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- PDB-6phe: Crystal structure of Methylglyoxal synthase from Elizabethkingia ... -

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基本情報

登録情報
データベース: PDB / ID: 6phe
タイトルCrystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1
要素Methylglyoxal synthase
キーワードLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / NUHP1
機能・相同性
機能・相同性情報


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / cytosol
類似検索 - 分子機能
Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Rossmann fold ...Methylglyoxal synthase / Methylglyoxal synthase, active site / Methylglyoxal synthase active site. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHATE ION / Methylglyoxal synthase
類似検索 - 構成要素
生物種Elizabethkingia anophelis NUHP1 (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
引用ジャーナル: TO BE PUBLISHED
タイトル: Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1
著者: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
履歴
登録2019年6月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年7月24日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Methylglyoxal synthase
B: Methylglyoxal synthase
C: Methylglyoxal synthase
D: Methylglyoxal synthase
E: Methylglyoxal synthase
F: Methylglyoxal synthase
G: Methylglyoxal synthase
H: Methylglyoxal synthase
I: Methylglyoxal synthase
J: Methylglyoxal synthase
K: Methylglyoxal synthase
L: Methylglyoxal synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)221,04826
ポリマ－219,67212
非ポリマー1,37614
水22,1761231
1
A: Methylglyoxal synthase
B: Methylglyoxal synthase
C: Methylglyoxal synthase
D: Methylglyoxal synthase
E: Methylglyoxal synthase
F: Methylglyoxal synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,64214
ポリマ－109,8366
非ポリマー8068
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint-176 kcal/mol
Surface area31050 Å2
手法PISA
2
G: Methylglyoxal synthase
H: Methylglyoxal synthase
I: Methylglyoxal synthase
J: Methylglyoxal synthase
K: Methylglyoxal synthase
L: Methylglyoxal synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)110,40612
ポリマ－109,8366
非ポリマー5706
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area21160 Å2
ΔGint-166 kcal/mol
Surface area30760 Å2
手法PISA
単位格子
Length a, b, c (Å)167.590, 167.590, 159.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 3 or (resid 4 and (name...
21(chain B and (resid 3 or (resid 4 and (name...
31(chain C and (resid 3 or (resid 4 and (name...
41(chain D and (resid 3 through 4 or resid 6...
51(chain E and (resid 3 or (resid 4 and (name...
61(chain F and (resid 3 or (resid 4 and (name...
71(chain G and (resid 3 or (resid 4 and (name...
81(chain H and (resid 3 or (resid 4 and (name...
91(chain I and (resid 3 or (resid 4 and (name...
101(chain J and (resid 3 or (resid 4 and (name...
111(chain K and (resid 3 or (resid 4 and (name...
121(chain L and (resid 3 or (resid 4 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 or (resid 4 and (name...A3
121(chain A and (resid 3 or (resid 4 and (name...A4
131(chain A and (resid 3 or (resid 4 and (name...A3 - 200
141(chain A and (resid 3 or (resid 4 and (name...A3 - 200
151(chain A and (resid 3 or (resid 4 and (name...A3 - 200
161(chain A and (resid 3 or (resid 4 and (name...A3 - 200
211(chain B and (resid 3 or (resid 4 and (name...B3
221(chain B and (resid 3 or (resid 4 and (name...B4
231(chain B and (resid 3 or (resid 4 and (name...B2 - 200
241(chain B and (resid 3 or (resid 4 and (name...B2 - 200
251(chain B and (resid 3 or (resid 4 and (name...B2 - 200
261(chain B and (resid 3 or (resid 4 and (name...B2 - 200
311(chain C and (resid 3 or (resid 4 and (name...C3
321(chain C and (resid 3 or (resid 4 and (name...C4
331(chain C and (resid 3 or (resid 4 and (name...C2 - 200
341(chain C and (resid 3 or (resid 4 and (name...C2 - 200
