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- PDB-5a8w: METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER WOLFEII A... -

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基本情報

登録情報
データベース: PDB / ID: 5a8w
タイトルMETHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER WOLFEII AT 1. 8 A RESOLUTION
要素
  • (METHYL-COENZYME M REDUCTASE ...) x 2
  • METHYL-COENZYME M II REDUCTASE
キーワードTRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / COENZYMES / DISULFIDES / MESNA / METALLOPORPHYRINS / METHANE / METHANOBACTERIUM / NICKEL / OXIDATION-REDUCTION / PHOSPHOTHREONINE
機能・相同性
機能・相同性情報


coenzyme-B sulfoethylthiotransferase / coenzyme-B sulfoethylthiotransferase activity / methanogenesis / metal ion binding
類似検索 - 分子機能
Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal ...Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase beta subunit, C-terminal domain / Methyl-coenzyme M reductase beta subunit, N-terminal domain / Methyl-coenzyme M reductase, alpha subunit, N-terminal / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, ferredoxin-like fold / Methyl-coenzyme M reductase, alpha subunit, C-terminal / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2 / Methyl-coenzyme M reductase alpha subunit, C-terminal domain / Methyl-coenzyme M reductase alpha subunit, N-terminal domain / Lambda Exonuclease; Chain A / Alpha-Beta Plaits / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
ACETATE ION / 1-THIOETHANESULFONIC ACID / FACTOR 430 / Coenzyme B / Methyl-coenzyme M reductase subunit beta / Methyl-coenzyme M reductase subunit gamma / Coenzyme-B sulfoethylthiotransferase
類似検索 - 構成要素
生物種METHANOTHERMOBACTER WOLFEII (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å
データ登録者Wagner, T. / Ermler, U.
引用ジャーナル: Angew.Chem.Int.Ed.Engl. / 年: 2016
タイトル: Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation.
著者: Wagner, T. / Kahnt, J. / Ermler, U. / Shima, S.
履歴
登録2015年7月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年8月3日Provider: repository / タイプ: Initial release
改定 1.12016年8月10日Group: Database references
改定 1.22016年9月28日Group: Database references
改定 1.32017年3月29日Group: Non-polymer description
改定 1.42024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: METHYL-COENZYME M II REDUCTASE
B: METHYL-COENZYME M REDUCTASE II
C: METHYL-COENZYME M REDUCTASE II
D: METHYL-COENZYME M II REDUCTASE
E: METHYL-COENZYME M REDUCTASE II
F: METHYL-COENZYME M REDUCTASE II
G: METHYL-COENZYME M II REDUCTASE
H: METHYL-COENZYME M REDUCTASE II
I: METHYL-COENZYME M REDUCTASE II
J: METHYL-COENZYME M II REDUCTASE
K: METHYL-COENZYME M REDUCTASE II
L: METHYL-COENZYME M REDUCTASE II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)561,29036
ポリマ－555,04912
非ポリマー6,24124
水52,5142915
1
A: METHYL-COENZYME M II REDUCTASE
B: METHYL-COENZYME M REDUCTASE II
C: METHYL-COENZYME M REDUCTASE II
D: METHYL-COENZYME M II REDUCTASE
E: METHYL-COENZYME M REDUCTASE II
F: METHYL-COENZYME M REDUCTASE II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)280,62718
ポリマ－277,5246
非ポリマー3,10212
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area57310 Å2
ΔGint-292.3 kcal/mol
Surface area61030 Å2
手法PISA
2
G: METHYL-COENZYME M II REDUCTASE
H: METHYL-COENZYME M REDUCTASE II
I: METHYL-COENZYME M REDUCTASE II
J: METHYL-COENZYME M II REDUCTASE
K: METHYL-COENZYME M REDUCTASE II
L: METHYL-COENZYME M REDUCTASE II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)280,66318
ポリマ－277,5246
非ポリマー3,13812
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area57400 Å2
ΔGint-282.2 kcal/mol
Surface area61030 Å2
手法PISA
単位格子
Length a, b, c (Å)110.391, 102.185, 118.739
Angle α, β, γ (deg.)89.20, 93.97, 90.98
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
22
/ NCSアンサンブル:
ID
1
2

