964.2592-3.00233.82590.2809-0.5676-0.62080.5849-0.4242-0.15130.22630.5159-0.14810.6556-0.0235-0.07720.69880.10590.636132.4113-21.25052.0684
1063.4483-0.59131.42032.5852-2.3035.93240.206-0.5596-0.27350.8922-0.0266-0.1554-0.27960.0751-0.01750.55060.0532-0.03940.69580.05950.773333.874-19.72787.6761
1071.7560.1595-0.47063.4927-1.52679.47880.1293-0.57910.5642-0.18190.2154-0.2206-0.50430.5826-0.04050.43520.0957-0.06040.5437-0.1490.850737.46530.1309-25.9792
1081.0743-0.5988-0.28822.9934-1.82664.2661-0.1401-0.1478-0.5166-0.02060.15540.5740.5166-0.35790.3460.46220.05140.01780.3957-0.25640.732425.3654-9.5945-24.438
1092.13860.7879-1.89282.4037-0.48731.8616-0.14850.16550.8705-0.09080.34920.798-0.5788-0.45090.46810.24320.12550.04820.3412-0.21230.746226.6865-2.5303-32.2576
1101.78541.0615-0.66172.5606-2.57634.8415-0.2794-0.15930.60920.27040.062-0.2719-0.5459-0.00220.08240.55290.0985-0.18250.4416-0.14451.10728.32566.1874-19.8247
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 104 )A1 - 104
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 266 )A105 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 290 )A267 - 290
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 406 )A291 - 406
5X-RAY DIFFRACTION5chain 'A' and (resid 407 through 548 )A407 - 548
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 73 )B2 - 73
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 206 )B74 - 206
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 307 )B207 - 307
9X-RAY DIFFRACTION9chain 'B' and (resid 308 through 361 )B308 - 361
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 20 )C2 - 20
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 45 )C21 - 45
12X-RAY DIFFRACTION12chain 'C' and (resid 46 through 63 )C46 - 63
13X-RAY DIFFRACTION13chain 'C' and (resid 64 through 84 )C64 - 84
14X-RAY DIFFRACTION14chain 'C' and (resid 85 through 136 )C85 - 136
15X-RAY DIFFRACTION15chain 'C' and (resid 137 through 197 )C137 - 197
16X-RAY DIFFRACTION16chain 'C' and (resid 198 through 234 )C198 - 234
17X-RAY DIFFRACTION17chain 'C' and (resid 235 through 266 )C235 - 266
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 29 )D2 - 29
19X-RAY DIFFRACTION19chain 'D' and (resid 30 through 127 )D30 - 127
20X-RAY DIFFRACTION20chain 'D' and (resid 128 through 150 )D128 - 150
21X-RAY DIFFRACTION21chain 'D' and (resid 151 through 213 )D151 - 213
22X-RAY DIFFRACTION22chain 'D' and (resid 214 through 235 )D214 - 235
23X-RAY DIFFRACTION23chain 'D' and (resid 236 through 309 )D236 - 309
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 104 )E1 - 104
25X-RAY DIFFRACTION25chain 'E' and (resid 105 through 191 )E105 - 191
26X-RAY DIFFRACTION26chain 'E' and (resid 192 through 303 )E192 - 303
27X-RAY DIFFRACTION27chain 'E' and (resid 304 through 456 )E304 - 456
28X-RAY DIFFRACTION28chain 'E' and (resid 457 through 505 )E457 - 505
29X-RAY DIFFRACTION29chain 'E' and (resid 506 through 547 )E506 - 547