351(chain C and (resid 3 or (resid 4 and (name...C2 - 200
361(chain C and (resid 3 or (resid 4 and (name...C2 - 200
411(chain D and (resid 3 through 4 or resid 6...D3 - 4
421(chain D and (resid 3 through 4 or resid 6...D6 - 8
431(chain D and (resid 3 through 4 or resid 6...D11 - 26
441(chain D and (resid 3 through 4 or resid 6...D3 - 200
451(chain D and (resid 3 through 4 or resid 6...D3 - 200
461(chain D and (resid 3 through 4 or resid 6...D3 - 200
471(chain D and (resid 3 through 4 or resid 6...D3 - 200
481(chain D and (resid 3 through 4 or resid 6...D3 - 200
491(chain D and (resid 3 through 4 or resid 6...D3 - 200
4101(chain D and (resid 3 through 4 or resid 6...D3 - 200
511(chain E and (resid 3 or (resid 4 and (name...E3
521(chain E and (resid 3 or (resid 4 and (name...E4
531(chain E and (resid 3 or (resid 4 and (name...E2 - 200
541(chain E and (resid 3 or (resid 4 and (name...E2 - 200
551(chain E and (resid 3 or (resid 4 and (name...E2 - 200
561(chain E and (resid 3 or (resid 4 and (name...E2 - 200
611(chain F and (resid 3 or (resid 4 and (name...F3
621(chain F and (resid 3 or (resid 4 and (name...F4
631(chain F and (resid 3 or (resid 4 and (name...F2 - 200
641(chain F and (resid 3 or (resid 4 and (name...F2 - 200
651(chain F and (resid 3 or (resid 4 and (name...F2 - 200
661(chain F and (resid 3 or (resid 4 and (name...F2 - 200
711(chain G and (resid 3 or (resid 4 and (name...G3
721(chain G and (resid 3 or (resid 4 and (name...G4
731(chain G and (resid 3 or (resid 4 and (name...G2 - 200
741(chain G and (resid 3 or (resid 4 and (name...G2 - 200
751(chain G and (resid 3 or (resid 4 and (name...G2 - 200
761(chain G and (resid 3 or (resid 4 and (name...G2 - 200
811(chain H and (resid 3 or (resid 4 and (name...H3
821(chain H and (resid 3 or (resid 4 and (name...H4
831(chain H and (resid 3 or (resid 4 and (name...H3 - 200
841(chain H and (resid 3 or (resid 4 and (name...H3 - 200
851(chain H and (resid 3 or (resid 4 and (name...H3 - 200
861(chain H and (resid 3 or (resid 4 and (name...H3 - 200
911(chain I and (resid 3 or (resid 4 and (name...I3
921(chain I and (resid 3 or (resid 4 and (name...I4
931(chain I and (resid 3 or (resid 4 and (name...I3 - 200
941(chain I and (resid 3 or (resid 4 and (name...I3 - 200
951(chain I and (resid 3 or (resid 4 and (name...I3 - 200
961(chain I and (resid 3 or (resid 4 and (name...I3 - 200
1011(chain J and (resid 3 or (resid 4 and (name...J3
1021(chain J and (resid 3 or (resid 4 and (name...J4
1031(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1041(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1051(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1061(chain J and (resid 3 or (resid 4 and (name...J3 - 200
1111(chain K and (resid 3 or (resid 4 and (name...K3
1121(chain K and (resid 3 or (resid 4 and (name...K4
1131(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1141(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1151(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1161(chain K and (resid 3 or (resid 4 and (name...K3 - 200
1211(chain L and (resid 3 or (resid 4 and (name...L3
1221(chain L and (resid 3 or (resid 4 and (name...L4
1231(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1241(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1251(chain L and (resid 3 or (resid 4 and (name...L3 - 200
1261(chain L and (resid 3 or (resid 4 and (name...L3 - 200

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要素

#1: タンパク質
Methylglyoxal synthase / MGS


分子量: 18305.998 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Elizabethkingia anophelis NUHP1 (バクテリア)
遺伝子: mgsA, BD94_2272 / プラスミド: ElanA.00692.a.B1
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
株 (発現宿主): BL21(DE3) / 参照: UniProt: A0A077EEZ5, methylglyoxal synthase
