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- PDB-9z9c: Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase f... -

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基本情報

登録情報
データベース: PDB / ID: 9z9c
タイトルCrystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form)
要素Glyceraldehyde-3-phosphate dehydrogenase
キーワードOXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
機能・相同性
機能・相同性情報


酸化還元酵素; アルデヒドまたはケトンに対し酸化酵素として働く; NAD又はNADPを用いる / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / glucose metabolic process / NAD binding / NADP binding
類似検索 - 分子機能
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
類似検索 - 構成要素
生物種Neisseria gonorrhoeae NCCP11945 (淋菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.3 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 米国
National Institutes of Health/Office of the DirectorS10OD030394 米国
引用ジャーナル: To be published
タイトル: Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form)
著者: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.
履歴
登録2025年11月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年11月26日Provider: repository / タイプ: Initial release

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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: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
I: Glyceraldehyde-3-phosphate dehydrogenase
J: Glyceraldehyde-3-phosphate dehydrogenase
K: Glyceraldehyde-3-phosphate dehydrogenase
L: Glyceraldehyde-3-phosphate dehydrogenase
M: Glyceraldehyde-3-phosphate dehydrogenase
N: Glyceraldehyde-3-phosphate dehydrogenase
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
T: Glyceraldehyde-3-phosphate dehydrogenase
U: Glyceraldehyde-3-phosphate dehydrogenase
V: Glyceraldehyde-3-phosphate dehydrogenase
W: Glyceraldehyde-3-phosphate dehydrogenase
X: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)899,98749
ポリマ-883,91524
非ポリマー16,07225
13,619756
1
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,9738
ポリマ-147,3194
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-121 kcal/mol
Surface area42710 Å2
手法PISA
2
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,1239
ポリマ-147,3194
非ポリマー2,8045
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-119 kcal/mol
Surface area43160 Å2
手法PISA
3
I: Glyceraldehyde-3-phosphate dehydrogenase
J: Glyceraldehyde-3-phosphate dehydrogenase
K: Glyceraldehyde-3-phosphate dehydrogenase
L: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,9738
ポリマ-147,3194
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19660 Å2
ΔGint-124 kcal/mol
Surface area43020 Å2
手法PISA
4
M: Glyceraldehyde-3-phosphate dehydrogenase
N: Glyceraldehyde-3-phosphate dehydrogenase
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,9738
ポリマ-147,3194
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-113 kcal/mol
Surface area43100 Å2
手法PISA
5
Q: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
T: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,9738
ポリマ-147,3194
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19560 Å2
ΔGint-118 kcal/mol
Surface area43140 Å2
手法PISA
6
U: Glyceraldehyde-3-phosphate dehydrogenase
V: Glyceraldehyde-3-phosphate dehydrogenase
W: Glyceraldehyde-3-phosphate dehydrogenase
X: Glyceraldehyde-3-phosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)149,9738
ポリマ-147,3194
非ポリマー2,6544
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area19550 Å2
ΔGint-122 kcal/mol
Surface area41890 Å2
手法PISA
単位格子
Length a, b, c (Å)105.534, 137.842, 157.786
Angle α, β, γ (deg.)85.95, 77.63, 86.88
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質 ...
Glyceraldehyde-3-phosphate dehydrogenase


分子量: 36829.789 Da / 分子数: 24 / 断片: residues 24-357 / 由来タイプ: 組換発現
由来: (組換発現) Neisseria gonorrhoeae NCCP11945 (淋菌)
遺伝子: NGK_2321 / プラスミド: NegoA.00617.a.B1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: B4RPP8, 酸化還元酵素; アルデヒドまたはケトンに対し酸化酵素として働く; NAD又はNADPを用いる
#2: 化合物...