NCS oper:
IDCodeMatrixベクター
1given(0.14615, 0.01886, -0.98908), (0.01878, -0.99969, -0.01628), (-0.98908, -0.0162, -0.14646)54.70775, -135.41515, 60.85105
2given(-0.99939, -0.0349, -0.00093), (-0.0349, 0.99939, 0.00273), (0.00084, 0.00276, -1)114.36598, 51.2539, -1.29854
3given(-0.14633, 0.0154, 0.98912), (0.0118, -0.99978, 0.01731), (0.98917, 0.01421, 0.14612)64.33155, -85.84843, -62.41743
4given(0.14582, 0.01873, -0.98913), (0.0188, -0.99969, -0.01616), (-0.98913, -0.01624, -0.14613)54.74264, -135.39137, 60.82265
5given(-0.99942, -0.03406, -0.00093), (-0.03406, 0.99942, 0.0022), (0.00086, 0.00223, -1)114.43179, 51.22232, -1.34264
6given(-0.14668, 0.01531, 0.98907), (0.01185, -0.99978, 0.01723), (0.98911, 0.01424, 0.14647)64.31837, -85.86157, -62.44341
7given(0.14698, 0.01575, -0.98901), (0.01796, -0.99975, -0.01325), (-0.98898, -0.01581, -0.14723)54.38477, -135.49632, 60.88938
8given(-0.99944, -0.03324, -0.00279), (-0.03324, 0.99945, 0.00028), (0.00278, 0.00037, -1)114.60445, 51.29135, -1.6152
9given(-0.14793, 0.01724, 0.98885), (0.01217, -0.99974, 0.01925), (0.98892, 0.01489, 0.14768)64.59094, -85.96172, -62.42006

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要素

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タンパク質 , 1種, 4分子 ADGJ

#1: タンパク質
METHYL-COENZYME M II REDUCTASE


分子量: 60929.172 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 由来: (天然) METHANOTHERMOBACTER WOLFEII (古細菌)
参照: UniProt: H7CHY2*PLUS, coenzyme-B sulfoethylthiotransferase

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METHYL-COENZYME M REDUCTASE ... , 2種, 8分子 BEHKCFIL

#2: タンパク質
METHYL-COENZYME M REDUCTASE II


分子量: 47144.555 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 由来: (天然) METHANOTHERMOBACTER WOLFEII (古細菌)
参照: UniProt: A0A1C7D1E4*PLUS, coenzyme-B sulfoethylthiotransferase
#3: タンパク質
METHYL-COENZYME M REDUCTASE II


分子量: 30688.428 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 由来: (天然) METHANOTHERMOBACTER WOLFEII (古細菌)
参照: UniProt: A0A1C7D1E5*PLUS, coenzyme-B sulfoethylthiotransferase

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非ポリマー , 6種, 2939分子

#4: 化合物
ChemComp-COM / 1-THIOETHANESULFONIC ACID / 2-メルカプトエタンスルホン酸


分子量: 142.197 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O3S2
#5: 化合物
ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE / N-(7-メルカプトヘプタノイル)-O-ホスホノ-L-トレオニン


分子量: 343.334 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C11H22NO7PS
#6: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C2H3O2
#7: 化合物
ChemComp-F43 / FACTOR 430


分子量: 906.580 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C42H51N6NiO13
#8: 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
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2915 / 由来タイプ: 天然 / 式: H2O

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詳細

配列の詳細METHANOTHERMOBACTER WOLFEII GENOME SEQUENCING IS ACTUALLY IN PROGRESS AND WILL BE RELEASED SOON. ...METHANOTHERMOBACTER WOLFEII GENOME SEQUENCING IS ACTUALLY IN PROGRESS AND WILL BE RELEASED SOON. THE SEQUENCE OF THIS STRUCTURE HAS BEEN CONFIRMED BY THE EARLY SEQUENCED INFORMATION

