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- PDB-6kja: E. coli ATCase holoenzyme mutant - G128/130A (catalytic chain) -

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基本情報

登録情報
データベース: PDB / ID: 6kja
タイトルE. coli ATCase holoenzyme mutant - G128/130A (catalytic chain)
要素
  • Aspartate carbamoyltransferase catalytic subunit
  • Aspartate carbamoyltransferase regulatory chain
キーワードTRANSFERASE / aspartate transcarbamoylase holoenzyme / de novo pyrimidine biosynthesis
機能・相同性
機能・相同性情報


aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutamine metabolic process / amino acid binding / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase ...Aspartate transcarbamylase regulatory subunit / Aspartate carbamoyltransferase regulatory subunit, C-terminal / Aspartate carbamoyltransferase regulatory subunit, N-terminal / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain superfamily / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain superfamily / Aspartate carbamoyltransferase regulatory chain, allosteric domain / Aspartate carbamoyltransferase regulatory chain, metal binding domain / Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate carbamoyltransferase / Aspartate/ornithine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Aspartate carbamoyltransferase catalytic subunit / Aspartate carbamoyltransferase regulatory chain
類似検索 - 構成要素
生物種Escherichia coli K-12 (大腸菌)
手法X線回折 / 分子置換 / 解像度: 3.064 Å
データ登録者Lei, Z. / Zheng, J. / Jia, Z.C.
資金援助 中国, カナダ, 2件
組織認可番号国
National Natural Science Foundation of China (NSFC)21773014 中国
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04427 カナダ
引用ジャーナル: Febs J. / 年: 2020
タイトル: New regulatory mechanism-based inhibitors of aspartate transcarbamoylase for potential anticancer drug development.
著者: Lei, Z. / Wang, B. / Lu, Z. / Wang, N. / Tan, H. / Zheng, J. / Jia, Z.
履歴
登録2019年7月22日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02020年3月11日Provider: repository / タイプ: Initial release
改定 1.12020年8月26日Group: Database references / Derived calculations / カテゴリ: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_dist_value / _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.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
改定 1.22023年11月22日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)154,7239
ポリマ－154,5266
非ポリマー1963
水19811
1
A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
ヘテロ分子

A: Aspartate carbamoyltransferase catalytic subunit
B: Aspartate carbamoyltransferase regulatory chain
C: Aspartate carbamoyltransferase catalytic subunit
D: Aspartate carbamoyltransferase regulatory chain
E: Aspartate carbamoyltransferase catalytic subunit
F: Aspartate carbamoyltransferase regulatory chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)309,44518
ポリマ－309,05312
非ポリマー3926
水18010
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area26510 Å2
ΔGint-83 kcal/mol
Surface area102290 Å2
手法PISA
単位格子
Length a, b, c (Å)127.408, 127.408, 197.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 6 or (resid 7...
21(chain C and (resid 2 through 77 or resid 86...
31(chain E and (resid 2 through 6 or (resid 7...
12(chain B and (resid 16 through 45 or (resid 46...
22(chain D and (resid 16 through 18 or (resid 19...
32(chain F and (resid 16 through 18 or (resid 19...

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
111ASNASNGLNGLN(chain A and (resid 2 through 6 or (resid 7...AA2 - 62 - 6
121LYSLYSLYSLYS(chain A and (resid 2 through 6 or (resid 7...AA77
131ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
141ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
151ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
161ASNASNVALVAL(chain A and (resid 2 through 6 or (resid 7...AA2 - 3092 - 309
211ASNASNALAALA(chain C and (resid 2 through 77 or resid 86...CC2 - 772 - 77
221GLUGLUTHRTHR(chain C and (resid 2 through 77 or resid 86...CC86 - 22886 - 228
231ARGARGARGARG(chain C and (resid 2 through 77 or resid 86...CC229229
241ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
251ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
261ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
271ALAALALEULEU(chain C and (resid 2 through 77 or resid 86...CC1 - 3101 - 310
311ASNASNGLNGLN(chain E and (resid 2 through 6 or (resid 7...EE2 - 62 - 6
321LYSLYSLYSLYS(chain E and (resid 2 through 6 or (resid 7...EE77
331ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
341ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
351ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
361ALAALALEULEU(chain E and (resid 2 through 6 or (resid 7...EE1 - 3101 - 310
112THRTHRGLYGLY(chain B and (resid 16 through 45 or (resid 46...BB16 - 4516 - 45
122LEULEULEULEU(chain B and (resid 16 through 45 or (resid 46...BB4646
132THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
142THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
152THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
162THRTHRASNASN(chain B and (resid 16 through 45 or (resid 46...BB16 - 15316 - 153
212THRTHRILEILE(chain D and (resid 16 through 18 or (resid 19...DD16 - 1816 - 18
222ASPASPHISHIS(chain D and (resid 16 through 18 or (resid 19...DD19 - 2019 - 20
232THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
242THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
252THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
262THRTHRASNASN(chain D and (resid 16 through 18 or (resid 19...DD16 - 15316 - 153
312THRTHRILEILE(chain F and (resid 16 through 18 or (resid 19...FF16 - 1816 - 18
322ASPASPHISHIS(chain F and (resid 16 through 18 or (resid 19...FF19 - 2019 - 20
332THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
342THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
352THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153
362THRTHRASNASN(chain F and (resid 16 through 18 or (resid 19...FF16 - 15316 - 153