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 24 / 由来タイプ: 合成 / : C21H27N7O14P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: NAD*YM
#3: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / : C6H14O4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 756 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.53 Å3/Da / 溶媒含有率: 51.35 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: Berkeley D8 : 25% PEG 3350, 0.10M MES pH 5.5, 5% iso-Propanol, 0.10M ammonium citrate dibasic. NegoA.00617.a.B1.PS38018 at 8 mg/mL. plate 20061 D8 drop 1, Puck: PSL-2202, Cryo: 80% crystallant + 20% PEG 200

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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: NSLS-II / ビームライン: 19-ID / 波長: 0.9786 Å
検出器タイプ: DECTRIS EIGER2 XE 9M / 検出器: PIXEL / 日付: 2025年6月28日
放射モノクロメーター: Double Crystal Si 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: 0.9786 Å / 相対比: 1
反射解像度: 2.3→49.02 Å / Num. obs: 374646 / % possible obs: 97.4 % / 冗長度: 3.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.13 / Rrim(I) all: 0.246 / Χ2: 0.89 / Net I/σ(I): 7.3 / Num. measured all: 1327731
反射 シェル解像度: 2.3→2.36 Å / % possible obs: 97.2 % / 冗長度: 3.5 % / Rmerge(I) obs: 1.008 / Num. measured all: 96270 / Num. unique obs: 27683 / CC1/2: 0.519 / Rpim(I) all: 0.64 / Rrim(I) all: 1.199 / Χ2: 0.96 / Net I/σ(I) obs: 1.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(dev_5438: ???)精密化
Aimlessデータスケーリング
XDSデータ削減
PHASER位相決定
PDB_EXTRACTデータ抽出
精密化構造決定の手法: 分子置換 / 解像度: 2.3→48.53 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 25.04 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2316 18761 5.01 %
Rwork0.1939 --
obs0.1958 374549 97.38 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 2.3→48.53 Å
タンパク質核酸リガンド溶媒全体
原子数58784 0 1066 756 60606
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00560801
X-RAY DIFFRACTIONf_angle_d0.73582736
X-RAY DIFFRACTIONf_dihedral_angle_d13.02522792
X-RAY DIFFRACTIONf_chiral_restr0.0499804
X-RAY DIFFRACTIONf_plane_restr0.00710632
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.32516030.278411879X-RAY DIFFRACTION97
2.33-2.350.33395860.267311902X-RAY DIFFRACTION97
2.35-2.380.3246220.265911747X-RAY DIFFRACTION97
2.38-2.410.30636370.26411808X-RAY DIFFRACTION97
2.41-2.440.31646360.261311836X-RAY DIFFRACTION97
2.44-2.480.30416120.250611863X-RAY DIFFRACTION97
2.48-2.510.30986720.243211826X-RAY DIFFRACTION97
2.51-2.550.30186200.246311850X-RAY DIFFRACTION97
2.55-2.590.2935780.243211848X-RAY DIFFRACTION97
2.59-2.630.29556060.251611678X-RAY DIFFRACTION96
2.63-2.680.30316130.24311705X-RAY DIFFRACTION96
2.68-2.730.26835950.217311970X-RAY DIFFRACTION98
2.73-2.780.2795990.218911920X-RAY DIFFRACTION98
2.78-2.840.26716240.207511844X-RAY DIFFRACTION98
2.84-2.90.27536590.21911845X-RAY DIFFRACTION98
2.9-2.970.2616300.212311973X-RAY DIFFRACTION98
2.97-3.040.2626320.216711842X-RAY DIFFRACTION98
3.04-3.120.25666130.224511925X-RAY DIFFRACTION98
3.12-3.210.25636540.217911898X-RAY DIFFRACTION98
3.21-3.320.24536330.201511887X-RAY DIFFRACTION98
