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- PDB-6s81: Crystal structure of methionine adenosyltransferase from Pyrococc... -

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基本情報

登録情報
データベース: PDB / ID: 6s81
タイトルCrystal structure of methionine adenosyltransferase from Pyrococcus furiosus
要素S-adenosylmethionine synthase
キーワードTRANSFERASE / S-adenosyl methionine synthesis / cofactor biosynthesis / cytoplasmic
機能・相同性
機能・相同性情報


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding
類似検索 - 分子機能
S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, archaea / S-adenosylmethionine synthase / S-adenosylmethionine synthetase, domain 3 / S-adenosylmethionine synthetase (AdoMet synthetase) / GMP Synthetase; Chain A, domain 3 - #10 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
: / S-adenosylmethionine synthase
類似検索 - 構成要素
生物種Pyrococcus furiosus (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.784 Å
データ登録者Degano, M. / Minici, C. / Porcelli, M.
資金援助 イタリア, 1件
組織認可番号国
Italian Association for Cancer Research イタリア
引用ジャーナル: J.Struct.Biol. / 年: 2020
タイトル: Structures of catalytic cycle intermediates of the Pyrococcus furiosus methionine adenosyltransferase demonstrate negative cooperativity in the archaeal orthologues.
著者: Minici, C. / Mosca, L. / Ilisso, C.P. / Cacciapuoti, G. / Porcelli, M. / Degano, M.
履歴
登録2019年7月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年2月5日Provider: repository / タイプ: Initial release
改定 1.12020年3月18日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
改定 1.22024年1月24日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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.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

