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- PDB-6kj8: E. coli ATCase holoenzyme mutant - G166P (catalytic chain) -

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基本情報

登録情報
データベース: PDB / ID: 6kj8
タイトルE. coli ATCase holoenzyme mutant - G166P (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: 3.011 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 / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)154,7599
ポリマ－154,5626
非ポリマー1963
水50428
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)309,51718
ポリマ－309,12512
非ポリマー3926
水21612
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area26900 Å2
ΔGint-97 kcal/mol
Surface area100680 Å2
手法PISA
単位格子
Length a, b, c (Å)126.592, 126.592, 196.490
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 1 through 5 or (resid 6...
21(chain C and (resid 1 through 6 or (resid 7...
31(chain E and (resid 1 through 5 or (resid 6...
12(chain B and (resid 16 or (resid 17 and (name...
22(chain D and (resid 16 through 58 or (resid 59...
32(chain F and (resid 16 or (resid 17 and (name...

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
111ALAALATYRTYR(chain A and (resid 1 through 5 or (resid 6...AA1 - 51 - 5
121GLNGLNLYSLYS(chain A and (resid 1 through 5 or (resid 6...AA6 - 76 - 7
131ALAALAVALVAL(chain A and (resid 1 through 5 or (resid 6...AA1 - 3091 - 309
141ALAALAVALVAL(chain A and (resid 1 through 5 or (resid 6...AA1 - 3091 - 309
151ALAALAVALVAL(chain A and (resid 1 through 5 or (resid 6...AA1 - 3091 - 309
161ALAALAVALVAL(chain A and (resid 1 through 5 or (resid 6...AA1 - 3091 - 309
211ALAALAGLNGLN(chain C and (resid 1 through 6 or (resid 7...CC1 - 61 - 6
221LYSLYSLYSLYS(chain C and (resid 1 through 6 or (resid 7...CC77
231ALAALAVALVAL(chain C and (resid 1 through 6 or (resid 7...CC1 - 3091 - 309
241ALAALAVALVAL(chain C and (resid 1 through 6 or (resid 7...CC1 - 3091 - 309
251ALAALAVALVAL(chain C and (resid 1 through 6 or (resid 7...CC1 - 3091 - 309
261ALAALAVALVAL(chain C and (resid 1 through 6 or (resid 7...CC1 - 3091 - 309
311ALAALATYRTYR(chain E and (resid 1 through 5 or (resid 6...EE1 - 51 - 5
321GLNGLNLYSLYS(chain E and (resid 1 through 5 or (resid 6...EE6 - 76 - 7
331ALAALALEULEU(chain E and (resid 1 through 5 or (resid 6...EE1 - 3101 - 310
341ALAALALEULEU(chain E and (resid 1 through 5 or (resid 6...EE1 - 3101 - 310
351ALAALALEULEU(chain E and (resid 1 through 5 or (resid 6...EE1 - 3101 - 310
361ALAALALEULEU(chain E and (resid 1 through 5 or (resid 6...EE1 - 3101 - 310
112THRTHRTHRTHR(chain B and (resid 16 or (resid 17 and (name...BB1616
122VALVALVALVAL(chain B and (resid 16 or (resid 17 and (name...BB1717
132LYSLYSASNASN(chain B and (resid 16 or (resid 17 and (name...BB13 - 15313 - 153
142LYSLYSASNASN(chain B and (resid 16 or (resid 17 and (name...BB13 - 15313 - 153
152LYSLYSASNASN(chain B and (resid 16 or (resid 17 and (name...BB13 - 15313 - 153
162LYSLYSASNASN(chain B and (resid 16 or (resid 17 and (name...BB13 - 15313 - 153
212THRTHRLEULEU(chain D and (resid 16 through 58 or (resid 59...DD16 - 5816 - 58