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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: 2.4 Å3/Da / 溶媒含有率: 49.01 % / 解説: NONE
結晶化pH: 7
詳細: 13% (W/V) PEG 4000, 100 MM SODIUM ACETATE PH 4.1, AND 200 MM AMMONIUM ACETATE AT ROOM TEMPERATURE. THICK SQUARE-SHAPED CRYSTALS WERE IMMERSED IN A SOLUTION CONTAINING 30% (V/V) ETHYLENE ...詳細: 13% (W/V) PEG 4000, 100 MM SODIUM ACETATE PH 4.1, AND 200 MM AMMONIUM ACETATE AT ROOM TEMPERATURE. THICK SQUARE-SHAPED CRYSTALS WERE IMMERSED IN A SOLUTION CONTAINING 30% (V/V) ETHYLENE GLYCOL, 14% (W/V) PEG 4000, 100 MM SODIUM ACETATE PH 4.1, AND 200 MM AMMONIUM ACETATE AS A CRYOPROTECTANT

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データ収集

回折平均測定温度: 77 K
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.97857
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年12月11日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97857 Å / 相対比: 1
反射解像度: 1.8→48.8 Å / Num. obs: 464655 / % possible obs: 96.9 % / Observed criterion σ(I): 2.1 / 冗長度: 2.7 % / Biso Wilson estimate: 14.76 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.5
反射 シェル解像度: 1.8→1.9 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
SCALAデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3POT