3.32-3.440.23936140.197511883X-RAY DIFFRACTION98
3.44-3.570.2276670.197711903X-RAY DIFFRACTION98
3.57-3.740.22626270.184411869X-RAY DIFFRACTION97
3.74-3.930.21016470.174711879X-RAY DIFFRACTION97
3.93-4.180.18556840.149111796X-RAY DIFFRACTION98
4.18-4.50.15886220.137811801X-RAY DIFFRACTION97
4.5-4.950.17455870.14111891X-RAY DIFFRACTION97
4.95-5.670.18166420.152611705X-RAY DIFFRACTION96
5.67-7.140.21015810.174612102X-RAY DIFFRACTION99
7.14-48.530.17256660.166711913X-RAY DIFFRACTION98
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.04360.09810.00170.1642-0.01520.1615-0.0515-0.0792-0.00950.0610.0009-0.14350.11940.0649-00.20810.0404-0.02040.33570.02190.300254.0478100.596966.4135
20.1022-0.1031-0.02890.1328-0.04520.0373-0.0540.0343-0.0692-0.090.0633-0.1296-0.00040.0044-00.21470.00110.0340.3566-0.02350.253450.4843108.821342.2155
30.0749-0.0473-0.03680.05320.00980.0647-0.1004-0.0410.1840.0322-0.02910.0784-0.2821-0.1083-0.03250.2603-0.0144-0.07490.37240.03440.305316.4022141.442244.2749
40.0299-0.00720.04020.0019-0.01840.1378-0.15560.13920.1823-0.13680.12630.1095-0.1626-0.12440.00020.3268-0.0647-0.10190.40820.08550.220920.6633137.698826.564
50.1409-0.00210.00910.2354-0.03960.1334-0.12760.08020.0229-0.11790.0987-0.03590.01870.0015-0.01230.221-0.0677-0.02530.36160.03970.189840.4134129.397735.0196
60.039-0.0194-0.00180.0578-0.06220.0575-0.09580.15930.193-0.03440.00870.0229-0.13750.1707-00.2227-0.0126-0.0650.331-0.00160.319348.353142.737563.3053
70.2077-0.00220.05830.23050.09260.1681-0.0853-0.06530.07370.11950.04360.04820.00690.0128-0.01880.20610.0408-0.04190.3187-0.03410.240133.2773134.279176.8698
80.0088-0.0198-0.00820.02340.010.029-0.10550.2634-0.02650.01680.06180.03840.04180.2175-00.2568-0.0118-0.00230.33670.00390.24116.775799.122347.872
90.02180.00760.0210.0224-0.01640.0529-0.12960.0524-0.01270.0172-0.1471-0.0453-0.04290.0714-0.00290.20890.03580.03530.3503-0.06570.276124.536697.606144.2409
100.28670.1159-0.11820.1914-0.05730.1968-0.05430.0069-0.04220.08760.03790.11390.018-0.00280.00030.17720.01380.0110.26610.00280.249213.8263108.774465.7416
110.025-0.00970.00840.0050.00410.0128-0.0584-0.0386-0.1188-0.14260.14940.0198-0.0431-0.02520.00040.5522-0.13590.09340.2749-0.03330.253391.6984119.0442-20.0371
120.01310.00830.01070.0181-0.00710.01460.0197-0.0164-0.1211-0.22250.14830.0013-0.0185-0.09190.00220.4556-0.06940.06770.2734-0.05480.284491.4068106.7855-18.412
130.00310.0009-0.00270.00290.0050.00030.05230.01850.0071-0.1632-0.0338-0.0889-0.0143-0.0436-00.7847-0.12850.15330.3931-0.08380.3804101.5538115.3376-25.0606
140.00650.0125-0.00030.0194-0.0120.0049-0.11670.01310.1323-0.24480.1726-0.0998-0.03370.048900.577-0.13020.1650.3474-0.0780.4525104.668124.5302-19.1546
150.0137-0.00310.01210.00460.0030.0253-0.11250.0192-0.0353-0.0464-0.0795-0.16090.00140.0461-0.02140.4513-0.16420.09460.2827-0.01530.3071101.748130.8368-14.1522
160.04990.01310.03190.02460.00350.0148-0.0563-0.0286-0.0276-0.0570.1121-0.0967-0.13350.1178-00.3913-0.04750.04790.2827-0.01210.305591.5885134.1623-1.7371