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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: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)178,10714
ポリマ－177,3554
非ポリマー75210
水15,997888
1
A: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,0898
ポリマ－88,6772
非ポリマー4116
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-56 kcal/mol
Surface area30190 Å2
手法PISA
2
B: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)89,0186
ポリマ－88,6772
非ポリマー3414
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-29 kcal/mol
Surface area30230 Å2
手法PISA
単位格子
Length a, b, c (Å)61.108, 133.900, 213.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 16 or resid 18...
21(chain B and (resid 2 through 16 or resid 18...
31(chain C and (resid 2 through 16 or resid 18...
41(chain D and (resid 2 through 16 or resid 18...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 2 through 16 or resid 18...A2 - 16
121(chain A and (resid 2 through 16 or resid 18...A18 - 109
131(chain A and (resid 2 through 16 or resid 18...A111 - 119
141(chain A and (resid 2 through 16 or resid 18...A121 - 133
151(chain A and (resid 2 through 16 or resid 18...A135 - 136
161(chain A and (resid 2 through 16 or resid 18...A138 - 157
171(chain A and (resid 2 through 16 or resid 18...A159 - 186
181(chain A and (resid 2 through 16 or resid 18...A188 - 2232
191(chain A and (resid 2 through 16 or resid 18...A234232
1101(chain A and (resid 2 through 16 or resid 18...A234 - 248
1111(chain A and (resid 2 through 16 or resid 18...A250 - 274
1121(chain A and (resid 2 through 16 or resid 18...A276 - 289
1131(chain A and (resid 2 through 16 or resid 18...A291 - 319
1141(chain A and (resid 2 through 16 or resid 18...A321 - 327
1151(chain A and (resid 2 through 16 or resid 18...A329 - 3369
1161(chain A and (resid 2 through 16 or resid 18...A371369
1171(chain A and (resid 2 through 16 or resid 18...A371 - 380
1181(chain A and (resid 2 through 16 or resid 18...A382 - 401
211(chain B and (resid 2 through 16 or resid 18...B2 - 16
221(chain B and (resid 2 through 16 or resid 18...B18 - 109
231(chain B and (resid 2 through 16 or resid 18...B111 - 19
241(chain B and (resid 2 through 16 or resid 18...B2 - 401
251(chain B and (resid 2 through 16 or resid 18...B135 - 136
261(chain B and (resid 2 through 16 or resid 18...B138 - 157
271(chain B and (resid 2 through 16 or resid 18...B159 - 186
281(chain B and (resid 2 through 16 or resid 18...B188 - 2232
291(chain B and (resid 2 through 16 or resid 18...B234232
2101(chain B and (resid 2 through 16 or resid 18...B234 - 248
2111(chain B and (resid 2 through 16 or resid 18...B250 - 274
2121(chain B and (resid 2 through 16 or resid 18...B276 - 289
2131(chain B and (resid 2 through 16 or resid 18...B291 - 319
2141(chain B and (resid 2 through 16 or resid 18...B321 - 327
2151(chain B and (resid 2 through 16 or resid 18...B329 - 3369
2161(chain B and (resid 2 through 16 or resid 18...B371369
2171(chain B and (resid 2 through 16 or resid 18...B371 - 380
2181(chain B and (resid 2 through 16 or resid 18...B382 - 401
311(chain C and (resid 2 through 16 or resid 18...C2 - 16
321(chain C and (resid 2 through 16 or resid 18...C18 - 109
331(chain C and (resid 2 through 16 or resid 18...C111 - 119
341(chain C and (resid 2 through 16 or resid 18...C121 - 133
351(chain C and (resid 2 through 16 or resid 18...C135 - 136
361(chain C and (resid 2 through 16 or resid 18...C138 - 142
371(chain C and (resid 2 through 16 or resid 18...C154 - 157
381(chain C and (resid 2 through 16 or resid 18...C159 - 1212
391(chain C and (resid 2 through 16 or resid 18...C214212
3101(chain C and (resid 2 through 16 or resid 18...C214 - 232
3111(chain C and (resid 2 through 16 or resid 18...C234 - 248
3121(chain C and (resid 2 through 16 or resid 18...C250 - 274
3131(chain C and (resid 2 through 16 or resid 18...C276 - 289
3141(chain C and (resid 2 through 16 or resid 18...C291 - 319
3151(chain C and (resid 2 through 16 or resid 18...C321 - 3335
3161(chain C and (resid 2 through 16 or resid 18...C337335
3171(chain C and (resid 2 through 16 or resid 18...C337 - 369
3181(chain C and (resid 2 through 16 or resid 18...C371 - 380
3191(chain C and (resid 2 through 16 or resid 18...C382 - 401
411(chain D and (resid 2 through 16 or resid 18...D2 - 16
421(chain D and (resid 2 through 16 or resid 18...D18 - 109
431(chain D and (resid 2 through 16 or resid 18...D111 - 119
441(chain D and (resid 2 through 16 or resid 18...D121 - 133
451(chain D and (resid 2 through 16 or resid 18...D135 - 136
461(chain D and (resid 2 through 16 or resid 18...D138 - 142
471(chain D and (resid 2 through 16 or resid 18...D154 - 157
481(chain D and (resid 2 through 16 or resid 18...D159 - 1212
491(chain D and (resid 2 through 16 or resid 18...D214212
4101(chain D and (resid 2 through 16 or resid 18...D214 - 232
4111(chain D and (resid 2 through 16 or resid 18...D234 - 248
4121(chain D and (resid 2 through 16 or resid 18...D250 - 274
4131(chain D and (resid 2 through 16 or resid 18...D276 - 289
4141(chain D and (resid 2 through 16 or resid 18...D291 - 319
4151(chain D and (resid 2 through 16 or resid 18...D321 - 3335
4161(chain D and (resid 2 through 16 or resid 18...D337335
4171(chain D and (resid 2 through 16 or resid 18...D337 - 369
4181(chain D and (resid 2 through 16 or resid 18...D371 - 380
4191(chain D and (resid 2 through 16 or resid 18...D382 - 401

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要素

#1: タンパク質
S-adenosylmethionine synthase / AdoMet synthase / Methionine adenosyltransferase