3pot


解像度: 1.8→48.658 Å / SU ML: 0.2 / σ(F): 1.96 / 位相誤差: 20.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2007 23252 5 %
Rwork0.1653 --
obs0.1671 464550 96.84 %
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
精密化ステップサイクル: LAST / 解像度: 1.8→48.658 Å
タンパク質核酸リガンド溶媒全体
原子数38697 0 405 2915 42017
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01640246
X-RAY DIFFRACTIONf_angle_d1.52954690
X-RAY DIFFRACTIONf_dihedral_angle_d16.58824265
X-RAY DIFFRACTIONf_chiral_restr0.0856031
X-RAY DIFFRACTIONf_plane_restr0.017246
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.31437600.282114398X-RAY DIFFRACTION95
1.8205-1.84190.30377800.263314393X-RAY DIFFRACTION95
1.8419-1.86430.287470.238314477X-RAY DIFFRACTION95
1.8643-1.88790.26217690.223514476X-RAY DIFFRACTION95
1.8879-1.91280.26697940.224514460X-RAY DIFFRACTION96
1.9128-1.9390.27757280.218114676X-RAY DIFFRACTION96
1.939-1.96670.25788240.212714616X-RAY DIFFRACTION96
1.9667-1.9960.24628010.198114500X-RAY DIFFRACTION96
1.996-2.02720.23177560.188514594X-RAY DIFFRACTION96
2.0272-2.06050.23957350.184514716X-RAY DIFFRACTION96
2.0605-2.0960.23587830.174514666X-RAY DIFFRACTION97
2.096-2.13410.21178320.167914648X-RAY DIFFRACTION97
2.1341-2.17520.21197670.166714741X-RAY DIFFRACTION97
2.1752-2.21960.21767820.167114689X-RAY DIFFRACTION97
2.2196-2.26780.21297290.161414734X-RAY DIFFRACTION97
2.2678-2.32060.20197840.16214775X-RAY DIFFRACTION97
2.3206-2.37860.20547900.157914715X-RAY DIFFRACTION97
2.3786-2.44290.19347480.154914784X-RAY DIFFRACTION97
2.4429-2.51480.19857370.15514861X-RAY DIFFRACTION97
2.5148-2.5960.19477460.149914815X-RAY DIFFRACTION98
2.596-2.68870.18788030.150714825X-RAY DIFFRACTION98
2.6887-2.79640.18787980.155914792X-RAY DIFFRACTION98
2.7964-2.92360.20188090.160614894X-RAY DIFFRACTION98
2.9236-3.07780.1987940.163914800X-RAY DIFFRACTION98
3.0778-3.27050.18917870.162114806X-RAY DIFFRACTION98
3.2705-3.5230.18738000.161914866X-RAY DIFFRACTION98
3.523-3.87740.16417530.146714842X-RAY DIFFRACTION98
3.8774-4.43810.15118090.129214867X-RAY DIFFRACTION98
4.4381-5.59030.15717330.133714998X-RAY DIFFRACTION98
5.5903-48.67540.16347740.154614874X-RAY DIFFRACTION98
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)
11.2079-0.10460.2771.7405-0.08480.61870.00710.1422-0.0053-0.1519-0.044-0.2430.09420.21460.03990.12480.02970.02480.20740.00550.122368.821-83.247421.6597
20.52880.03340.03271.1895-0.4140.68760.02440.0877-0.0347-0.2011-0.00920.06370.0906-0.0426-0.01980.0940.0081-0.00990.1112-0.00380.070331.9065-76.6761-0.2979
30.3245-0.00270.07670.342-0.03970.44630.02980.0358-0.0387-0.019-0.00310.01690.06370.0285-0.02990.08850.0086-0.00810.0896-0.00160.078841.8715-90.557423.7661
40.7409-0.81430.26781.2229-0.10620.6139-0.0010.08340.0084-0.1031-0.0057-0.12630.11490.14340.01440.15580.03060.01720.196400.110552.4705-78.93085.025
50.42230.2755-0.01851.1571-0.54210.878-0-0.0768-0.01780.18680.02980.11310.0211-0.0848-0.00930.09820.00830.02310.1712-0.01010.091421.4637-72.35456.2526
62.49491.3966-1.16471.7642-0.8782.28390.0632-0.25850.07970.1404-0.0962-0.0254-0.20990.12910.08650.11950.0158-0.05040.11150.01070.088229.2937-42.269143.2907
73.96332.38281.43193.12530.71151.62230.2534-0.50010.03590.3979-0.21820.07040.0378-0.2453-0.02170.17950.0099-0.00480.20820.00020.114719.124-52.013553.1548
81.23220.4937-0.32380.74420.1141.2884-0.0739-0.0470.004-0.01530.0388-0.00950.0201-0.02030.02380.09260.0036-0.01810.12210.00750.072723.8686-51.751738.421