170.00180.00010.00250.00220.0021-0.0020.0506-0.01470.0248-0.08650.09390.0146-0.0267-0.163900.2823-0.05020.10640.2475-0.0830.3865104.7646111.34493.9428
180.06470.05630.02880.046-0.00380.05610.0417-0.0179-0.0278-0.1176-0.0069-0.0106-0.06390.021700.3327-0.02940.02350.2833-0.03190.268994.2758127.70037.4525
190.0056-0.00330.00530.0028-0.00130.0040.07520.11410.0589-0.13350.05940.0078-0.0875-0.062400.34280.00380.02070.29990.02910.356276.6571130.75824.1982
20-0.0057-0.00560.00420.0198-0.01590.0099-0.0157-0.092-0.03460.02880.16870.0773-0.007-0.1261-00.3369-0.02660.02410.2796-0.01610.304881.229126.48657.615
210.03610.04380.00930.03340.00830.0091-0.108-0.02120.1397-0.04980.08620.03220.040.0722-00.407-0.03370.00370.279-0.00120.243888.0659127.9846-4.1766
220.156-0.02070.06490.0790.01340.1435-0.0495-0.0907-0.13790.0307-0.0342-0.0208-0.0846-0.0888-0.00190.21580.015-0.02250.348-0.01920.263683.624798.027236.5357
230.04740.0630.02430.1609-0.21990.2201-0.0008-0.0152-0.02490.04510.0095-0.0642-0.0621-0.0098-00.2651-0.0214-0.04130.2413-0.04390.233492.6714119.172326.1829
240.122-0.13230.15050.195-0.20280.2345-0.12540.0706-0.1254-0.11550.1617-0.705-0.08250.1412-0.02940.2913-0.07310.12220.3588-0.11770.8241119.204498.72999.8112
250.0289-0.0068-0.02680.0089-0.0070.03660.02350.02120.0407-0.07130.0024-0.1678-0.02570.02990.01770.17760.03090.36030.3158-0.29450.8233118.297880.87051.8486
260.01710.02860.05990.02490.03360.0427-0.0207-0.0035-0.0341-0.20950.018-0.23070.00250.1163-00.3483-0.02390.08720.2981-0.05810.335998.194185.3519-1.359
270.0557-0.0880.02510.1144-0.0337-0.0088-0.1248-0.0663-0.0543-0.0940.1302-0.24980.10440.0291-0.00010.2744-0.02140.05620.2634-0.06130.36398.355378.429611.1824
280.0349-0.0834-0.02530.10630.03040.11570.0839-0.00390.0928-0.06950.01590.2205-0.1029-0.04050.00020.2697-0.011-0.06540.28290.03540.235560.0124104.38454.3011
290.07520.0365-0.04450.0892-0.05720.0447-0.0528-0.04940.0281-0.19360.11550.07380.1899-0.07020.02160.3602-0.0634-0.09790.32280.00460.244267.431283.8536-3.6215
30-0.001-0.0014-0.00140.00340.00550.0073-0.02450.0180.0237-0.11520.05630.1345-0.0245-0.146-00.2254-0.0064-0.00060.2871-0.02650.291879.807593.924416.3131
310.0628-0.05630.07780.1095-0.06340.0588-0.0303-0.08340.0079-0.24850.0306-0.04450.08310.0445-00.4014-0.048-0.02760.2679-0.03120.218580.718882.6955-3.3508
320.3164-0.14550.05970.45240.13110.1156-0.15630.05110.1144-0.42490.1685-0.1770.0620.02820.00450.4581-0.0428-0.00110.2862-0.01330.197977.929389.9167-9.7447
330.0141-0.0105-0.00060.00370.00450.0089-0.01070.11320.0059-0.00480.0572-0.09490.0388-0.0313-00.23690.0273-0.05880.2986-0.02090.4738126.339933.032882.989
340.01410.00650.00560.00860.01560.0117-0.02220.02920.12690.14120.011-0.1766-0.0757-0.038200.29750.0065-0.05130.3420.00440.4342125.240745.346382.7805
350.0182-0.0043-0.00350.0066-0.0030.0027-0.1073-0.0823-0.0981-0.07880.0058-0.11490.02460.046200.310.00330.00370.4634-0.00570.5416133.076235.958973.9816
360.00590.00040.01570.00810.01870.0318-0.09870.0171-0.0675-0.15750.1287-0.29050.13380.020.00020.27880.06380.0060.3051-0.04370.488125.022125.052571.1832