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Aspartate carbamoyltransferase catalytic subunit / Aspartate transcarbamylase / ATCase


分子量: 34365.156 Da / 分子数: 3 / 変異: G128A, G130A / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 株: K-12 / 遺伝子: pyrB, b4245, JW4204 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A786, aspartate carbamoyltransferase
#2: タンパク質 Aspartate carbamoyltransferase regulatory chain


分子量: 17143.625 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 株: K-12 / 遺伝子: pyrI / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A7F3
#3: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Zn
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 11 / 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

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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: 3 Å3/Da / 溶媒含有率: 58.93 %
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: 0.1 M HEPES pH 7.0, 30% Jeffamine M-600 pH 7.0, and 10% glycerol

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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: 回転陽極 / タイプ: RIGAKU R-AXIS IV / 波長: 1.54 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2016年10月15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: 1.54 Å / 相対比: 1
反射解像度: 3.04→50 Å / Num. obs: 36586 / % possible obs: 99.8 % / 冗長度: 4.8 % / CC1/2: 0.999 / Net I/σ(I): 16
反射 シェル解像度: 3.04→3.09 Å / Num. unique obs: 1813 / CC1/2: 0.88

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1ZA1

1za1


解像度: 3.064→42.287 Å / SU ML: 0.47 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 31.6 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2834 1966 5.62 %
Rwork0.2488 33032 -
obs0.2507 34998 98.64 %
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 max: 165.93 Å2 / Biso mean: 68.8878 Å2 / Biso min: 23.92 Å2
精密化ステップサイクル: final / 解像度: 3.064→42.287 Å
タンパク質核酸リガンド溶媒全体
原子数10005 0 3 11 10019
Biso mean--57.83 56.69 -
残基数----1311
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2712X-RAY DIFFRACTION4.25TORSIONAL
12C2712X-RAY DIFFRACTION4.25TORSIONAL
13E2712X-RAY DIFFRACTION4.25TORSIONAL
21B1182X-RAY DIFFRACTION4.25TORSIONAL
22D1182X-RAY DIFFRACTION4.25TORSIONAL
23F1182X-RAY DIFFRACTION4.25TORSIONAL
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 (%)
3.0644-3.1410.39671380.33742360100
3.141-3.22590.39591390.32862338100
3.2259-3.32080.33931340.3163231699
3.3208-3.42790.38331440.30632390100
3.4279-3.55040.36311460.30042355100
3.5504-3.69250.3281410.2884232799
3.6925-3.86040.28921380.2681234899
3.8604-4.06380.32121410.2658231697
4.0638-4.31810.29661380.2355232198
4.3181-4.65120.2521370.2138232897
4.6512-5.11850.19431410.2005236498
5.1185-5.85750.24111410.2224237098
5.8575-7.37350.31021470.2565243799
7.3735-42.2870.20941410.1999246296
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)
10.02250.0103-0.0055-0.02220.022-0.02460.43080.2288-0.5216-0.02510.30260.26360.2709-0.04-0-1.49520.79650.6440.6229-0.6809-0.0326-16.870220.4201-64.8139
20.0182-0.0005-0.0085-0.002-0.0169-0.00020.10670.2941-0.3630.32390.1104-0.0470.0368-0.06-0-0.93810.1437-0.08390.6765-0.22310.3297-26.72820.6722-53.5694
30.0147-0.0153-0.0352-0.0254-0.002-0.03010.27930.0185-0.43940.72040.0185-0.2113-0.2960.09750-1.70621.73020.5107-0.6119-0.87860.5322-0.31849.585-49.7173
40.02540.021-0.06630.05450.02090.0502-0.0230.20630.0183-0.01760.0508-0.387-0.0187-0.1134-0-0.34040.0948-0.47941.0217-0.52980.46010.139321.2332-58.3121
5-0.00090.00030.0038-0.00050.0004-0.0013-0.0044-0.0016-0.01040.02660.0186-0.00070.0036-0.0108-00.94210.0465-0.05010.8414-0.16680.9331-40.338-15.6297-35.2173