222ILEILEASNASN(chain D and (resid 16 through 58 or (resid 59...DD59 - 6359 - 63
232THRTHRASNASN(chain D and (resid 16 through 58 or (resid 59...DD16 - 15316 - 153
242THRTHRASNASN(chain D and (resid 16 through 58 or (resid 59...DD16 - 15316 - 153
252THRTHRASNASN(chain D and (resid 16 through 58 or (resid 59...DD16 - 15316 - 153
262THRTHRASNASN(chain D and (resid 16 through 58 or (resid 59...DD16 - 15316 - 153
312THRTHRTHRTHR(chain F and (resid 16 or (resid 17 and (name...FF1616
322VALVALVALVAL(chain F and (resid 16 or (resid 17 and (name...FF1717
332ALAALAASNASN(chain F and (resid 16 or (resid 17 and (name...FF11 - 15311 - 153
342ALAALAASNASN(chain F and (resid 16 or (resid 17 and (name...FF11 - 15311 - 153
352ALAALAASNASN(chain F and (resid 16 or (resid 17 and (name...FF11 - 15311 - 153
362ALAALAASNASN(chain F and (resid 16 or (resid 17 and (name...FF11 - 15311 - 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: 34377.172 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: 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, b4244, JW4203 / 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: 28 / 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: 2.94 Å3/Da / 溶媒含有率: 58.17 %
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: 0.1M 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1月12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→50 Å / Num. obs: 37126 / % possible obs: 100 % / 冗長度: 8.8 % / CC1/2: 0.996 / Net I/σ(I): 16.1
反射 シェル解像度: 3→3.05 Å / Num. unique obs: 1823 / CC1/2: 0.811

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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: 3.011→47.869 Å / SU ML: 0.41 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 26.49 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2474 1988 5.44 %
Rwork0.2106 34587 -
obs0.2126 36575 99.63 %
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: 186.42 Å2 / Biso mean: 60.697 Å2 / Biso min: 22.56 Å2
精密化ステップサイクル: final / 解像度: 3.011→47.869 Å
タンパク質核酸リガンド溶媒全体
原子数10027 0 3 28 10058
Biso mean--47.66 48.33 -
残基数----1312
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2721X-RAY DIFFRACTION10.31TORSIONAL
12C2721X-RAY DIFFRACTION10.31TORSIONAL
13E2721X-RAY DIFFRACTION10.31TORSIONAL
21B1149X-RAY DIFFRACTION10.31TORSIONAL
22D1149X-RAY DIFFRACTION10.31TORSIONAL
23F1149X-RAY DIFFRACTION10.31TORSIONAL
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 (%)
3.011-3.0860.36861410.3023243599
3.086-3.16940.39691430.29052439100
3.1694-3.26260.35261340.28042420100
3.2626-3.36790.3141410.28462451100
3.3679-3.48830.29011420.26282458100
3.4883-3.62790.31121420.22592448100
3.6279-3.79290.25841400.2112445100
3.7929-3.99280.24011440.19912463100
3.9928-4.24280.22511460.19012477100
4.2428-4.57020.18821420.16642483100
4.5702-5.02970.16171380.16432468100
5.0297-5.75640.22381440.19052502100
5.7564-7.24840.24341450.21992520100
7.2484-47.8690.2431460.1921257897
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)