#2: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 12 / 由来タイプ: 合成 / 式: PO4
#3: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1231 / 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: 2.56 Å3/Da / 溶媒含有率: 51.98 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5
詳細: Rigaku Reagents JCSG+ screen, condition a11: 50% (V/V) MPD, 200mM ammonium phosphate monobasic, Tris base / HCl pH 8.5. ElanA.00692.a.B1.PS38386 at 18.2mg/ml: cryo: direct: tray: 2978372 a11: puck vsf3-5

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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: APS / ビームライン: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2018年3月15日
放射モノクロメーター: C(111) / 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: 0.97872 Å / 相対比: 1
反射解像度: 2.1→48.61 Å / Num. obs: 132174 / % possible obs: 99.9 % / 冗長度: 9.996 % / Biso Wilson estimate: 29.637 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.107 / Χ2: 1.014 / Net I/σ(I): 19.3 / Num. measured all: 1321165 / Scaling rejects: 28
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.1510.0420.5594.596838964596430.9280.588100
2.15-2.2110.050.4485.694739942794270.9520.471100
2.21-2.2810.0520.3796.6692161916991680.9650.399100
2.28-2.3510.0580.3247.789695891889180.9730.341100
2.35-2.4210.0630.3128.187240867086690.9740.329100
2.42-2.5110.070.259.9484053834783470.9840.263100
2.51-2.610.0520.23110.6781532811181110.9850.243100
2.6-2.7110.0590.18812.8678396779577940.9910.198100
2.71-2.8310.0580.16614.4875244748174810.9920.175100
2.83-2.9710.0390.13317.7272182719071900.9950.14100
2.97-3.1310.0280.10721.6168249680668060.9970.113100
3.13-3.3210.0190.08925.2465056649364930.9980.094100
3.32-3.5510.0090.07130.4360976609260920.9980.074100
3.55-3.839.9780.05238.2656746568956870.9990.055100
3.83-4.29.9630.04244.4252513527552710.9990.04499.9
4.2-4.79.9110.03749.1647238477347660.9990.03999.9
4.7-5.429.8670.03946.4941738424542300.9990.04199.6
5.42-6.649.7520.04341.6535371364236270.9990.04599.6
6.64-9.399.570.03347.45270542858282710.03598.9
9.39-48.618.6930.02552.24141441702162710.02695.6

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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
XSCALEデータスケーリング
PHENIX(dev_3500)精密化
PDB_EXTRACT3.25データ抽出
MOLREP位相決定
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 1vmd

1vmd


解像度: 2.1→48.61 Å / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 18.41
Rfactor反射数%反射Selection details
Rfree0.1841 2162 1.64 %0
Rwork0.1475 ---
obs0.1481 132058 99.88 %-
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: 99.16 Å2 / Biso mean: 28.5545 Å2 / Biso min: 7.73 Å2
精密化ステップサイクル: final / 解像度: 2.1→48.61 Å
タンパク質核酸リガンド溶媒全体
原子数14161 0 76 1238 15475
Biso mean--24.01 38.3 -
残基数----1817
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00715180
X-RAY DIFFRACTIONf_angle_d0.87320784
X-RAY DIFFRACTIONf_dihedral_angle_d14.8229376
X-RAY DIFFRACTIONf_chiral_restr0.062356
X-RAY DIFFRACTIONf_plane_restr0.0052702
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A6559X-RAY DIFFRACTION6.544TORSIONAL
12B6559X-RAY DIFFRACTION6.544TORSIONAL
13C6559X-RAY DIFFRACTION6.544TORSIONAL
14D6559X-RAY DIFFRACTION6.544TORSIONAL
15E6559X-RAY DIFFRACTION6.544TORSIONAL
16F6559X-RAY DIFFRACTION6.544TORSIONAL
17G6559X-RAY DIFFRACTION6.544TORSIONAL
18H6559X-RAY DIFFRACTION6.544TORSIONAL
19I6559X-RAY DIFFRACTION6.544TORSIONAL
110J6559X-RAY DIFFRACTION6.544TORSIONAL
111K6559X-RAY DIFFRACTION6.544TORSIONAL
112L6559X-RAY DIFFRACTION6.544TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.14890.26721340.197485658699100
2.1489-2.20260.2591130.172585788691100
2.2026-2.26220.22881390.164585778716100
2.2622-2.32870.18891480.161785798727100
2.3287-2.40390.21191450.161985758720100
2.4039-2.48980.24321300.158886188748100