90.77310.1460.17950.66470.16650.60970.00110.00860.0436-0.0453-0.0034-0.039-0.0608-0.0604-0.0050.11750.00610.00560.12070.01380.117727.9344-76.976149.8391
100.8011-0.07090.05660.66710.1180.48380.0237-0.1276-0.11170.1591-0.0020.02660.1169-0.0336-0.01840.1375-0.0118-0.01330.13650.03180.106836.6952-93.578859.9836
110.64630.0385-0.01470.41840.00870.42430.00060.00350.0605-0.01130.0165-0.0099-0.040.0041-0.0190.11280.0022-0.00210.12430.00810.10442.2015-80.190748.2329
125.87684.1134-3.65026.4966-2.73783.7417-0.0054-0.1320.48480.15670.14820.5617-0.078-0.1509-0.18260.10720.052-0.02140.1527-0.00030.11724.2465-68.214359.0604
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147.08764.1728-2.63053.3942-0.28923.33710.3059-0.30610.68270.4025-0.20020.2118-0.498-0.2056-0.10140.21930.0056-0.01630.1798-0.04240.137245.4114-71.440668.4936
150.5331-0.2589-0.44590.62770.29980.7388-0.0166-0.07280.04310.10240.045-0.09940.03650.1213-0.02510.09880.0066-0.03170.12470.01160.107461.0241-85.908452.3871
162.18240.65351.08783.1175-0.19972.54140.02240.0773-0.0050.09990.0173-0.408-0.06770.3120.01810.0770.0163-0.01560.18070.01710.140575.9587-86.26543.2153
176.4994.2221.03477.9074-0.34591.84080.1504-0.175-0.62340.2679-0.1044-0.80910.08910.2098-0.07280.14650.0316-0.04170.17520.02440.138974.1615-96.976450.9151
186.269-2.00110.491.0229-0.12570.19130.09180.2523-0.4536-0.0462-0.05490.13480.10610.0167-0.03240.134-0.009-0.02650.10030.00450.091847.8387-104.343742.6066
197.3064-0.30570.00440.01720.0020.0037-0.0223-0.161-0.83910.042-0.00720.29890.2181-0.15470.04470.1457-0.0347-0.00270.13970.02850.204417.2355-97.241845.5772
200.2091-0.21370.08421.1786-0.2450.83880.04440.11730.0937-0.1532-0.0712-0.247-0.02290.13440.02830.1023-0.00730.03440.18960.03240.144840.5936-51.3692-11.1212
210.5533-0.08310.14660.6706-0.12050.4742-0.0341-0.03460.06840.0964-0.0147-0.1287-0.04980.10520.04220.0811-0.0133-0.01980.12430.01610.129457.0179-57.341927.2895
220.3617-0.03960.09580.3009-0.05840.4584-0.03330.01930.07510.0408-0.0148-0.0492-0.0680.06490.050.0707-0.0146-0.01860.08230.01410.093535.5907-44.374317.333
230.39190.00010.09651.4881-0.85120.7634-0.02250.13010.0814-0.05830.004-0.1967-0.02860.1550.01960.1042-0.0106-0.0030.20860.04530.175155.9369-55.60029.5277
242.98371.04931.60991.62540.6833.1601-0.069-0.2980.1890.0364-0.02870.2495-0.1417-0.34120.12060.10030.020.04520.1907-0.010.1423-5.4344-51.788934.5796
251.8742-2.6188-1.15474.22711.62370.88610.09110.1229-0.1061-0.0717-0.1270.16190.0106-0.10290.01630.0865-0.0051-0.03780.13570.00910.08614.793-85.515525.2324
261.3879-0.13420.16982.4811.01641.5482-0.0192-0.115-0.08260.0867-0.00260.26890.1306-0.18970.03010.0879-0.0192-0.01110.14290.03960.096912.0449-87.162635.0788
273.9293-1.73891.82120.7689-0.80610.843-0.0402-0.13220.16020.13890.07160.10190.0099-0.1305-0.03330.1414-0.0080.02220.14260.00010.127522.3234-77.729826.846
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381.32-0.64290.42550.88250.41540.7670.0305-0.0802-0.00820.0773-0.00140.08290.0991-0.0992-0.02440.1015-0.02630.01410.16820.02070.113651.6851-30.9502-22.6641
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410.61491.01070.22411.73070.24650.46890.0255-0.1128-0.00310.1169-0.00930.11150.0528-0.14250.0010.1487-0.02390.01010.20740.01240.124464.7387-29.4297-6.4731
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490.72970.1828-0.01620.7275-0.1420.4425-0.00520.1224-0.1034-0.14890.0272-0.02480.09470.0246-0.0150.1386-0.0018-0.01310.1458-0.02770.099480.8191-43.5891-61.4117
500.51950.0148-0.04990.56760.08080.3405-0.00270.02530.05570.00710.01610.0145-0.02380.0021-0.02060.1138-0.0044-0.00840.1290.00230.10474.9486-30.236-49.7174