10.05670.01260.02090.01420.0117-0.02421.0729-0.2865-1.2667-0.0876-0.0963-0.10090.4043-0.3075-00.2620.33960.70040.0542-0.2194-0.7595-8.7936-24.7848-31.5181
2-0.01550.01290.01890.01090.0090.00070.15870.0456-0.2681-0.06430.1598-0.13850.1601-0.0518-00.41230.11720.09990.2187-0.02910.166-6.7786-39.6005-21.0259
3-0.0319-0.0828-0.141-0.0128-0.0688-0.06650.2759-0.02760.1186-0.03660.0036-0.18730.1780.093900.3120.08390.22440.29530.03440.3687-5.7303-18.9411-22.3876
40.0158-0.0699-0.15280.0597-0.0060.1276-0.1632-0.42710.8662-0.425-0.1725-0.2105-0.2267-0.2645-0-0.0688-0.2040.62630.11560.18830.3687-9.8943-3.2927-14.754
50.0215-0.03340.0174-0.0122-0.0094-0.0144-0.0361-0.06610.1408-0.04790.0214-0.02480.1556-0.0086-00.49020.01010.18790.26730.03480.2831-17.2248-14.901-26.6305
60.007-0.006-0.00230.00570.00190.00370.01710.0146-0.050.01280.0109-0.07050.00920.0371-00.86310.16780.12171.01420.22071.459139.9331-31.5748-9.1114
7-0.0065-0.0211-0.00460.0056-0.01250.01160.13240.1751-0.0627-0.0415-0.0661-0.01210.1835-0.001900.6032-0.00460.03950.67830.0750.644929.4143-33.8083-3.3859
8-0.00670.0018-0.00460.00110.006-0.0014-0.0323-0.06810.00330.00460.0448-0.0888-0.00710.0297-00.7056-0.0231-0.08190.87580.14251.056737.1127-30.4063.0235
90.00760.00250.00490.0057-0.0003-0.00280.00920.08270.1014-0.161-0.1114-0.03410.06840.0664-00.68680.07150.08650.91480.16511.009632.9724-28.3409-10.6379
100.00040.002-0.00150.00120.00130.00020.02490.0192-0.02240.04040.0425-0.05230.03520.0421-00.7453-0.1750.26361.15630.36131.10247.0892-31.1656-14.2904
11-0.0011-0.0049-0.0007-0.0055-0.0014-0.0011-0.0766-0.01950.0117-0.0574-0.0527-0.02790.01530.14700.62720.11330.16990.82390.391.398229.9797-20.6514-14.2219
120.00620.04380.06030.0002-0.03770.0474-0.01030.0271-0.17190.0298-0.04-0.2011-0.1018-0.176800.26990.02550.09810.20430.04510.463311.1093-24.0828-10.8964
130.00990.0046-0.00520.00730.00980.00310.0939-0.02280.0776-0.05710.0760.0744-0.030.0076-00.38420.00260.01250.5096-0.00790.504513.6899-19.9848-3.296
140.0041-0.016-0.00430.06070.02050.00180.4714-0.0918-0.181-0.14370.38830.51430.3734-0.137400.5970.3037-0.0896-0.092-0.551-0.011-13.7645-62.8903-33.0441
15-0.0004-0.0088-0.02790.0037-0.018-0.00470.0150.18480.0769-0.2444-0.17890.5746-0.00170.0876-00.50920.3417-0.2395-0.53550.4835-0.1223-19.0005-47.4907-31.5514
160.03080.0163-0.04290.0245-0.049-0.03450.0355-0.0286-0.2356-0.2081-0.05610.0504-0.05030.1468-00.41850.0937-0.06170.242-0.00740.2599-22.9975-48.0719-23.3101
170.0057-0.0090.00250.0251-0.00390.00220.1289-0.3285-0.2641-0.1539-0.0460.08750.00530.1531-00.35130.0605-0.12410.2747-0.06410.3272-15.6419-59.0684-22.8295
180.00020.02610.0020.034-0.00620.04620.2461-0.033-0.30820.06330.0657-0.2344-0.0879-0.112200.44460.1177-0.10430.3068-0.12440.3305-0.6635-67.0019-17.3802
190.06920.05550.01860.0495-0.00750.0653-0.0007-0.08210.06320.07210.1621-0.11130.0767-0.028800.39060.0432-0.06790.2252-0.09890.46651.6663-66.6595-12.7112
200.00750.0210.00430.0297-0.00910.01820.0765-0.18540.0127-0.01990.1131-0.30790.0344-0.0355-00.31850.0495-0.05860.3258-0.1120.36849.1477-56.5632-11.2162