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480.16230.0307-0.06310.08370.14180.3503-0.1143-0.0299-0.06020.53740.1713-0.00290.1631-0.13450.20461.01280.20670.20140.257-0.02540.107977.9041122.0269132.0177
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520.10160.0244-0.0020.15370.12070.251-0.03150.0477-0.0997-0.0259-0.0333-0.0077-0.0876-0.0487-0.00330.24050.0182-0.03660.2605-0.00650.206187.8102102.251476.1633
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540.0016-0.01220.01650.0468-0.05610.0666-0.0759-0.0272-0.0590.06090.11340.0616-0.0246-0.1255-0.01370.37940.00360.29170.3931-0.01460.90753.2796101.9886102.6052
550.00820.0050.00260.0054-0.00670.0088-0.03420.0588-0.02570.0142-0.05780.1326-0.0732-0.0009-00.29960.00610.0510.3497-0.07330.576361.0365109.413497.0156
560.0178-0.0028-0.00060.0034-0.0040.00140.0245-0.0892-0.03480.12990.18980.1042-0.0467-0.133200.45950.08470.05970.5139-0.03630.921246.3051107.0292101.8448
570.002-0.0015-0.00320.00340.00530.01350.0068-0.0277-0.04160.04450.05010.0449-0.0346-0.16450.05220.6160.15990.61920.6640.15760.982749.602296.6089115.5547
580.02260.0394-0.02090.0694-0.03310.01560.0490.024-0.0284-0.01260.1133-0.02960.02-0.14520.12220.5983-0.22130.64770.43450.16121.011354.169884.3226113.2045
590.0651-0.03130.06430.1324-0.07510.1398-0.2356-0.0305-0.24350.41380.03440.33050.124-0.0536-0.49620.77640.02380.3580.16530.06010.476173.538590.8274116.435
600.11380.09690.08530.0920.08630.3845-0.02740.0533-0.04840.4538-0.03970.58050.18760.0094-0.01590.4495-0.03380.15150.23900.50272.741684.6395104.3702
610.55620.124-0.42670.0208-0.09280.37520.06190.2608-0.13530.33670.0014-0.5231-0.1461-0.11790.16910.42110.1253-0.33930.27-0.13540.4149106.9747113.0652111.6456
620.04070.0001-0.06080.0149-0.02640.1441-0.1284-0.0127-0.14430.1278-0.2399-0.1549-0.16360.0214-0.03920.49640.0196-0.22470.3441-0.16090.9132116.6071114.3026107.7118
630.05810.0238-0.07470.02910.01230.2157-0.05830.02470.05350.0566-0.1019-0.2290.11440.0929-0.08980.55070.2443-0.27050.3347-0.06670.76113.849195.9817109.7781
640.1194-0.0596-0.01270.0237-0.01390.0207-0.02530.014-0.01760.57220.1087-0.37180.20640.02230.1291.0820.3723-0.4110.14240.01560.3515100.498689.8137122.2936
650.3620.0627-0.13720.0639-0.01550.1741-0.0910.0902-0.03350.72760.15-0.21380.2919-0.07250.13310.75670.1533-0.070.12480.02540.207690.894992.3344113.5094
660.0013-0.0054-0.01460.0731-0.01490.07110.0306-0.00970.00080.2020.01080.0010.1265-0.10.06551.11630.2287-0.06510.0792-0.16910.099990.3952101.8509126.8094
670.3814-0.12230.21610.3019-0.26540.2532-0.18450.01690.00170.2032-0.05320.09990.0904-0.0392-0.07910.86830.05820.11130.2928-0.03810.245484.694789.4287124.6277
680.055-0.01370.02120.0075-0.02060.0639-0.00930.01910.01080.04-0.0234-0.0373-0.03480.0089-0.06620.8190.2898-0.6850.3686-0.14510.3682108.8998100.9809121.3204
690.0104-0.0032-0.00620.0012-0.00510.00970.04990.10350.14120.0580.0597-0.0705-0.0014-0.0942-00.28710.03530.04720.34030.06250.401539.807162.2487108.885