30X-RAY DIFFRACTION30chain 'F' and (resid 2 through 100 )F2 - 100
31X-RAY DIFFRACTION31chain 'F' and (resid 101 through 121 )F101 - 121
32X-RAY DIFFRACTION32chain 'F' and (resid 122 through 206 )F122 - 206
33X-RAY DIFFRACTION33chain 'F' and (resid 207 through 307 )F207 - 307
34X-RAY DIFFRACTION34chain 'F' and (resid 308 through 325 )F308 - 325
35X-RAY DIFFRACTION35chain 'F' and (resid 326 through 361 )F326 - 361
36X-RAY DIFFRACTION36chain 'G' and (resid 2 through 20 )G2 - 20
37X-RAY DIFFRACTION37chain 'G' and (resid 21 through 45 )G21 - 45
38X-RAY DIFFRACTION38chain 'G' and (resid 46 through 63 )G46 - 63
39X-RAY DIFFRACTION39chain 'G' and (resid 64 through 221 )G64 - 221
40X-RAY DIFFRACTION40chain 'G' and (resid 222 through 266 )G222 - 266
41X-RAY DIFFRACTION41chain 'H' and (resid 2 through 29 )H2 - 29
42X-RAY DIFFRACTION42chain 'H' and (resid 30 through 73 )H30 - 73
43X-RAY DIFFRACTION43chain 'H' and (resid 74 through 98 )H74 - 98
44X-RAY DIFFRACTION44chain 'H' and (resid 99 through 127 )H99 - 127
45X-RAY DIFFRACTION45chain 'H' and (resid 128 through 167 )H128 - 167
46X-RAY DIFFRACTION46chain 'H' and (resid 168 through 213 )H168 - 213
47X-RAY DIFFRACTION47chain 'H' and (resid 214 through 235 )H214 - 235
48X-RAY DIFFRACTION48chain 'H' and (resid 236 through 259 )H236 - 259
49X-RAY DIFFRACTION49chain 'H' and (resid 260 through 309 )H260 - 309
50X-RAY DIFFRACTION50chain 'I' and (resid 1 through 31 )I1 - 31
51X-RAY DIFFRACTION51chain 'I' and (resid 32 through 118 )I32 - 118
52X-RAY DIFFRACTION52chain 'I' and (resid 119 through 143 )I119 - 143
53X-RAY DIFFRACTION53chain 'I' and (resid 144 through 191 )I144 - 191
54X-RAY DIFFRACTION54chain 'I' and (resid 192 through 220 )I192 - 220
55X-RAY DIFFRACTION55chain 'I' and (resid 221 through 266 )I221 - 266
56X-RAY DIFFRACTION56chain 'I' and (resid 267 through 318 )I267 - 318
57X-RAY DIFFRACTION57chain 'I' and (resid 319 through 456 )I319 - 456
58X-RAY DIFFRACTION58chain 'I' and (resid 457 through 505 )I457 - 505
59X-RAY DIFFRACTION59chain 'I' and (resid 506 through 548 )I506 - 548
60X-RAY DIFFRACTION60chain 'J' and (resid 2 through 25 )J2 - 25
61X-RAY DIFFRACTION61chain 'J' and (resid 26 through 157 )J26 - 157
62X-RAY DIFFRACTION62chain 'J' and (resid 158 through 206 )J158 - 206
63X-RAY DIFFRACTION63chain 'J' and (resid 207 through 307 )J207 - 307
64X-RAY DIFFRACTION64chain 'J' and (resid 308 through 361 )J308 - 361
65X-RAY DIFFRACTION65chain 'K' and (resid 2 through 20 )K2 - 20
66X-RAY DIFFRACTION66chain 'K' and (resid 21 through 45 )K21 - 45
67X-RAY DIFFRACTION67chain 'K' and (resid 46 through 63 )K46 - 63
68X-RAY DIFFRACTION68chain 'K' and (resid 64 through 117 )K64 - 117
69X-RAY DIFFRACTION69chain 'K' and (resid 118 through 162 )K118 - 162
70X-RAY DIFFRACTION70chain 'K' and (resid 163 through 221 )K163 - 221
71X-RAY DIFFRACTION71chain 'K' and (resid 222 through 250 )K222 - 250