515.7453-4.5384-4.22947.27223.16634.24720.05110.14970.5803-0.28650.1041-0.5948-0.10650.1374-0.1630.1167-0.0633-0.04040.16390.02020.134692.4424-17.5931-60.5178
521.05640.1227-0.04290.85730.0510.20780.0490.2092-0.0399-0.27620.00040.15640.0051-0.0516-0.03870.1636-0.0091-0.04940.1759-0.00450.09456.1557-39.9887-60.2166
536.1555-3.4525-1.82712.05830.49742.74380.2990.53320.7421-0.3645-0.2242-0.1786-0.49250.067-0.08620.23-0.0047-0.01510.18310.0690.171871.4355-21.5788-70.2313
540.68070.124-0.20360.7474-0.2780.63020.00140.09060.0495-0.1420.02870.0990.0241-0.0866-0.03240.1043-0.0112-0.02580.11440.0070.095356.2967-36.5575-53.9205
550.5643-0.37210.4391.0972-0.23381.3244-0.0013-0.0484-0.0718-0.02610.10690.31820.0749-0.2586-0.06590.0865-0.0366-0.02250.16350.0150.120943.4773-40.4119-40.9897
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631.82881.7425-0.94382.7962-1.39330.82750.103-0.1077-0.11350.095-0.1201-0.1143-0.01940.1167-0.01430.10850.0014-0.02850.14-0.00630.0805102.5772-35.0339-26.5492
641.4007-0.11170.28922.7198-1.43361.9839-0.02630.0875-0.0427-0.0782-0.0273-0.25620.10350.16240.06920.08480.0073-0.0160.1359-0.03410.0854105.343-36.2588-36.593
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660.2948-0.0893-0.05580.36960.08120.5427-0.02770.01670.014-0.01010.0125-0.034-0.00570.03960.01660.0961-0.0155-0.01490.12730.00890.1244109.8686-0.6656-19.9005
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680.2701-0.0007-0.1660.66310.28320.9503-0.0377-0.0570.01410.2008-0.0154-0.2169-0.0540.17960.03610.1039-0.0164-0.06120.1573-0.0010.1639112.07454.91215.6455
693.76231.2303-1.91692.6363-3.68755.1616-0.07530.0397-0.5318-0.1792-0.2141-0.4390.57650.47590.34040.14920.0635-0.02160.18590.02970.2171124.5325-12.4409-8.309
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712.36610.21421.711.8919-0.68661.8477-0.1451-0.34950.09680.350.05190.041-0.2163-0.32110.06350.13150.0193-0.00850.1743-0.02920.094191.23014.97115.3081
721.42731.5313-0.15774.321-1.83294.72010.0846-0.25620.04070.7322-0.1494-0.2007-0.17440.17920.05120.07590.0225-0.02380.1873-0.03210.1197100.66975.422519.0899
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747.7527-0.9512-2.52397.9775.26829.52010.20190.60310.6339-0.6286-0.1068-0.1594-1.1312-0.0261-0.11960.1892-0.0243-0.0320.13090.06790.179105.550211.9926-40.3945
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 5 THROUGH 95 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 96 THROUGH 242 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 243 THROUGH 516 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 517 THROUGH 552 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 2 THROUGH 58 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 59 THROUGH 93 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 94 THROUGH 115 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 116 THROUGH 184 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 185 THROUGH 244 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 245 THROUGH 321 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 322 THROUGH 407 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 408 THROUGH 443 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 2 THROUGH 58 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 59 THROUGH 80 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 81 THROUGH 158 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 159 THROUGH 199 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 200 THROUGH 216 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 217 THROUGH 249 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 250 THROUGH 264 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 4 THROUGH 77 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 78 THROUGH 242 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 243 THROUGH 516 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 517 THROUGH 552 )
