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- PDB-5a8r: METHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARBURGEN... -

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基本情報

登録情報
データベース: PDB / ID: 5a8r
タイトルMETHYL-COENZYME M REDUCTASE II FROM METHANOTHERMOBACTER MARBURGENSIS AT 2.15 A RESOLUTION
要素
  • (METHYL-COENZYME M REDUCTASE II SUBUNIT ...) x 2
  • METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
キーワードTRANSFERASE / POST-TRANSLATIONAL MODIFICATION / BINDING SITES / CATALYSIS / COENZYMES / DISULFIDES / HYDROGEN / HYDROGEN BONDING / LIGANDS / MESNA / METALLOPORPHYRINS / METHANE / METHANOBACTERIUM / MODELS / MOLECULAR / NICKEL / OXIDATION-REDUCTION / OXIDOREDUCTASES / PHOSPHOTHREONINE / PROTEIN CONFORMATION / PROTEIN FOLDING / PROTEIN STRUCTURE
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 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit ...Methyl-coenzyme M Reductase; Chain B, domain 2 / Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M Reductase; Chain A, domain 1 / Methyl-coenzyme M Reductase; Chain A, domain 1 / Alpha-Beta Plaits - #470 / Methyl-coenzyme M reductase, gamma subunit / Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1 / Methyl-coenzyme M reductase, gamma subunit superfamily / Methyl-coenzyme M reductase gamma subunit / Methyl-coenzyme M reductase, beta subunit / Methyl coenzyme M reductase, alpha subunit / Methyl-coenzyme M reductase, beta subunit, C-terminal / Methyl-coenzyme M reductase, beta subunit, N-terminal / 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
1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B / Methyl-coenzyme M reductase II subunit beta / Methyl-coenzyme M reductase II subunit alpha / Methyl-coenzyme M reductase II subunit gamma
類似検索 - 構成要素
生物種METHANOTHERMOBACTER MARBURGENSIS (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.15 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16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年8月10日Provider: repository / タイプ: Initial release
改定 1.12016年9月28日Group: Database references
改定 1.22017年3月29日Group: Non-polymer description
改定 2.02019年4月24日Group: Data collection / Derived calculations / Polymer sequence
カテゴリ: entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
改定 2.12019年5月15日Group: Data collection / Experimental preparation / カテゴリ: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
改定 2.22024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_conn_type / 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.ptnr1_symmetry / _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.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.ptnr3_symmetry / _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_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

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集合体

登録構造単位
A: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
B: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
C: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
D: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
E: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
F: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
G: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
H: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
I: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
J: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
K: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
L: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)559,56531
ポリマ－553,72312
非ポリマー5,84219
水32,7871820
1
A: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
B: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
C: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
D: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
E: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
F: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)279,76315
ポリマ－276,8616
非ポリマー2,9029
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area57460 Å2
ΔGint-297.9 kcal/mol
Surface area60850 Å2
手法PISA
2
G: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
H: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
I: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
J: METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA
K: METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA
L: METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)279,80216
ポリマ－276,8616
非ポリマー2,94110
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56790 Å2
ΔGint-286.1 kcal/mol
Surface area60840 Å2
手法PISA
単位格子
Length a, b, c (Å)216.660, 246.610, 103.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDモデル要素
11L-2007-