分子量: 44338.660 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (古細菌)
株: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / 遺伝子: mat, PF1866 / プラスミド: pET22b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q8TZW1, methionine adenosyltransferase
#2: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mn
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#4: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H13NO4S / コメント: pH緩衝剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 888 / 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: 2.46 Å3/Da / 溶媒含有率: 49.96 %
結晶化温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 0.1 M MES pH 5.5, 0.05 M Mn(HCOO)2, 30% v/v PEG MME 550

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.97625 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2010年1月30日 / 詳細: Mirrors
放射モノクロメーター: Si111 / 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: 0.97625 Å / 相対比: 1
反射解像度: 1.78→133.9 Å / Num. obs: 166737 / % possible obs: 99.9 % / 冗長度: 13.2 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.073 / Rrim(I) all: 0.267 / Net I/σ(I): 8.2 / Num. measured all: 2208219 / Scaling rejects: 28
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.8812.35.085294645239460.4741.4885.3050.699.4
5.64-133.912.60.0557203257110.9990.0160.05730.499.9

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
Aimless0.7.1データスケーリング
PHENIX精密化
PDB_EXTRACT3.25データ抽出
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1p7l, 1rg9, 3iml, 1qm4

1p7l

1rg9

3iml

1qm4


解像度: 1.784→106.55 Å / SU ML: 0.27 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.16
Rfactor反射数%反射
Rfree0.2311 8245 4.98 %
Rwork0.2095 --
obs0.2106 165455 99.14 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 102.47 Å2 / Biso mean: 35.1319 Å2 / Biso min: 16.92 Å2
精密化ステップサイクル: final / 解像度: 1.784→106.55 Å
タンパク質核酸リガンド溶媒全体
原子数12260 0 32 888 13180
Biso mean--38.01 37.28 -
残基数----1578
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00512639
X-RAY DIFFRACTIONf_angle_d0.71717158
X-RAY DIFFRACTIONf_chiral_restr0.0531998
X-RAY DIFFRACTIONf_plane_restr0.0052233
X-RAY DIFFRACTIONf_dihedral_angle_d11.8427854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8817X-RAY DIFFRACTION8.871TORSIONAL
12B8817X-RAY DIFFRACTION8.871TORSIONAL
13C8817X-RAY DIFFRACTION8.871TORSIONAL
14D8817X-RAY DIFFRACTION8.871TORSIONAL
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 (%)
1.784-1.80430.43382460.4284479091
1.8043-1.82550.4522470.4243488694
1.8255-1.84780.37532580.3949522199
1.8478-1.87120.38882780.3737516199
1.8712-1.89580.33262420.3344523799
1.8958-1.92180.31572670.3167523699
1.9218-1.94920.36252590.30995207100
1.9492-1.97830.33332780.2936521499
1.9783-2.00920.32162900.2732518799
2.0092-2.04220.27222970.2663520699
2.0422-2.07740.25232800.2631515199
2.0774-2.11520.27123030.25635239100
2.1152-2.15580.28012540.22825199100
2.1558-2.19990.23352680.21415270100
2.1999-2.24770.20492950.19765196100
2.2477-2.30.24122790.19685241100
2.3-2.35750.23372800.18785255100
2.3575-2.42130.23312590.19145235100
2.4213-2.49250.23982860.18675256100
2.4925-2.5730.21242610.17895286100
2.573-2.66490.21312940.18245257100
2.6649-2.77160.22592740.19645267100
2.7716-2.89780.2352880.19215278100
2.8978-3.05060.21843050.19725282100
3.0506-3.24170.20852620.20065322100
3.2417-3.4920.22872770.19295306100