21-0.0290.08330.0827-0.0011-0.0144-0.08830.0895-0.18870.2135-0.32130.07680.0284-0.04880.1905-00.51670.2199-0.11820.0587-0.07660.1979-3.1629-51.909-25.8015
22-0.0044-0.00410.00190.00910.0044-0.0045-0.04620.13610.0002-0.1714-0.02860.06590.0569-0.0785-00.58050.05-0.11930.49140.29181.1748-40.3922-90.3155-3.1031
23-0.01240.01640.02250.0250.0171-0.00840.09890.08690.04650.1073-0.0014-0.12860.231-0.1719-00.0114-0.8821-0.6802-0.7957-0.29160.786-44.0118-84.1379-8.7911
240.0028-0.00330.00340.00130.0020.0007-0.00840.0220.0420.03920.007-0.0028-0.03920.015701.1425-0.179-0.20280.7140.13691.4614-35.0295-90.0662-7.4763
250.00220.001-0.0006-0.0008-0-0.0026-0.0198-0.00540.003-0.0229-0.02080.03150.0179-0.0068-01.328-0.3192-0.03241.484-0.08351.4657-49.9331-98.0065-16.0561
260.0582-0.0171-0.02030.003-0.0290.02980.06330.1086-0.37860.04010.06230.2939-0.0523-0.2409-00.3580.0241-0.2557-0.03170.16710.6188-30.1989-73.2888-11.2971
270.00460.0089-0.0209-0.00340.00770.0170.0426-0.0252-0.2775-0.31080.1631-0.0931-0.05360.192300.36630.0467-0.21230.40160.08480.5088-22.4057-75.5493-9.1463
280.08660.1315-0.10460.08310.22050.04780.0758-0.0455-0.0281-0.0934-0.0319-0.0372-0.00480.0147-00.43460.1092-0.05590.2865-0.01240.1795-36.0407-33.2984-30.7422
290.0128-0.06840.07040.11790.0374-0.06650.4393-0.44610.2244-0.0696-0.18110.1958-0.12570.3101-00.31410.1223-0.16710.11970.06520.2235-42.0328-31.7809-23.11
300.0713-0.04070.0224-0.0081-0.00550.07790.2487-0.1938-0.3178-0.0920.04070.2321-0.43450.2043-00.29040.1108-0.23420.29940.05370.5368-56.0835-44.6327-15.3424
310.01930.02770.0022-0.0096-0.026-0.03370.24190.1996-0.2755-0.1194-0.23870.0957-0.123-0.210100.39140.0504-0.13320.3113-0.04070.3383-42.0338-45.52-27.4017
320.0059-0.01330.0002-0.0003-0.00280.00240.0885-0.05460.00050.08350.23150.05730.1343-0.1793-00.7130.0193-0.0780.5452-0.01970.6574-54.65197.1965-7.4743
330.0138-0.00640.00870.01120.02440.0077-0.2434-0.01010.0213-0.2048-0.1479-0.11-0.17250.013400.568-0.0229-0.11370.48450.02180.6998-49.78719.8316-6.5215
340.0053-0.0028-0.00580.010.01580.001-0.0771-0.0261-0.01370.0083-0.02420.1132-0.1017-0.03900.95150.1373-0.13370.7501-0.16591.1596-58.569410.6875-5.3771
350.0089-0.0030.00670.0015-0.00570.0099-0.05190.07990.0338-0.095-0.05820.0283-0.0022-0.0115-00.7024-0.02760.03080.385-0.01170.5034-53.77283.6562-18.1544
360.0025-0.00330.00130.00610.00230.0030.0636-0.0024-0.0270.05060.0076-0.04820.03710.02200.34250.1540.01250.6039-0.01050.567-59.923-2.5681-8.5465
370.00370.0001-0.0020.0025-0.00030.0009-0.0510.05350.1089-0.0296-0.0329-0.0378-0.0587-0.0131-00.8899-0.0069-0.36510.92980.23511.2409-59.106613.9206-17.6312
380.0266-0.00240.0030.0005-0.00090.0014-0.13960.01770.1157-0.0207-0.10840.04860.0073-0.0927-00.48050.0636-0.10590.34470.06140.783-61.76942.9956-17.8225
390.01860.0114-0.01260.0076-0.00450.0043-0.2536-0.05970.0836-0.0388-0.0858-0.1033-0.00350.0181-00.27560.0273-0.03010.29470.08090.26-46.2678-14.4849-11.0528