HOH

非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(0.98908, -0.12913, -0.07098), (-0.12907, -0.99162, 0.00546), (-0.07109, 0.00376, -0.99746)5.77749, 92.80326, -6.43632
2given(0.03692, 0.11514, -0.99266), (0.04851, 0.99196, 0.11687), (0.99814, -0.05247, 0.03104)-59.89064, -57.84676, 49.63807
3given(0.09358, -0.12344, 0.98793), (-0.08697, -0.9895, -0.1154), (0.99181, -0.07512, -0.10334)-42.36803, 33.87555, 50.24358
4given(0.98865, -0.13177, -0.0722), (-0.13182, -0.99127, 0.00404), (-0.07211, 0.00552, -0.99738)5.9371, 92.58008, -6.53967
5given(0.03808, 0.11327, -0.99283), (0.05256, 0.99195, 0.11518), (0.99789, -0.05657, 0.03182)-59.69933, -57.55694, 49.74099
6given(0.09284, -0.12411, 0.98791), (-0.08996, -0.98919, -0.11582), (0.99161, -0.07812, -0.10301)-42.43921, 33.63229, 50.31127
7given(0.98885, -0.13152, -0.06977), (-0.1317, -0.99129, 0.00209), (-0.06944, 0.00712, -0.99756)5.83942, 92.61015, -6.42697
8given(0.03971, 0.11506, -0.99256), (0.05062, 0.99184, 0.117), (0.99793, -0.05489, 0.03357)-59.67875, -57.65757, 49.64801
9given(0.08979, -0.12901, 0.98757), (-0.08971, -0.98859, -0.12099), (0.99191, -0.07773, -0.10034)-42.40379, 33.75019, 50.28413

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要素

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METHYL-COENZYME M REDUCTASE II SUBUNIT ... , 2種, 8分子 ADGJBEHK

#1: タンパク質
METHYL-COENZYME M REDUCTASE II SUBUNIT ALPHA / MCR II ALPHA / METHYL-COENZYME M REDUCTASE II


分子量: 60811.102 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM)
由来: (天然) METHANOTHERMOBACTER MARBURGENSIS (古細菌)
株: MARBURG
参照: UniProt: P58815, coenzyme-B sulfoethylthiotransferase
#2: タンパク質
METHYL-COENZYME M REDUCTASE II SUBUNIT GAMMA / MCR II GAMMA / METHYL-COENZYME M REDUCTASE II


分子量: 47039.332 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM)
由来: (天然) METHANOTHERMOBACTER MARBURGENSIS (古細菌)
株: MARBURG
参照: UniProt: D9PXZ6, coenzyme-B sulfoethylthiotransferase

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タンパク質 , 1種, 4分子 CFIL

#3: タンパク質
METHYL-COENZYME M REDUCTASE II, SUBUNIT BETA / METHYL-COENZYME M REDUCTASE II


分子量: 30580.283 Da / 分子数: 4 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM)
由来: (天然) METHANOTHERMOBACTER MARBURGENSIS (古細菌)
株: MARBURG
参照: UniProt: P58816, coenzyme-B sulfoethylthiotransferase

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非ポリマー , 5種, 1839分子

#4: 化合物
ChemComp-COM / 1-THIOETHANESULFONIC ACID


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


分子量: 343.334 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C11H22NO7PS
#6: 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
#7: 化合物
ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 7 / 由来タイプ: 合成 / 式: K
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1820 / 由来タイプ: 天然 / 式: H2O

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詳細

非ポリマーの詳細DIDEHYDROASPARTATE (DYA): DIDEHYDROASPARTATE IS AN ASPARTATE CONTAINING A DOUBLE BOND BETWEEN THE C ...DIDEHYDROASPARTATE (DYA): DIDEHYDROASPARTATE IS AN ASPARTATE CONTAINING A DOUBLE BOND BETWEEN THE C ALPHA AND C BETA
配列の詳細RESIDUE 402 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 447 IS A THIOGLYCINE. RESIDUE 452 IS A ...RESIDUE 402 IS A C2-(S)-METHYLGLUTAMINE. RESIDUE 447 IS A THIOGLYCINE. RESIDUE 452 IS A DIDEHYDROASPARTATE. RESIDUE 454 IS A S-METHYLCYSTEINE

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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: 2.5 Å3/Da / 溶媒含有率: 50.92 % / 解説: NONE
結晶化温度: 281 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7
詳細: 160 MM POTASSIUM ACETATE, 40% (V/V) PENTAERYTHRITOL PROPOXYLATE 426 (5/4 PO/OH), 100 MM TRIS PH 8.0, AND 3% (W/V) TRIMETHYLAMINE N-OXIDE DEHYDRATE AT 8 DEGREE CELSIUS