72X-RAY DIFFRACTION72chain 'K' and (resid 251 through 266 )K251 - 266
73X-RAY DIFFRACTION73chain 'L' and (resid 2 through 29 )L2 - 29
74X-RAY DIFFRACTION74chain 'L' and (resid 30 through 98 )L30 - 98
75X-RAY DIFFRACTION75chain 'L' and (resid 99 through 171 )L99 - 171
76X-RAY DIFFRACTION76chain 'L' and (resid 172 through 197 )L172 - 197
77X-RAY DIFFRACTION77chain 'L' and (resid 198 through 288 )L198 - 288
78X-RAY DIFFRACTION78chain 'L' and (resid 289 through 309 )L289 - 309
79X-RAY DIFFRACTION79chain 'M' and (resid 1 through 48 )M1 - 48
80X-RAY DIFFRACTION80chain 'M' and (resid 49 through 143 )M49 - 143
81X-RAY DIFFRACTION81chain 'M' and (resid 144 through 220 )M144 - 220
82X-RAY DIFFRACTION82chain 'M' and (resid 221 through 266 )M221 - 266
83X-RAY DIFFRACTION83chain 'M' and (resid 267 through 318 )M267 - 318
84X-RAY DIFFRACTION84chain 'M' and (resid 319 through 365 )M319 - 365
85X-RAY DIFFRACTION85chain 'M' and (resid 366 through 456 )M366 - 456
86X-RAY DIFFRACTION86chain 'M' and (resid 457 through 505 )M457 - 505
87X-RAY DIFFRACTION87chain 'M' and (resid 506 through 548 )M506 - 548
88X-RAY DIFFRACTION88chain 'N' and (resid 2 through 25 )N2 - 25
89X-RAY DIFFRACTION89chain 'N' and (resid 26 through 100 )N26 - 100
90X-RAY DIFFRACTION90chain 'N' and (resid 101 through 121 )N101 - 121
91X-RAY DIFFRACTION91chain 'N' and (resid 122 through 157 )N122 - 157
92X-RAY DIFFRACTION92chain 'N' and (resid 158 through 206 )N158 - 206
93X-RAY DIFFRACTION93chain 'N' and (resid 207 through 320 )N207 - 320
94X-RAY DIFFRACTION94chain 'N' and (resid 321 through 361 )N321 - 361
95X-RAY DIFFRACTION95chain 'O' and (resid 2 through 20 )O2 - 20
96X-RAY DIFFRACTION96chain 'O' and (resid 21 through 45 )O21 - 45
97X-RAY DIFFRACTION97chain 'O' and (resid 46 through 63 )O46 - 63
98X-RAY DIFFRACTION98chain 'O' and (resid 64 through 117 )O64 - 117
99X-RAY DIFFRACTION99chain 'O' and (resid 118 through 162 )O118 - 162
100X-RAY DIFFRACTION100chain 'O' and (resid 163 through 221 )O163 - 221
101X-RAY DIFFRACTION101chain 'O' and (resid 222 through 250 )O222 - 250
102X-RAY DIFFRACTION102chain 'O' and (resid 251 through 266 )O251 - 266
103X-RAY DIFFRACTION103chain 'P' and (resid 2 through 29 )P2 - 29
104X-RAY DIFFRACTION104chain 'P' and (resid 30 through 98 )P30 - 98
105X-RAY DIFFRACTION105chain 'P' and (resid 99 through 127 )P99 - 127
106X-RAY DIFFRACTION106chain 'P' and (resid 128 through 171 )P128 - 171
107X-RAY DIFFRACTION107chain 'P' and (resid 172 through 197 )P172 - 197
108X-RAY DIFFRACTION108chain 'P' and (resid 198 through 224 )P198 - 224
109X-RAY DIFFRACTION109chain 'P' and (resid 225 through 259 )P225 - 259
110X-RAY DIFFRACTION110chain 'P' and (resid 260 through 309 )P260 - 309

+
万見について

-
お知らせ

-
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

-
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

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