2.4898-2.58950.20821540.159985728726100
2.5895-2.70730.19071100.155586608770100
2.7073-2.85010.19541530.153286208773100
2.8501-3.02860.18131220.146286578779100
3.0286-3.26240.19081640.146686698833100
3.2624-3.59060.16961680.138686698837100
3.5906-4.10990.16031570.120187458902100
4.1099-5.17710.14121740.123687808954100
5.1771-48.62250.17981510.16099032918399
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)
13.93320.7377-1.89692.6572-0.62514.9339-0.1212-0.0238-0.3688-0.0971-0.01880.42270.3156-0.36250.04820.1585-0.05630.0070.1680.05180.2346-24.271837.87571.9388
21.85390.7815-0.53923.0715-0.91562.8249-0.0730.1663-0.0798-0.19760.17750.31130.0471-0.3616-0.06790.0915-0.0032-0.00580.15310.04760.1936-22.846249.515967.3528
32.9186-0.8616-0.78651.7865-1.41643.7764-0.033-0.09410.30050.19740.20630.2113-0.27440.2198-0.2070.1161-0.02420.04160.1304-0.00140.1406-16.760250.415576.046
46.2329-4.59561.88598.6893-5.85084.9663-0.10740.33370.28980.064-0.0078-0.3496-0.4330.40640.05530.2736-0.03940.0040.1904-0.01360.1902-9.734839.742361.7719
51.74552.4675-0.46624.8809-1.36740.2058-0.15330.17990.0476-0.26780.1326-0.07010.0072-0.08590.04790.1581-0.01470.01110.12770.02840.1604-11.139945.285976.9007
64.52530.33-0.19032.89951.65335.4591-0.4443-0.3895-0.21850.3734-0.19540.5984-0.4788-0.4469-0.19560.27150.01160.07760.2060.03040.1923-21.512346.247589.4526
75.9765.2088-3.1374.9466-3.2732.04020.8181-1.00620.37351.0465-0.74160.1994-0.6720.61-0.19740.4148-0.07990.01290.2603-0.03870.2127-5.022558.439184.5296
86.75053.34181.11349.1309-3.21482.0770.2523-0.54240.5605-0.0025-0.5444-0.5875-0.49361.614-0.00250.2489-0.12150.02250.41450.02930.28129.002667.92574.4855
95.47081.63760.23572.8398-0.20612.05140.0179-0.0746-0.5606-0.2612-0.10480.14420.2250.0140.08760.19280.00240.00390.0878-0.01270.1757-7.51629.517984.3481
106.31922.9559-4.74373.1913-3.16664.15990.349-0.27520.38190.5363-0.101-0.0107-0.89950.1437-0.26790.2275-0.02320.00210.1326-0.02410.13661.530146.422889.7123
112.9590.7159-2.14493.0346-0.11545.9982-0.0536-0.1082-0.24460.2858-0.01790.21940.2763-0.36420.07370.1512-0.0079-0.00010.1610.04190.1087-3.183234.275693.0239
124.625-0.9044-3.59462.41561.51443.17260.0323-0.6854-0.10660.28430.0644-0.32380.06061.008-0.26030.1884-0.0215-0.00240.22730.00740.17198.340139.54592.4002
132.45140.4387-0.24322.2572.44023.1138-0.0762-0.0573-0.1-0.0030.0338-0.05850.21650.12610.02830.17210.03160.01060.10940.02970.14636.061231.714281.9585
143.3888-2.0288-0.95186.65892.37684.8374-0.27810.2063-0.3438-0.08380.06610.41160.5076-0.10040.1830.1858-0.0420.04360.11070.0130.1191-3.813931.930281.7283
152.6199-3.1466-1.69249.5342-2.47256.45230.0160.4041-0.3665-0.0733-0.0633-0.317-0.17660.27440.00340.2027-0.00720.02020.2185-0.01820.30065.255847.711375.5766
160.6723-0.9624-1.07945.64595.69945.75230.05420.07940.0344-0.26620.2813-0.3757-0.20760.3676-0.32780.2044-0.00540.00390.14540.00060.1963-5.414835.993574.3306
174.56791.7931-0.7675.1054-0.93661.36-0.02920.0432-0.35570.15310.05650.0350.1754-0.20390.00950.1554-0.02660.01810.16640.01250.1239-14.798935.0886.7985
184.4199-1.24731.51238.16634.65314.2746-0.31390.6324-0.1887-0.2162-0.16810.61710.7031-1.04470.46480.3025-0.1051-0.01730.2897-0.0790.2809-8.096223.144259.0202
194.6387-0.36460.76162.043-0.27572.7236-0.11960.0531-0.3063-0.14310.0732-0.12020.20450.20020.01910.2550.01680.05690.092-0.01220.152913.70521.716159.4117
201.8037-1.2418-1.66872.15091.32893.372-0.15960.0582-0.4026-0.1097-0.0560.02360.4535-0.12440.17540.26850.00370.06890.0817-0.01210.21417.393918.418262.9222
212.2139-1.61561.091.9099-1.62842.984-0.0527-0.08720.1703-0.14150.0274-0.04290.1681-0.28840.11840.22420.00830.01280.1646-0.0160.20597.71729.420360.5479