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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: SLS / ビームライン: X10SA / 波長: 1.00005
検出器タイプ: DECTRIS PILATUS / 検出器: PIXEL / 日付: 2013年11月30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: 2.15→69.31 Å / Num. obs: 300218 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / 冗長度: 4.2 % / Biso Wilson estimate: 24.86 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.7
反射 シェル解像度: 2.15→2.27 Å / 冗長度: 4.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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
MOSFLMデータ削減
SCALAデータスケーリング
MOLREP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: 2.15→55.361 Å / SU ML: 0.2 / σ(F): 1.33 / 位相誤差: 18.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1963 15159 5.1 %
Rwork0.1562 --
obs0.1582 300017 99.89 %
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: 2.15→55.361 Å
タンパク質核酸リガンド溶媒全体
原子数38608 0 367 1820 40795
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00639752
X-RAY DIFFRACTIONf_angle_d1.0853945
X-RAY DIFFRACTIONf_dihedral_angle_d13.26514685
X-RAY DIFFRACTIONf_chiral_restr0.0435925
X-RAY DIFFRACTIONf_plane_restr0.0057135
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17440.28724980.23389438X-RAY DIFFRACTION100
2.1744-2.20.2885020.23049407X-RAY DIFFRACTION100
2.2-2.22680.27755100.22299400X-RAY DIFFRACTION100
2.2268-2.2550.27714860.21969489X-RAY DIFFRACTION100
2.255-2.28470.2734980.21319407X-RAY DIFFRACTION100
2.2847-2.3160.25784950.20049411X-RAY DIFFRACTION100
2.316-2.34910.24724890.19619474X-RAY DIFFRACTION100
2.3491-2.38420.23935060.18989372X-RAY DIFFRACTION100
2.3842-2.42140.24755250.19059407X-RAY DIFFRACTION100
2.4214-2.46110.23985140.18829417X-RAY DIFFRACTION99
2.4611-2.50360.24394980.18149403X-RAY DIFFRACTION100
2.5036-2.54910.22645160.17139357X-RAY DIFFRACTION99
2.5491-2.59810.22115050.16829462X-RAY DIFFRACTION100
2.5981-2.65110.22694990.17049467X-RAY DIFFRACTION100
2.6511-2.70880.20835060.16299451X-RAY DIFFRACTION100
2.7088-2.77180.21645140.16259420X-RAY DIFFRACTION100
2.7718-2.84110.21925290.15949444X-RAY DIFFRACTION100
2.8411-2.91790.20645050.15789492X-RAY DIFFRACTION100
2.9179-3.00380.20184810.15899489X-RAY DIFFRACTION100
3.0038-3.10070.21084740.16159499X-RAY DIFFRACTION100
3.1007-3.21150.20255070.16119499X-RAY DIFFRACTION100
3.2115-3.34010.20344770.15799548X-RAY DIFFRACTION100
3.3401-3.49210.17885150.14849476X-RAY DIFFRACTION100
3.4921-3.67620.16515130.13479536X-RAY DIFFRACTION100
3.6762-3.90640.16375340.12739512X-RAY DIFFRACTION100
3.9064-4.2080.14935230.11669558X-RAY DIFFRACTION100
4.208-4.63120.13954950.11479607X-RAY DIFFRACTION100
4.6312-5.30090.14535280.12339640X-RAY DIFFRACTION100
5.3009-6.67680.17455140.15279723X-RAY DIFFRACTION100
6.6768-55.37950.16425030.142710053X-RAY DIFFRACTION100
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)
10.42530.08440.01520.5843-0.21320.0838-0.0697-0.1394-0.0430.19170.04420.1850.0129-0.2841-0.00280.2521-0.05770.12250.273-0.00610.2423-107.048439.94628.6728
20.39960.29490.01170.7922-0.18030.298-0.0494-0.032-0.00740.141-0.00480.16270.0614-0.2199-0.01510.1283-0.03820.08890.1456-0.03530.1487-102.619544.393415.7685
30.87440.1913-0.04541.10490.00560.6298-0.00690.02390.217-0.02140.00120.104-0.27110.01130.02110.1983-0.0138-0.00960.0968-0.0120.1427-87.091181.3767-4.2079