400.00140.02720.0238-0.00040.03180.04530.0393-0.1055-0.0471-0.04620.07130.1676-0.0751-0.0162-00.39250.0098-0.02250.32320.04460.3461-50.0531-16.925-13.4818
410.0035-0.01380.00890.0098-0.00630.00020.06350.0772-0.1083-0.077-0.02590.18470.0515-0.032900.34540.0124-0.00720.38380.04950.3492-53.9745-15.7074-5.3307
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 66 )A1 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 98 )A67 - 98
3X-RAY DIFFRACTION3chain 'A' and (resid 99 through 166 )A99 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 265 )A167 - 265
5X-RAY DIFFRACTION5chain 'A' and (resid 266 through 309 )A266 - 309
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 19 )B13 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 41 )B20 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 57 )B42 - 57
9X-RAY DIFFRACTION9chain 'B' and (resid 58 through 85 )B58 - 85
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 92 )B86 - 92
11X-RAY DIFFRACTION11chain 'B' and (resid 93 through 101 )B93 - 101
12X-RAY DIFFRACTION12chain 'B' and (resid 102 through 143 )B102 - 143
13X-RAY DIFFRACTION13chain 'B' and (resid 144 through 153 )B144 - 153
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 32 )C1 - 32
15X-RAY DIFFRACTION15chain 'C' and (resid 33 through 52 )C33 - 52
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 106 )C53 - 106
17X-RAY DIFFRACTION17chain 'C' and (resid 107 through 149 )C107 - 149
18X-RAY DIFFRACTION18chain 'C' and (resid 150 through 195 )C150 - 195
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 236 )C196 - 236
20X-RAY DIFFRACTION20chain 'C' and (resid 237 through 265 )C237 - 265
21X-RAY DIFFRACTION21chain 'C' and (resid 266 through 309 )C266 - 309
22X-RAY DIFFRACTION22chain 'D' and (resid 16 through 26 )D16 - 26
23X-RAY DIFFRACTION23chain 'D' and (resid 27 through 74 )D27 - 74
24X-RAY DIFFRACTION24chain 'D' and (resid 75 through 84 )D75 - 84
25X-RAY DIFFRACTION25chain 'D' and (resid 85 through 93 )D85 - 93
26X-RAY DIFFRACTION26chain 'D' and (resid 94 through 123 )D94 - 123
27X-RAY DIFFRACTION27chain 'D' and (resid 124 through 153 )D124 - 153
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 87 )E1 - 87
29X-RAY DIFFRACTION29chain 'E' and (resid 88 through 166 )E88 - 166
30X-RAY DIFFRACTION30chain 'E' and (resid 167 through 265 )E167 - 265
31X-RAY DIFFRACTION31chain 'E' and (resid 266 through 310 )E266 - 310
32X-RAY DIFFRACTION32chain 'F' and (resid 11 through 32 )F11 - 32
33X-RAY DIFFRACTION33chain 'F' and (resid 33 through 50 )F33 - 50
34X-RAY DIFFRACTION34chain 'F' and (resid 51 through 62 )F51 - 62
35X-RAY DIFFRACTION35chain 'F' and (resid 63 through 74 )F63 - 74
36X-RAY DIFFRACTION36chain 'F' and (resid 75 through 81 )F75 - 81
37X-RAY DIFFRACTION37chain 'F' and (resid 82 through 89 )F82 - 89
38X-RAY DIFFRACTION38chain 'F' and (resid 90 through 101 )F90 - 101
39X-RAY DIFFRACTION39chain 'F' and (resid 102 through 114 )F102 - 114
40X-RAY DIFFRACTION40chain 'F' and (resid 115 through 143 )F115 - 143
41X-RAY DIFFRACTION41chain '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