221.3279-0.4325-1.37293.29191.56325.05220.0008-0.0959-0.11920.1987-0.0128-0.05010.14540.02270.0290.17130.00330.04810.14360.00120.149619.873928.092662.7072
235.5361-1.7131-2.62564.00114.24354.8318-0.0914-0.27461.1580.27790.7379-1.20140.10961.0332-0.5730.25850.0278-0.02830.3623-0.08450.31917.724842.583782.3607
240.38990.90910.34574.19282.43044.897-0.03720.02190.0181-0.52020.0503-0.0983-0.0911-0.2215-0.00180.14620.03550.03150.21740.00560.174124.590335.740147.2016
255.5972-2.201-0.86783.47750.60774.0778-0.1242-0.1269-0.19190.13030.1357-0.18970.170.2720.00350.0793-0.02130.0310.1247-0.0180.185331.382840.329359.2057
261.7991-1.40521.53292.5205-0.55832.2631-0.03810.14660.2285-0.02440.0061-0.1408-0.10240.06130.00210.12990.01960.08840.15320.01630.172525.166746.590652.5503
275.7033-0.8596-3.0968.4977-2.5548.78670.0521-0.10270.1418-0.52620.02250.6264-0.35820.1335-0.0920.23760.0033-0.02850.1875-0.00160.19415.69546.658966.0255
283.9194-0.90791.83141.7817-1.09492.968-0.02170.1117-0.0846-0.15240.11340.0559-0.0653-0.0081-0.08680.1481-0.01370.03780.1080.00280.167320.343832.573552.2956
293.543-0.35894.76254.7107-1.94196.99061.01640.9852-1.1351-0.4104-0.75560.8390.6481-0.1031-0.19980.34990.0498-0.05850.2781-0.07530.33290.356137.284539.0688
303.38910.2084-0.59583.69010.21661.69450.0220.07650.2609-0.79080.0076-0.7649-0.24410.0422-0.16140.25750.04780.10170.1480.05670.22529.345163.846741.8484
312.1324-0.7853-0.09011.7713-1.21552.35180.34560.6491-0.2207-0.5461-0.27020.1699-0.2733-0.4734-0.10950.36820.1325-0.00970.3146-0.00810.1137-2.068355.012435.1869
323.3255-0.30340.42462.0236-0.39240.62750.1630.21310.0107-0.4555-0.2077-0.1262-0.1572-0.17380.08730.23570.06550.04940.1710.01780.11739.535850.06340.1647
334.98891.4715-2.62992.572-1.61322.50460.1120.0003-0.20480.1215-0.1552-0.07240.0201-0.03720.03490.23020.0181-0.00310.1786-0.00830.12911.840352.101447.2935
345.4467-1.59842.35570.6897-0.33871.46670.086-0.0068-0.2682-0.11860.0177-0.00450.07110.0134-0.12660.18930.02810.04270.14150.01750.13173.553660.409449.562
357.2483.4527-0.50815.73481.21173.99110.18720.3325-0.1026-0.7193-0.0169-0.9036-0.26680.2904-0.05840.30860.0370.11210.16380.05850.27097.030872.914342.5871
365.8959-5.53144.82915.5744-4.32674.1047-0.6085-0.1081.0840.6011-0.0542-0.474-0.70490.27140.76390.29570.0005-0.05730.26980.02220.444823.331559.262.8823
375.4914-0.9092.54960.1393-0.63594.51910.28030.0426-0.2011-0.1766-0.0601-0.00330.1427-0.4507-0.19420.17720.0104-0.0110.11120.02080.14-10.952568.945454.7685
383.6545-1.31970.49554.0762-1.47072.78820.03230.01710.3497-0.2226-0.104-0.2812-0.17880.24310.09920.1471-0.01350.02790.0634-0.01610.13660.921874.614761.0631
398.31575.9573-4.23625.1296-5.19447.3470.2227-0.75550.19961.0685-0.36-0.2271-0.53350.28530.11220.2043-0.0015-0.0270.1542-0.01150.1260.851274.965570.5352
402.43341.7760.21571.5391-0.33492.95730.0109-0.03240.1192-0.01960.00480.1563-0.0162-0.1074-0.03550.10470.00660.02760.07230.01080.1425-8.354766.163567.7815
412.27791.8936-2.79843.2186-1.25743.98030.17280.4256-0.0012-0.10930.08630.28810.1252-0.3632-0.29830.14720.01210.00660.08770.01450.1334-8.663666.092257.8626
429.8328-2.0099-2.51198.1682-2.78216.81240.0656-0.58560.0130.18470.03430.07680.5782-0.2102-0.10410.2203-0.02960.01240.2697-0.0170.22776.73757.753465.5994
434.36463.022-0.72983.31150.2410.52020.1682-0.3812-0.13270.1334-0.2404-0.07460.0380.02620.09430.19070.00610.03590.15710.02120.1385-3.586861.814154.1665
446.51960.1634-1.86855.328-3.12073.21760.04340.38980.2065-0.39970.07750.38360.0729-0.1944-0.14030.20460.0541-0.01840.16850.03270.0938-10.639971.575945.6503
456.68043.7426-1.0674.78880.0724.773-0.53740.51280.1695-0.93261.04661.16310.8148-0.3305-0.35550.3504-0.121-0.11260.32640.00590.2824-20.184945.17952.8124
461.6996-0.69160.03153.7871-2.11534.1106-0.0356-0.12880.04690.09220.02010.07940.01650.0004-0.05190.07560.0212-0.03230.1337-0.00770.163555.855445.06255.8084