3.492-3.84350.19422630.17895379100
3.8435-4.39960.17352770.1645386100
4.3996-5.54310.18152820.16365441100
5.5431-106.550.21952960.2208561999
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)
10.0773-0.0408-0.34540.6006-0.03511.2375-0.0023-0.07180.0615-0.00610.0706-0.0734-0.05520.0932-0.08210.18130.00280.00350.2811-0.02170.2587-29.886113.6292-9.6368
21.17580.0168-0.02930.4131-0.39762.2997-0.0713-0.0564-0.1072-0.14160.14730.19840.20320.1539-0.09850.22330.0040.03570.2815-0.03640.2122-24.67674.9258-28.8623
32.5132-1.267-0.28556.5423-2.20743.16780.10330.01560.3417-0.30670.0361-0.2558-0.38020.1384-0.06970.3364-0.03710.06190.2645-0.03030.2867-21.385520.3666-31.0189
40.5118-0.0685-0.01910.5116-0.09071.7713-0.06350.16490.0801-0.1444-0.0031-0.132-0.24660.05690.06370.2535-0.0371-0.01360.27540.02090.261-27.545915.5099-21.9444
53.0659-0.9146-1.46941.41620.4442.51060.01230.05030.2118-0.0498-0.0256-0.28060.02120.4046-0.00250.21350.0493-0.00030.3670.00290.3123-18.01850.6365-5.7478
60.52510.3123-0.48820.3451-0.13132.372-0.0803-0.088-0.0868-0.03810.0157-0.11360.35880.28080.0690.25770.05930.01480.2823-0.00940.2621-24.34-4.5969-10.7756
71.4463-0.34660.4691.7527-0.45482.3657-0.1012-0.12940.1850.10170.1198-0.1286-0.37870.03430.02110.2670.0032-0.03230.2841-0.04340.2956-31.733622.50280.2501
80.2239-0.1524-0.19610.73040.16440.8078-0.01990.05480.07350.04490.07090.0419-0.0741-0.0282-0.07230.18620.00790.00190.23820.02370.2489-31.005713.16-71.6206
90.91750.08080.0920.12840.37491.9975-0.0451-0.0164-0.1170.1250.065-0.1280.1519-0.0537-0.02740.24030.03250.04540.23330.0180.2215-36.34024.7553-52.2891
102.32251.96980.31977.27962.71333.57990.1625-0.24020.14070.3926-0.13270.1009-0.2376-0.21320.02650.30090.06780.04260.25680.04430.2502-39.279520.2863-50.3698
110.50560.0746-0.14680.4972-0.00061.8183-0.05690.0614-0.00440.03370.03610.09310.1392-0.2050.02870.1933-0.00350.00680.22320.01690.2539-36.71440.3713-68.4392
121.68480.24650.26561.54440.40732.1057-0.07450.1540.2297-0.11280.05410.0685-0.3124-0.03340.01590.2515-0.0084-0.02520.24660.05240.3103-29.120221.8191-81.6492
130.2451-0.1584-0.36020.4809-0.22081.4648-0.0169-0.0386-0.0113-0.03150.02410.05490.1321-0.2674-0.02140.2368-0.0120.00530.33570.00930.2426-48.02722.3454-15.9993
141.4013-0.1852-0.26080.38580.22211.40230.01890.12480.087-0.1169-0.061-0.2531-0.0893-0.04130.00970.2682-0.00470.01850.28740.00410.2242-41.915810.9812-34.3326
152.1117-2.1901-0.59366.51490.27872.84220.0630.0823-0.154-0.7006-0.0201-0.09590.4460.05020.00670.3776-0.02770.01570.32080.03320.24-43.3358-4.7171-37.8702
161.06520.07040.21442.1578-0.24331.7174-0.12720.0285-0.2045-0.11590.18770.09250.1447-0.1766-0.04430.3033-0.05250.02430.292-0.00960.2201-42.35122.6354-37.679
171.3286-0.1917-0.31971.47440.2021.6004-0.07480.2224-0.3018-0.25650.1025-0.17260.56150.024-0.0130.452-0.01460.04890.3695-0.05880.3056-43.146-12.3925-16.1529
182.16480.24593.08081.89020.54977.41540.0430.2937-0.1047-0.00060.0920.27270.1778-0.702-0.14630.17830.03020.02450.49270.02260.3119-60.688614.9559-19.3477
190.6004-0.14990.0150.9178-0.8663.66710.0215-0.01250.19210.11230.11610.1675-0.6251-0.6589-0.12870.37190.1370.03560.39040.02570.332-57.289626.3552-19.3728
200.10950.2093-0.04010.7292-0.77691.5353-0.03210.01710.0182-0.08150.0514-0.01110.0932-0.1687-0.01780.23050.00470.01270.3008-0.00920.2488-46.45292.5694-13.9812