700.0137-0.0136-0.00340.01750.00240.01140.15550.06110.2079-0.0042-0.01360.09740.0953-0.042200.26310.01570.01470.31120.02880.381731.067757.7049116.4179
710.12960.0499-0.13320.04490.02110.13170.01610.21870.0183-0.12850.0239-0.08460.03130.0438-00.30640.00410.06170.36660.01570.309549.540654.3418102.5299
720.0209-0.0059-0.03850.0050.00630.0363-0.06270.13940.008-0.16130.0566-0.00150.1552-0.027-00.32360.02030.04470.3543-0.00280.283150.719438.0279111.5707
730.04040.0032-0.01030.0082-0.01580.09420.0266-0.06960.12020.0674-0.0039-0.0343-0.02640.1191-00.25410.01770.02660.3521-0.0120.334564.469449.9439121.2214
740.0106-0.0004-0.01730.00460.01620.02460.07570.01370.0637-0.10920.0686-0.0097-0.00570.063300.27320.01120.05250.33050.01280.343356.457254.8667112.9502
750.2971-0.21970.02580.3327-0.01750.0418-0.1414-0.4164-0.27040.12030.09680.1220.32940.1104-0.03760.47880.1148-0.02090.45830.03280.225153.870519.25149.89
760.02680.00340.00220.0046-0.00690.00470.0739-0.207-0.03190.0350.0698-0.15870.0529-0.04560.00740.40060.1639-0.09330.3853-0.05460.334571.446819.4933142.0692
770.06120.0459-0.02810.0944-0.0750.04750.0041-0.01990.08930.00140.0253-0.11070.17030.077500.35680.08370.00830.3426-0.02510.295163.567628.5781126.1092
780.07850.07150.01740.11360.02740.0542-0.13890.3239-0.2641-0.08220.0732-0.08990.3282-0.0374-0.01040.4666-0.08910.01970.3632-0.06080.203732.936916.3349112.4032
790.19560.0144-0.03030.12960.0380.15870.05360.04430.08880.10220.03360.09970.1823-0.11640.0010.3382-0.102-0.0030.36070.01210.269420.260127.8126130.5044
800.0494-0.05170.05780.461-0.27940.22590.0451-0.04330.2046-0.19580.0795-0.04930.11180.27630.02740.1885-0.00710.04060.3505-0.08950.388552.186660.9127146.2477
810.1624-0.0888-0.18710.09340.21160.43390.020.00640.10360.08210.0580.08490.0275-0.0480.00060.2577-0.00030.04980.2871-0.03330.313129.392652.0672146.5144
820.22660.06920.11660.05120.04380.6479-0.09560.0244-0.5044-0.01240.01670.0061-0.07570.0446-0.02930.22370.00240.04560.2529-0.02990.481487.94752.724722.8324
830.52570.2717-0.11720.3556-0.11350.0742-0.54920.0854-0.8254-0.35220.0703-1.11190.2836-0.013-0.87370.30870.04750.159-0.00940.14311.053674.604832.68930.981
840.0782-0.0565-0.07970.27350.25240.24630.0132-0.0286-0.0032-0.0430.24510.1014-0.04770.05280.08640.3333-0.1054-0.06930.3670.180.354933.326731.006523.5812
850.0049-0.0251-0.02060.10620.06420.0508-0.1799-0.0460.1062-0.21060.32950.449-0.0811-0.05140.00280.2918-0.0782-0.09950.43750.18210.511429.039737.739824.9797
860.00440.00660.00180.15320.14750.1646-0.1231-0.0238-0.13560.13480.32410.1370.1572-0.13820.02430.2615-0.04630.02420.33670.1190.403832.732223.084536.051
870.1365-0.02340.12030.0136-0.06250.532-0.09420.0364-0.2556-0.44360.1322-0.48010.14-0.1456-0.00620.4115-0.10080.18760.2673-0.02110.651750.186216.328626.8234
880.0047-0.00390.00370.00360.00370.005-0.06410.0735-0.02730.0546-0.1423-0.03770.0765-0.153-00.28090.00750.02190.31480.05160.346752.257940.055439.0504
890.0337-0.01190.10130.0088-0.04870.2916-0.1032-0.0559-0.31730.0094-0.1288-0.0688-0.0443-0.083-0.03350.2985-0.00850.10490.25730.02490.491555.730424.162233.7637