474.1206-2.2395-1.8832.69010.9312.1904-0.03950.083-0.26810.04860.00310.31630.0691-0.1610.04940.092-0.0036-0.04090.1217-0.00780.170654.686437.772652.8206
482.6711-0.03741.40810.59310.61092.61910.0478-0.0263-0.08990.0516-0.1872-0.12110.54110.23160.15210.23940.0445-0.00740.14740.00350.207164.653940.951258.0104
493.2095-2.0584-1.62812.40850.94732.93740.09730.13190.2563-0.2393-0.0442-0.2480.01460.2029-0.03760.1439-0.0007-0.00590.13630.01990.18667.599750.287547.5142
503.85-0.0562-0.46252.62030.35083.2737-0.04210.19580.2324-0.07-0.09040.0058-0.2097-0.11290.09070.21280.0183-0.07510.08030.01090.119969.489162.380957.8062
512.8285-0.85861.61863.0248-1.32583.8494-0.16260.08590.3825-0.08070.0024-0.069-0.27380.21320.14960.2148-0.0209-0.06650.09430.01670.194375.779766.003361.3302
523.1422-1.562-0.68083.45682.13076.4158-0.1331-0.1598-0.2927-0.06040.0165-0.14780.15550.68370.13830.22040.0014-0.00820.15450.05440.202675.58354.852358.9484
531.6085-0.1752.03493.4402-2.31444.64890.0499-0.13660.06670.2056-0.0492-0.0247-0.0956-0.0762-0.00110.13720.0094-0.01880.1058-0.01050.133163.419455.813862.1428
544.36483.00220.71455.5801-3.17614.0399-0.3417-0.5783-0.83210.70290.76560.4526-0.1498-0.9699-0.37710.41370.05090.06360.40290.07290.318967.78641.327482.0904
554.90951.2357-1.13124.2742-0.32951.66740.06380.04260.73180.00050.0845-0.1104-0.10670.128-0.11730.18940.0179-0.04730.16720.00730.167192.882655.871681.5961
565.90711.69124.16713.96612.86044.3180.2351-0.1807-0.3340.56410.0482-0.07310.67670.1853-0.2920.25870.0029-0.0220.1950.02090.121485.763240.563689.3696
572.8381-0.51210.89681.3651-0.82433.4451-0.0578-0.0170.06010.06840.04360.0319-0.2414-0.05760.01940.17810.0074-0.03430.1054-0.02160.105481.579251.406683.7004
588.5782-3.50291.62464.89881.80767.540.05650.36540.1042-0.2310.09050.58270.1674-0.4275-0.120.2898-0.0161-0.01070.25370.00830.322279.178836.901974.0515
590.6247-1.2716-0.12064.6097-3.2713.6590.0573-0.00130.0438-0.21870.30560.34530.0751-0.3437-0.32670.1563-0.0018-0.05140.16270.00730.171891.55946.981575.4628
606.27530.1265-0.73386.1504-2.64812.28950.18960.31480.775-0.23230.08360.1105-0.01060.1639-0.30940.2481-0.0771-0.06070.2038-0.00410.288101.16255.093482.0713
614.59750.0004-0.80822.6224-2.39594.6979-0.57450.9370.0625-0.452-0.1693-0.6615-0.46141.69861.04570.393-0.11690.00760.4990.09950.398190.707761.813155.7656
622.3186-0.36170.0732.744-0.06824.0636-0.0405-0.11140.09070.11580.0886-0.3326-0.06620.446-0.03380.0782-0.0092-0.03850.215-0.02970.2622106.801840.480672.0597
632.15910.13310.96882.47351.89622.3955-0.07880.14290.0612-0.09340.2646-0.4210.04850.4098-0.04960.08250.00190.00170.2137-0.02460.2295104.965835.036765.4542
642.7332-4.7546-2.66348.9465.18633.1733-0.0030.7344-0.0439-0.4991-0.33750.14650.4688-0.40.28940.323-0.0667-0.02470.36390.02210.320693.43545.16559.125
654.02173.08210.50766.08921.36331.5943-0.0133-0.0261-0.13810.17840.0324-0.1430.15420.1514-0.01090.14490.0209-0.01990.1475-0.03270.164598.109838.613878.0476
664.65924.77054.44745.22055.01075.35310.551-1.0008-0.13980.9285-0.54150.03210.0832-0.9912-0.05420.448-0.109-0.01960.3260.01440.241681.445320.691177.1166
673.504-0.2253-1.80481.6441-0.35844.561-0.024-0.01220.1745-0.05940.1218-0.19690.26390.6736-0.04220.13010.0338-0.01590.1762-0.02460.159894.770115.611352.2994
684.7092-3.3415-2.5928.64865.75124.12260.0296-0.0106-0.38290.1672-0.2720.72830.151-0.41070.28080.16970.01560.00410.14310.00040.194377.25212.3461.8335
696.42850.082-0.36725.02330.14651.5886-0.01620.312-0.3423-0.35650.0473-0.06110.19020.1791-0.03570.21720.04110.0040.08220.00960.109789.5747.575657.3097
704.66194.72213.32225.66935.32866.82820.1486-0.5828-0.34610.8077-0.3336-0.02080.7950.09410.12840.25520.02970.00920.13680.01970.187883.9729.346569.1478