40.21430.07440.05170.1918-0.03490.451-0.03080.00380.07810.12030.00030.072-0.0922-0.03910.02850.12410.00430.02140.06-0.03060.0887-89.094167.36156.1478
50.1730.05640.04870.09930.16690.29030.0134-0.07250.01770.1303-0.01890.0255-0.02530.0018-0.12470.39970.0120.03850.1444-0.05150.0314-82.879857.487439.6585
60.0993-0.02020.04230.2702-0.04250.2163-0.0186-0.06260.0220.2013-0.0054-0.01840.00990.03430.00320.23510.01230.01180.1069-0.02140.0737-79.982353.511225.9584
70.31890.12730.18520.1474-0.08450.7254-0.06370.01060.11630.10240.05120.199-0.1009-0.21150.00150.12650.01350.07960.1552-0.00910.1916-103.635360.337510.158
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 51 THROUGH 105 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 106 THROUGH 142 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 143 THROUGH 343 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 344 THROUGH 389 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 390 THROUGH 515 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 516 THROUGH 551 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 2 THROUGH 48 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 49 THROUGH 78 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 79 THROUGH 115 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 116 THROUGH 146 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 147 THROUGH 184 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 185 THROUGH 246 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 247 THROUGH 277 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 278 THROUGH 407 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 408 THROUGH 443 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 3 THROUGH 43 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 44 THROUGH 58 )
19X-RAY DIFFRACTION19CHAIN C AND (RESID 59 THROUGH 80 )
20X-RAY DIFFRACTION20CHAIN C AND (RESID 81 THROUGH 181 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 182 THROUGH 216 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 217 THROUGH 249 )
23X-RAY DIFFRACTION23CHAIN C AND (RESID 250 THROUGH 264 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 4 THROUGH 50 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 51 THROUGH 105 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 106 THROUGH 142 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 143 THROUGH 515 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 516 THROUGH 551 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 2 THROUGH 58 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 59 THROUGH 126 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 127 THROUGH 184 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 185 THROUGH 246 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 247 THROUGH 277 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 278 THROUGH 407 )
35X-RAY DIFFRACTION35CHAIN E AND (RESID 408 THROUGH 443 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 3 THROUGH 58 )
37X-RAY DIFFRACTION37CHAIN F AND (RESID 59 THROUGH 80 )
38X-RAY DIFFRACTION38CHAIN F AND (RESID 81 THROUGH 181 )