60.0034-0.0021-0.00290.0035-0.00140.00050.0340.0112-0.0076-0.04970.04370.035-0.0196-0.0596-00.624-0.1928-0.07480.6308-0.20370.8458-46.1989-5.6083-38.4311
7-0.00530.00110.00250.01020.00280.0006-0.01240.0812-0.03830.0461-0.04740.00620.04310.030900.9862-0.2964-0.20840.8934-0.3511.2238-43.7598-14.4909-39.2863
80.0036-0.00690.00340.00670.0025-0.0045-0.02550.01130.0234-0.008-0.0021-0.05510.0474-0.0311-00.9338-0.0166-0.12060.8456-0.17141.2917-40.1121-17.704-42.4114
90.0027-0.0075-0.00070.00460.0036-0.0039-0.0150.0210.0468-0.02-0.0452-0.06450.0329-0.0203-00.9943-0.08170.07180.8672-0.21851.1771-39.2084-20.6584-47.0346
100.0042-0.0019-0.01280.0016-0.0031-0.00010.01160.0251-0.08280.02960.00710.0181-0.0119-0.0213-00.31450.01750.0070.5109-0.10750.6661-30.22785.4825-43.8592
110.00080.00450.00430.00170.0011-0.0024-0.0527-0.0244-0.11990.0052-0.0246-0.0370.0401-0.0118-00.37710.1233-0.24970.5266-0.20080.9329-22.3583-1.5766-44.986
120.00150.00060.00160.0022-0.00090.0017-0.00450.00260.0324-0.0001-0.017-0.01690.02840.020900.85330.19450.07960.8248-0.08920.8937-24.2269-1.5586-36.3818
130.05820.033-0.00370.02930.0669-0.0440.69090.540.27330.8520.13750.27460.0971-0.1138-0-1.42530.09780.04230.97140.09720.3741-38.246443.1189-59.8305
140.06420.0164-0.01810.05190.00860.0350.13150.07450.04110.49670.31550.18480.0315-0.0067-00.2197-0.0097-0.030.69970.15610.3415-57.528731.963-46.674
150.0295-0.02530.03340.035-0.00790.0016-0.0020.2902-0.36730.12340.05920.15610.18210.10690-0.24150.0147-0.24250.79940.140.1921-46.725325.829-57.3378
160.0011-0.0018-0.0037-0.0004-0.00440.0001-0.0212-0.01860.0104-0.0234-0.0090.0209-0.0211-0.001500.9980.25380.0961.09650.10061.3139-58.218579.7221-36.2614
17-0.00080.0007-0.00150.0007-0.0013-0.0016-0.01220.0205-0.032-0.0144-0.00270.0407-0.01490.029500.75560.1534-0.03590.57930.10981.1933-46.201679.5149-39.6034
180.0016-0.0024-0.00180.0037-0.0006-0.0017-0.0121-0.01070.0202-0.0114-0.0303-0.03220.0101-0.0226-01.19710.19330.03141.1248-0.0291.4795-57.040384.9927-32.1185
190.0005-0.00260.00010.0004-0.0009-0.0011-0.0231-0.0052-0.02880.02310.01760.0244-0.0004-0.004701.09150.13270.02841.02720.20571.2646-52.410184.9946-45.4837
200.00250.0004-0.0007-0.0003-0.0014-0.0005-0.0148-0.0222-0.0169-0.04390.0180.0205-0.0105-0.0034-00.69640.17820.11190.97010.07991.3055-57.691772.8594-44.5836
210.0007-0.0015-0.00230.00020.00060.0013-0.0051-0.01030.00630.0117-0.00390.01040.00520.001301.3936-0.00640.07141.35250.17891.4025-59.093688.434-47.9723
220.0053-0.0011-0.0030.0245-0.0043-0.0014-0.01940.0057-0.0336-0.012-0.0056-0.0007-0.05150.0068-01.11110.07260.01130.99930.07041.3775-63.000980.9662-47.7227
230.004-0.00470.00140.01-0.00740.00710.0616-0.01240.07930.04870.0356-0.0320.00880.023500.30260.02330.15090.68040.20180.9723-47.77559.7268-44.2431
240.00190.00080.0020.0063-0.00580.00230.0084-0.02630.03270.0197-0.07170.02180.0461-0.040400.28530.05080.33140.62660.30310.8251-53.636255.5487-44.4454
250.00180.0016-0.00380.00090.00060.00070.00350.00020.02590.02480.0122-0.0042-0.0093-0.0192-00.6859-0.01920.18960.8515-0.00830.9143-53.804658.6856-36.5973
260.0151-0.03410.00830.0630.06230.01380.10820.29140.01430.42490.4244-0.01730.10170.1681-0-0.0647-0.04360.20591.00780.14140.1753-10.801847.8339-63.3916
270.01680.0165-0.02990.0147-0.0214-0.02990.28240.47380.0290.32690.2558-0.17950.12110.0033-00.07630.07850.02310.77620.09590.2498-5.753547.5867-57.0922
280.0529-0.00650.00540.0247-0.00350.00860.18080.11940.35120.56210.26550.28410.28410.1701-00.3332-0.03340.21810.60250.3930.6046-10.384171.2743-49.1874
290.02790.01410.04370.0110.01240.00090.24130.28280.19120.03550.27910.3759-0.01490.1482-0-0.3021-0.14690.33710.97520.43590.3117-18.771659.6248-60.4576