24X-RAY DIFFRACTION24CHAIN E AND (RESID 2 THROUGH 32 )
25X-RAY DIFFRACTION25CHAIN E AND (RESID 33 THROUGH 78 )
26X-RAY DIFFRACTION26CHAIN E AND (RESID 79 THROUGH 161 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 162 THROUGH 184 )
28X-RAY DIFFRACTION28CHAIN E AND (RESID 185 THROUGH 407 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 408 THROUGH 443 )
30X-RAY DIFFRACTION30CHAIN F AND (RESID 2 THROUGH 58 )
31X-RAY DIFFRACTION31CHAIN F AND (RESID 59 THROUGH 80 )
32X-RAY DIFFRACTION32CHAIN F AND (RESID 81 THROUGH 180 )
33X-RAY DIFFRACTION33CHAIN F AND (RESID 181 THROUGH 194 )
34X-RAY DIFFRACTION34CHAIN F AND (RESID 195 THROUGH 216 )
35X-RAY DIFFRACTION35CHAIN F AND (RESID 217 THROUGH 249 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 250 THROUGH 264 )
37X-RAY DIFFRACTION37CHAIN G AND (RESID 5 THROUGH 54 )
38X-RAY DIFFRACTION38CHAIN G AND (RESID 55 THROUGH 95 )
39X-RAY DIFFRACTION39CHAIN G AND (RESID 96 THROUGH 242 )
40X-RAY DIFFRACTION40CHAIN G AND (RESID 243 THROUGH 516 )
41X-RAY DIFFRACTION41CHAIN G AND (RESID 517 THROUGH 552 )
42X-RAY DIFFRACTION42CHAIN H AND (RESID 2 THROUGH 32 )
43X-RAY DIFFRACTION43CHAIN H AND (RESID 33 THROUGH 58 )
44X-RAY DIFFRACTION44CHAIN H AND (RESID 59 THROUGH 93 )
45X-RAY DIFFRACTION45CHAIN H AND (RESID 94 THROUGH 115 )
46X-RAY DIFFRACTION46CHAIN H AND (RESID 116 THROUGH 146 )
47X-RAY DIFFRACTION47CHAIN H AND (RESID 147 THROUGH 184 )
48X-RAY DIFFRACTION48CHAIN H AND (RESID 185 THROUGH 244 )
49X-RAY DIFFRACTION49CHAIN H AND (RESID 245 THROUGH 321 )
50X-RAY DIFFRACTION50CHAIN H AND (RESID 322 THROUGH 407 )
51X-RAY DIFFRACTION51CHAIN H AND (RESID 408 THROUGH 443 )
52X-RAY DIFFRACTION52CHAIN I AND (RESID 2 THROUGH 58 )
53X-RAY DIFFRACTION53CHAIN I AND (RESID 59 THROUGH 80 )
54X-RAY DIFFRACTION54CHAIN I AND (RESID 81 THROUGH 158 )
55X-RAY DIFFRACTION55CHAIN I AND (RESID 159 THROUGH 181 )
56X-RAY DIFFRACTION56CHAIN I AND (RESID 182 THROUGH 216 )
57X-RAY DIFFRACTION57CHAIN I AND (RESID 217 THROUGH 264 )
58X-RAY DIFFRACTION58CHAIN J AND (RESID 5 THROUGH 54 )
59X-RAY DIFFRACTION59CHAIN J AND (RESID 55 THROUGH 95 )
60X-RAY DIFFRACTION60CHAIN J AND (RESID 96 THROUGH 242 )
61X-RAY DIFFRACTION61CHAIN J AND (RESID 243 THROUGH 552 )
62X-RAY DIFFRACTION62CHAIN K AND (RESID 2 THROUGH 32 )
63X-RAY DIFFRACTION63CHAIN K AND (RESID 33 THROUGH 78 )
64X-RAY DIFFRACTION64CHAIN K AND (RESID 79 THROUGH 161 )
65X-RAY DIFFRACTION65CHAIN K AND (RESID 162 THROUGH 184 )
66X-RAY DIFFRACTION66CHAIN K AND (RESID 185 THROUGH 407 )
67X-RAY DIFFRACTION67CHAIN K AND (RESID 408 THROUGH 443 )
68X-RAY DIFFRACTION68CHAIN L AND (RESID 2 THROUGH 58 )
69X-RAY DIFFRACTION69CHAIN L AND (RESID 59 THROUGH 80 )
70X-RAY DIFFRACTION70CHAIN L AND (RESID 81 THROUGH 158 )
71X-RAY DIFFRACTION71CHAIN L AND (RESID 159 THROUGH 181 )
72X-RAY DIFFRACTION72CHAIN L AND (RESID 182 THROUGH 216 )
73X-RAY DIFFRACTION73CHAIN L AND (RESID 217 THROUGH 249 )
74X-RAY DIFFRACTION74CHAIN L AND (RESID 250 THROUGH 264 )

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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