712.25061.71810.69212.92840.51663.1961-0.00760.0319-0.04480.1273-0.02-0.16610.02760.23250.05530.10110.05180.00220.1057-0.01370.135892.387918.542462.1705
728.5589-1.785.67842.78222.36859.6632-0.1475-0.49350.28410.2812-0.0073-0.0189-0.59330.47760.08620.29110.0030.00340.33530.06120.247876.387926.20964.3937
733.08221.26941.16414.10830.88171.60850.0346-0.03160.1358-0.0872-0.0659-0.07730.01090.21250.02960.14780.0364-0.00360.13970.020.088689.361519.502149.2895
748.86184.50882.06863.61060.79393.185-0.19090.5928-0.2596-1.52530.6154-1.5159-1.0462-0.0981-0.41120.4966-0.0920.14620.40550.01130.3156103.888140.265450.2052
753.3954-0.15020.26712.8506-0.38092.4360.17330.251-0.1198-0.3364-0.11930.11010.26520.1211-0.01890.21080.0809-0.01840.1712-0.03890.1280.198224.084637.1185
765.4968-3.238-3.09193.79462.60594.10150.48060.63940.4073-0.7341-0.2798-0.2228-0.22230.0292-0.19320.31290.09090.02550.23950.03930.183478.992335.350532.4988
776.6893-2.81310.28874.3291.46823.25770.07310.026-0.11720.0361-0.11220.3282-0.017-0.16550.06590.16250.0196-0.02040.1457-0.0160.130572.430627.94542.9924
782.5182-2.87633.03659.86610.12965.9041-0.06910.48790.42360.33280.24050.3557-0.4515-0.0104-0.12550.28470.01320.00840.29830.05550.346186.511438.362448.3817
794.1586-1.1897-1.38711.1637-0.14421.72520.0452-0.01620.0924-0.22040.00990.15040.0148-0.0079-0.07340.19050.0541-0.02660.1439-0.00680.138679.082320.903345.8863
804.5314-6.0393-1.04138.21212.21782.7574-0.746-0.0693-0.80221.02220.01821.06771.0088-0.22070.88840.2079-0.06350.09330.2108-0.00240.468165.679317.953354.5716
813.8422-4.2058-2.08867.1248-0.99845.4827-0.3047-0.9433-0.20921.83450.03850.8118-0.2985-0.27770.09680.44360.02090.13670.2909-0.01170.341357.117429.947767.8427
822.7044-0.62410.05214.02451.04885.776-0.0963-0.22720.26390.33520.1265-0.069-0.4886-0.2611-0.01750.18350.00970.04560.09230.04520.2048-18.24351.358680.7509
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 19 through 38 )G19 - 38
2X-RAY DIFFRACTION2chain 'G' and (resid 39 through 78 )G39 - 78
3X-RAY DIFFRACTION3chain 'G' and (resid 79 through 88 )G79 - 88
4X-RAY DIFFRACTION4chain 'G' and (resid 89 through 100 )G89 - 100
5X-RAY DIFFRACTION5chain 'G' and (resid 101 through 127 )G101 - 127
6X-RAY DIFFRACTION6chain 'G' and (resid 128 through 134 )G128 - 134
7X-RAY DIFFRACTION7chain 'G' and (resid 135 through 146 )G135 - 146
8X-RAY DIFFRACTION8chain 'G' and (resid 147 through 153 )G147 - 153
9X-RAY DIFFRACTION9chain 'H' and (resid 3 through 18 )H3 - 18
10X-RAY DIFFRACTION10chain 'H' and (resid 19 through 31 )H19 - 31
11X-RAY DIFFRACTION11chain 'H' and (resid 32 through 44 )H32 - 44
12X-RAY DIFFRACTION12chain 'H' and (resid 45 through 55 )H45 - 55
13X-RAY DIFFRACTION13chain 'H' and (resid 56 through 78 )H56 - 78
14X-RAY DIFFRACTION14chain 'H' and (resid 79 through 88 )H79 - 88
15X-RAY DIFFRACTION15chain 'H' and (resid 89 through 100 )H89 - 100
16X-RAY DIFFRACTION16chain 'H' and (resid 101 through 118 )H101 - 118
17X-RAY DIFFRACTION17chain 'H' and (resid 119 through 138 )H119 - 138
18X-RAY DIFFRACTION18chain 'H' and (resid 139 through 153 )H139 - 153
19X-RAY DIFFRACTION19chain 'I' and (resid 3 through 31 )I3 - 31
20X-RAY DIFFRACTION20chain 'I' and (resid 32 through 78 )I32 - 78
21X-RAY DIFFRACTION21chain 'I' and (resid 79 through 100 )I79 - 100
22X-RAY DIFFRACTION22chain 'I' and (resid 101 through 138 )I101 - 138
23X-RAY DIFFRACTION23chain 'I' and (resid 139 through 153 )I139 - 153
24X-RAY DIFFRACTION24chain 'J' and (resid 3 through 18 )J3 - 18
25X-RAY DIFFRACTION25chain 'J' and (resid 19 through 44 )J19 - 44
26X-RAY DIFFRACTION26chain 'J' and (resid 45 through 88 )J45 - 88
27X-RAY DIFFRACTION27chain 'J' and (resid 89 through 100 )J89 - 100
28X-RAY DIFFRACTION28chain 'J' and (resid 101 through 138 )J101 - 138