900.13850.03080.24540.0260.0780.5969-0.21830.0921-0.2799-0.19610.0089-0.290.0304-0.019-0.31150.2676-0.0250.23120.2173-0.01130.568561.168622.93926.6785
910.0039-0.001-0.0119-0.00170.00010.0378-0.10020.0165-0.0821-0.08310.0192-0.12450.1398-0.0466-0.06020.7396-0.34110.71510.4058-0.20090.554558.109119.416712.5079
920.2022-0.00210.25290.0233-0.0760.2881-0.186-0.1101-0.22-0.6730.1488-0.57130.0419-0.0076-0.13820.4513-0.17590.24030.2822-0.02510.604152.101722.823320.3373
930.0018-0.01010.00780.0555-0.02190.01560.0559-0.0220.0331-0.2544-0.0043-0.0398-0.02430.11480.0481.136-0.49520.23890.5716-0.03060.264855.865244.0877-3.8843
940.0189-0.00940.01770.0660.02540.0306-0.03890.0126-0.0309-0.08940.03490.0081-0.03560.0431-0.00570.8108-0.56990.09250.3583-0.18420.261355.898936.69224.4305
950.1083-0.03770.02470.0936-0.09420.1075-0.05630.05530.055-0.0964-0.0327-0.05030.01620.0153-0.0660.9915-0.38740.17270.3591-0.24870.577360.827137.6057-8.4435
960.0338-0.00850.01630.0114-0.0110.0106-0.0169-0.01690.0608-0.056-0.0169-0.02950.05330.003-0.01341.0882-0.56550.2350.6551-0.05560.637158.150957.6502-4.5734
970.31210.1332-0.05960.6208-0.24060.5636-0.37420.25920.0282-0.86940.61650.06920.2772-0.17141.46280.4541-0.2342-0.29260.4240.31410.122745.907962.424510.0608
980.0076-0.00580.00620.00040.00440.0094-0.10690.04950.01640.269-0.032-0.0682-0.09680.00700.65470.0372-0.04010.3570.04370.23358.232458.707452.9929
990.013-0.0095-0.00630.00180.00240.01950.02950.0372-0.12830.3215-0.0942-0.06270.0405-0.076-0.00280.51630.002-0.11260.35590.06880.310961.181948.471250.7538
1000.01470.00450.01030.0024-0.00330.0112-0.0895-0.08530.00930.2072-0.01370.1546-0.0041-0.055-0.00010.96220.23660.33530.59030.12550.526143.616157.994756.3886
1010.00170.004-0.00260.0249-0.01390.01070.0426-0.05580.06860.0928-0.06320.06650.0246-0.0501-0.01590.7920.20090.3610.4790.04290.408543.701867.195251.435
1020.37810.0963-0.01470.0398-0.01320.004-0.09570.03180.26480.25960.16030.2668-0.0636-0.12780.00450.4490.09480.10870.22850.01320.288849.194774.567637.7201
1030.06910.0336-0.0120.0397-0.04520.0249-0.0509-0.00190.07770.34390.22560.3984-0.0065-0.1518-00.28620.0250.06030.33150.06930.359345.380763.028129.1637
1040.01950.0078-0.01240.00760.00260.0054-0.06860.07390.00950.16760.00190.0044-0.0668-0.003400.35450.0311-0.05350.3017-0.02230.300762.952676.319428.619
1050.10280.10890.08450.09520.05360.1103-0.0350.10850.10230.28690.09840.1852-0.05650.12450.01580.36410.03730.00920.26990.02840.298556.643270.272333.0098
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 334 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 84 )
4X-RAY DIFFRACTION4chain 'B' and (resid 85 through 150 )
5X-RAY DIFFRACTION5chain 'B' and (resid 151 through 334 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 69 )
7X-RAY DIFFRACTION7chain 'C' and (resid 70 through 333 )
8X-RAY DIFFRACTION8chain 'D' and (resid 2 through 46 )
9X-RAY DIFFRACTION9chain 'D' and (resid 47 through 69 )
10X-RAY DIFFRACTION10chain 'D' and (resid 70 through 333 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 33 )