300.0008-0.00030.001-0.00010.0043-0.0010.0320.0135-0.00010.04190.0074-0.03920.00590.0203-00.5514-0.1013-0.14620.6796-0.07370.713734.171147.8434-38.4557
310.0006-0.0096-0.00050.002-0.01220.0051-0.02740.0301-0.04480.0385-0.0878-0.11590.03840.054200.36570.0983-0.02910.8506-0.05030.627632.617740.2101-40.4145
320.0027-0.00080.00020.00110.0018-0.00130.01370.0089-0.0029-0.0123-0.0110.0312-0.0114-0.002900.5706-0.111-0.28350.8359-0.08870.671727.34250.5744-46.078
330.0068-0.0049-0.00390.0090.00390.0017-0.0003-00.01420.0032-0.00430.0131-0.0077-0.0057-00.89360.02790.21951.019-0.17471.024141.450344.1102-48.9124
340.00230.0010.0090.0026-0.00790.0102-0.01180.0072-0.0276-0.0405-0.0748-0.0048-0.0055-0.0085-00.3026-0.04330.04110.9066-0.0520.629825.682249.7288-48.6412
350.00190.00110.0091-0.0007-0.01290.0197-0.01690.0248-0.01950.064-0.00580.0209-0.13470.038-00.4009-0.0105-0.00190.7313-0.04710.45649.37551.4331-45.7124
360.00090.0007-0.00140.00090.00120.0013-0.00440.0083-0.01390.0123-0.00010.025500.0035-00.4632-0.1083-0.07560.6591-0.12850.51213.265954.7192-38.4349
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 66 )A2 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 134 )A67 - 134
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 247 )A135 - 247
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 309 )A248 - 309
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 25 )B16 - 25
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 41 )B26 - 41
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 74 )B42 - 74
8X-RAY DIFFRACTION8chain 'B' and (resid 75 through 89 )B75 - 89
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 99 )B90 - 99
10X-RAY DIFFRACTION10chain 'B' and (resid 100 through 123 )B100 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 143 )B124 - 143
12X-RAY DIFFRACTION12chain 'B' and (resid 144 through 153 )B144 - 153
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 149 )C1 - 149
14X-RAY DIFFRACTION14chain 'C' and (resid 150 through 247 )C150 - 247
15X-RAY DIFFRACTION15chain 'C' and (resid 248 through 310 )C248 - 310
16X-RAY DIFFRACTION16chain 'D' and (resid 16 through 25 )D16 - 25
17X-RAY DIFFRACTION17chain 'D' and (resid 26 through 41 )D26 - 41
18X-RAY DIFFRACTION18chain 'D' and (resid 42 through 57 )D42 - 57
19X-RAY DIFFRACTION19chain 'D' and (resid 58 through 67 )D58 - 67
20X-RAY DIFFRACTION20chain 'D' and (resid 68 through 81 )D68 - 81
21X-RAY DIFFRACTION21chain 'D' and (resid 82 through 89 )D82 - 89
22X-RAY DIFFRACTION22chain 'D' and (resid 90 through 99 )D90 - 99
23X-RAY DIFFRACTION23chain 'D' and (resid 100 through 130 )D100 - 130
24X-RAY DIFFRACTION24chain 'D' and (resid 131 through 143 )D131 - 143
25X-RAY DIFFRACTION25chain 'D' and (resid 144 through 153 )D144 - 153
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 87 )E1 - 87
27X-RAY DIFFRACTION27chain 'E' and (resid 88 through 149 )E88 - 149
28X-RAY DIFFRACTION28chain 'E' and (resid 150 through 265 )E150 - 265
29X-RAY DIFFRACTION29chain 'E' and (resid 266 through 310 )E266 - 310
30X-RAY DIFFRACTION30chain 'F' and (resid 16 through 25 )F16 - 25
31X-RAY DIFFRACTION31chain 'F' and (resid 26 through 67 )F26 - 67
32X-RAY DIFFRACTION32chain 'F' and (resid 68 through 81 )F68 - 81
33X-RAY DIFFRACTION33chain 'F' and (resid 82 through 89 )F82 - 89
34X-RAY DIFFRACTION34chain 'F' and (resid 90 through 109 )F90 - 109
35X-RAY DIFFRACTION35chain 'F' and (resid 110 through 143 )F110 - 143
36X-RAY DIFFRACTION36chain 'F' and (resid 144 through 153 )F144 - 153

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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