211.3101-0.0524-0.93071.202-0.33320.7797-0.05780.0773-0.0676-0.12150.04920.04280.1316-0.36310.03020.2193-0.04090.00580.3226-0.00740.2417-53.4234-6.9506-5.5111
220.23860.1513-0.32750.54540.03051.5378-0.01990.0244-0.03090.0708-0.0019-0.09010.12170.30520.0310.21470.04190.00160.3001-0.00180.2396-12.96241.8165-65.0952
231.48790.2012-0.480.3939-0.05521.5492-0.0641-0.0860.11530.0482-0.01050.2003-0.09940.16930.06080.25590.0264-0.00940.24930.00770.1912-19.005910.7155-46.8554
242.32492.5149-0.49127.2388-0.45332.68230.1231-0.2358-0.14520.798-0.17930.07860.32790.0250.0830.37680.06550.03160.3149-0.00290.2551-17.7145-4.9408-43.1024
250.4827-0.3313-0.14840.2281-0.06871.6325-0.1182-0.0832-0.12530.12080.04840.0490.29670.13470.07590.3090.0360.05050.29560.03980.262-18.3017-5.347-54.24
260.7501-0.0691-0.39340.96190.79443.4063-0.0803-0.06270.08150.04560.0642-0.1842-0.28920.67580.02520.2522-0.0793-0.03510.41240.02520.324-1.762721.4059-61.3007
270.5756-0.0239-0.07230.59840.03941.9394-0.0646-0.01220.11890.07980.0232-0.0476-0.18420.17420.03250.2382-0.0258-0.02210.24940.01690.2708-11.561520.9562-61.417
281.3048-0.019-0.35621.01690.21652.1051-0.0917-0.1243-0.10290.07490.0529-0.01860.2550.24360.03440.20460.05320.01650.2580.02260.2029-11.3559-6.3507-73.2223
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 54 )A2 - 54
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 91 )A55 - 91
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 119 )A92 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 170 )A120 - 170
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 191 )A171 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 313 )A192 - 313
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 401 )A314 - 401
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 54 )B2 - 54
9X-RAY DIFFRACTION9chain 'B' and (resid 55 through 91 )B55 - 91
10X-RAY DIFFRACTION10chain 'B' and (resid 92 through 119 )B92 - 119
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 313 )B120 - 313
12X-RAY DIFFRACTION12chain 'B' and (resid 314 through 401 )B314 - 401
13X-RAY DIFFRACTION13chain 'C' and (resid 2 through 54 )C2 - 54
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 91 )C55 - 91
15X-RAY DIFFRACTION15chain 'C' and (resid 92 through 119 )C92 - 119
16X-RAY DIFFRACTION16chain 'C' and (resid 120 through 143 )C120 - 143
17X-RAY DIFFRACTION17chain 'C' and (resid 144 through 170 )C144 - 170
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 191 )C171 - 191
19X-RAY DIFFRACTION19chain 'C' and (resid 192 through 266 )C192 - 266
20X-RAY DIFFRACTION20chain 'C' and (resid 267 through 354 )C267 - 354
21X-RAY DIFFRACTION21chain 'C' and (resid 355 through 401 )C355 - 401
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 54 )D2 - 54
23X-RAY DIFFRACTION23chain 'D' and (resid 55 through 91 )D55 - 91
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 119 )D92 - 119
25X-RAY DIFFRACTION25chain 'D' and (resid 120 through 170 )D120 - 170
26X-RAY DIFFRACTION26chain 'D' and (resid 171 through 247 )D171 - 247
27X-RAY DIFFRACTION27chain 'D' and (resid 248 through 298 )D248 - 298
28X-RAY DIFFRACTION28chain 'D' and (resid 299 through 401 )D299 - 401

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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://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

他の情報も見る