29X-RAY DIFFRACTION29chain 'J' and (resid 139 through 153 )J139 - 153
30X-RAY DIFFRACTION30chain 'K' and (resid 3 through 18 )K3 - 18
31X-RAY DIFFRACTION31chain 'K' and (resid 19 through 55 )K19 - 55
32X-RAY DIFFRACTION32chain 'K' and (resid 56 through 78 )K56 - 78
33X-RAY DIFFRACTION33chain 'K' and (resid 79 through 100 )K79 - 100
34X-RAY DIFFRACTION34chain 'K' and (resid 101 through 127 )K101 - 127
35X-RAY DIFFRACTION35chain 'K' and (resid 128 through 138 )K128 - 138
36X-RAY DIFFRACTION36chain 'K' and (resid 139 through 153 )K139 - 153
37X-RAY DIFFRACTION37chain 'L' and (resid 3 through 18 )L3 - 18
38X-RAY DIFFRACTION38chain 'L' and (resid 19 through 44 )L19 - 44
39X-RAY DIFFRACTION39chain 'L' and (resid 45 through 55 )L45 - 55
40X-RAY DIFFRACTION40chain 'L' and (resid 56 through 78 )L56 - 78
41X-RAY DIFFRACTION41chain 'L' and (resid 79 through 88 )L79 - 88
42X-RAY DIFFRACTION42chain 'L' and (resid 89 through 100 )L89 - 100
43X-RAY DIFFRACTION43chain 'L' and (resid 101 through 126 )L101 - 126
44X-RAY DIFFRACTION44chain 'L' and (resid 127 through 138 )L127 - 138
45X-RAY DIFFRACTION45chain 'L' and (resid 139 through 153 )L139 - 153
46X-RAY DIFFRACTION46chain 'A' and (resid 3 through 31 )A3 - 31
47X-RAY DIFFRACTION47chain 'A' and (resid 32 through 78 )A32 - 78
48X-RAY DIFFRACTION48chain 'A' and (resid 79 through 100 )A79 - 100
49X-RAY DIFFRACTION49chain 'A' and (resid 101 through 153 )A101 - 153
50X-RAY DIFFRACTION50chain 'B' and (resid 2 through 31 )B2 - 31
51X-RAY DIFFRACTION51chain 'B' and (resid 32 through 78 )B32 - 78
52X-RAY DIFFRACTION52chain 'B' and (resid 79 through 100 )B79 - 100
53X-RAY DIFFRACTION53chain 'B' and (resid 101 through 139 )B101 - 139
54X-RAY DIFFRACTION54chain 'B' and (resid 140 through 153 )B140 - 153
55X-RAY DIFFRACTION55chain 'C' and (resid 2 through 18 )C2 - 18
56X-RAY DIFFRACTION56chain 'C' and (resid 19 through 36 )C19 - 36
57X-RAY DIFFRACTION57chain 'C' and (resid 37 through 88 )C37 - 88
58X-RAY DIFFRACTION58chain 'C' and (resid 89 through 100 )C89 - 100
59X-RAY DIFFRACTION59chain 'C' and (resid 101 through 126 )C101 - 126
60X-RAY DIFFRACTION60chain 'C' and (resid 127 through 139 )C127 - 139
61X-RAY DIFFRACTION61chain 'C' and (resid 140 through 153 )C140 - 153
62X-RAY DIFFRACTION62chain 'D' and (resid 3 through 44 )D3 - 44
63X-RAY DIFFRACTION63chain 'D' and (resid 45 through 88 )D45 - 88
64X-RAY DIFFRACTION64chain 'D' and (resid 89 through 100 )D89 - 100
65X-RAY DIFFRACTION65chain 'D' and (resid 101 through 138 )D101 - 138
66X-RAY DIFFRACTION66chain 'D' and (resid 139 through 153 )D139 - 153
67X-RAY DIFFRACTION67chain 'E' and (resid 2 through 18 )E2 - 18
68X-RAY DIFFRACTION68chain 'E' and (resid 19 through 31 )E19 - 31
69X-RAY DIFFRACTION69chain 'E' and (resid 32 through 44 )E32 - 44
70X-RAY DIFFRACTION70chain 'E' and (resid 45 through 55 )E45 - 55
71X-RAY DIFFRACTION71chain 'E' and (resid 56 through 88 )E56 - 88
72X-RAY DIFFRACTION72chain 'E' and (resid 89 through 100 )E89 - 100
73X-RAY DIFFRACTION73chain 'E' and (resid 101 through 139 )E101 - 139
74X-RAY DIFFRACTION74chain 'E' and (resid 140 through 153 )E140 - 153
75X-RAY DIFFRACTION75chain 'F' and (resid 2 through 44 )F2 - 44
76X-RAY DIFFRACTION76chain 'F' and (resid 45 through 68 )F45 - 68
77X-RAY DIFFRACTION77chain 'F' and (resid 69 through 88 )F69 - 88
78X-RAY DIFFRACTION78chain 'F' and (resid 89 through 100 )F89 - 100
79X-RAY DIFFRACTION79chain 'F' and (resid 101 through 134 )F101 - 134
80X-RAY DIFFRACTION80chain 'F' and (resid 135 through 146 )F135 - 146
81X-RAY DIFFRACTION81chain 'F' and (resid 147 through 153 )F147 - 153
82X-RAY DIFFRACTION82chain 'G' and (resid 2 through 18 )G2 - 18

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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