39X-RAY DIFFRACTION39CHAIN F AND (RESID 182 THROUGH 201 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 202 THROUGH 216 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 217 THROUGH 230 )
42X-RAY DIFFRACTION42CHAIN F AND (RESID 231 THROUGH 263 )
43X-RAY DIFFRACTION43CHAIN G AND (RESID 4 THROUGH 50 )
44X-RAY DIFFRACTION44CHAIN G AND (RESID 51 THROUGH 105 )
45X-RAY DIFFRACTION45CHAIN G AND (RESID 106 THROUGH 142 )
46X-RAY DIFFRACTION46CHAIN G AND (RESID 143 THROUGH 203 )
47X-RAY DIFFRACTION47CHAIN G AND (RESID 204 THROUGH 343 )
48X-RAY DIFFRACTION48CHAIN G AND (RESID 344 THROUGH 389 )
49X-RAY DIFFRACTION49CHAIN G AND (RESID 390 THROUGH 515 )
50X-RAY DIFFRACTION50CHAIN G AND (RESID 516 THROUGH 551 )
51X-RAY DIFFRACTION51CHAIN H AND (RESID 2 THROUGH 32 )
52X-RAY DIFFRACTION52CHAIN H AND (RESID 33 THROUGH 59 )
53X-RAY DIFFRACTION53CHAIN H AND (RESID 60 THROUGH 126 )
54X-RAY DIFFRACTION54CHAIN H AND (RESID 127 THROUGH 161 )
55X-RAY DIFFRACTION55CHAIN H AND (RESID 162 THROUGH 184 )
56X-RAY DIFFRACTION56CHAIN H AND (RESID 185 THROUGH 243 )
57X-RAY DIFFRACTION57CHAIN H AND (RESID 244 THROUGH 277 )
58X-RAY DIFFRACTION58CHAIN H AND (RESID 278 THROUGH 407 )
59X-RAY DIFFRACTION59CHAIN H AND (RESID 408 THROUGH 443 )
60X-RAY DIFFRACTION60CHAIN I AND (RESID 2 THROUGH 43 )
61X-RAY DIFFRACTION61CHAIN I AND (RESID 44 THROUGH 58 )
62X-RAY DIFFRACTION62CHAIN I AND (RESID 59 THROUGH 80 )
63X-RAY DIFFRACTION63CHAIN I AND (RESID 81 THROUGH 181 )
64X-RAY DIFFRACTION64CHAIN I AND (RESID 182 THROUGH 216 )
65X-RAY DIFFRACTION65CHAIN I AND (RESID 217 THROUGH 230 )
66X-RAY DIFFRACTION66CHAIN I AND (RESID 231 THROUGH 249 )
67X-RAY DIFFRACTION67CHAIN I AND (RESID 250 THROUGH 263 )
68X-RAY DIFFRACTION68CHAIN J AND (RESID 4 THROUGH 50 )
69X-RAY DIFFRACTION69CHAIN J AND (RESID 51 THROUGH 105 )
70X-RAY DIFFRACTION70CHAIN J AND (RESID 106 THROUGH 142 )
71X-RAY DIFFRACTION71CHAIN J AND (RESID 143 THROUGH 203 )
72X-RAY DIFFRACTION72CHAIN J AND (RESID 204 THROUGH 343 )
73X-RAY DIFFRACTION73CHAIN J AND (RESID 344 THROUGH 389 )
74X-RAY DIFFRACTION74CHAIN J AND (RESID 390 THROUGH 515 )
75X-RAY DIFFRACTION75CHAIN J AND (RESID 516 THROUGH 551 )
76X-RAY DIFFRACTION76CHAIN K AND (RESID 2 THROUGH 48 )
77X-RAY DIFFRACTION77CHAIN K AND (RESID 49 THROUGH 101 )
78X-RAY DIFFRACTION78CHAIN K AND (RESID 102 THROUGH 161 )
79X-RAY DIFFRACTION79CHAIN K AND (RESID 162 THROUGH 184 )
80X-RAY DIFFRACTION80CHAIN K AND (RESID 185 THROUGH 246 )
81X-RAY DIFFRACTION81CHAIN K AND (RESID 247 THROUGH 277 )
82X-RAY DIFFRACTION82CHAIN K AND (RESID 278 THROUGH 407 )
83X-RAY DIFFRACTION83CHAIN K AND (RESID 408 THROUGH 443 )
84X-RAY DIFFRACTION84CHAIN L AND (RESID 2 THROUGH 22 )
85X-RAY DIFFRACTION85CHAIN L AND (RESID 23 THROUGH 35 )
86X-RAY DIFFRACTION86CHAIN L AND (RESID 36 THROUGH 53 )
87X-RAY DIFFRACTION87CHAIN L AND (RESID 54 THROUGH 80 )
88X-RAY DIFFRACTION88CHAIN L AND (RESID 81 THROUGH 181 )
89X-RAY DIFFRACTION89CHAIN L AND (RESID 182 THROUGH 199 )
90X-RAY DIFFRACTION90CHAIN L AND (RESID 200 THROUGH 216 )
91X-RAY DIFFRACTION91CHAIN L AND (RESID 217 THROUGH 230 )
92X-RAY DIFFRACTION92CHAIN L AND (RESID 231 THROUGH 249 )
93X-RAY DIFFRACTION93CHAIN L AND (RESID 250 THROUGH 264 )

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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