12X-RAY DIFFRACTION12chain 'E' and (resid 34 through 67 )
13X-RAY DIFFRACTION13chain 'E' and (resid 68 through 84 )
14X-RAY DIFFRACTION14chain 'E' and (resid 85 through 111 )
15X-RAY DIFFRACTION15chain 'E' and (resid 112 through 129 )
16X-RAY DIFFRACTION16chain 'E' and (resid 130 through 179 )
17X-RAY DIFFRACTION17chain 'E' and (resid 180 through 199 )
18X-RAY DIFFRACTION18chain 'E' and (resid 200 through 254 )
19X-RAY DIFFRACTION19chain 'E' and (resid 255 through 278 )
20X-RAY DIFFRACTION20chain 'E' and (resid 279 through 303 )
21X-RAY DIFFRACTION21chain 'E' and (resid 304 through 333 )
22X-RAY DIFFRACTION22chain 'F' and (resid 2 through 129 )
23X-RAY DIFFRACTION23chain 'F' and (resid 130 through 334 )
24X-RAY DIFFRACTION24chain 'G' and (resid 4 through 111 )
25X-RAY DIFFRACTION25chain 'G' and (resid 112 through 150 )
26X-RAY DIFFRACTION26chain 'G' and (resid 151 through 249 )
27X-RAY DIFFRACTION27chain 'G' and (resid 250 through 333 )
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 111 )
29X-RAY DIFFRACTION29chain 'H' and (resid 112 through 179 )
30X-RAY DIFFRACTION30chain 'H' and (resid 180 through 199 )
31X-RAY DIFFRACTION31chain 'H' and (resid 200 through 265 )
32X-RAY DIFFRACTION32chain 'H' and (resid 266 through 333 )
33X-RAY DIFFRACTION33chain 'I' and (resid 1 through 33 )
34X-RAY DIFFRACTION34chain 'I' and (resid 34 through 67 )
35X-RAY DIFFRACTION35chain 'I' and (resid 68 through 84 )
36X-RAY DIFFRACTION36chain 'I' and (resid 85 through 129 )
37X-RAY DIFFRACTION37chain 'I' and (resid 130 through 179 )
38X-RAY DIFFRACTION38chain 'I' and (resid 180 through 199 )
39X-RAY DIFFRACTION39chain 'I' and (resid 200 through 254 )
40X-RAY DIFFRACTION40chain 'I' and (resid 255 through 278 )
41X-RAY DIFFRACTION41chain 'I' and (resid 279 through 333 )
42X-RAY DIFFRACTION42chain 'J' and (resid 2 through 95 )
43X-RAY DIFFRACTION43chain 'J' and (resid 96 through 334 )
44X-RAY DIFFRACTION44chain 'K' and (resid 2 through 84 )
45X-RAY DIFFRACTION45chain 'K' and (resid 85 through 333 )
46X-RAY DIFFRACTION46chain 'L' and (resid 2 through 129 )
47X-RAY DIFFRACTION47chain 'L' and (resid 130 through 333 )
48X-RAY DIFFRACTION48chain 'M' and (resid 1 through 84 )
49X-RAY DIFFRACTION49chain 'M' and (resid 85 through 179 )
50X-RAY DIFFRACTION50chain 'M' and (resid 180 through 199 )
51X-RAY DIFFRACTION51chain 'M' and (resid 200 through 334 )
52X-RAY DIFFRACTION52chain 'N' and (resid 1 through 150 )
53X-RAY DIFFRACTION53chain 'N' and (resid 151 through 334 )
54X-RAY DIFFRACTION54chain 'O' and (resid 3 through 37 )
55X-RAY DIFFRACTION55chain 'O' and (resid 38 through 57 )
56X-RAY DIFFRACTION56chain 'O' and (resid 58 through 91 )
57X-RAY DIFFRACTION57chain 'O' and (resid 92 through 124 )
58X-RAY DIFFRACTION58chain 'O' and (resid 125 through 150 )
59X-RAY DIFFRACTION59chain 'O' and (resid 151 through 254 )
60X-RAY DIFFRACTION60chain 'O' and (resid 255 through 333 )
61X-RAY DIFFRACTION61chain 'P' and (resid 3 through 56 )
62X-RAY DIFFRACTION62chain 'P' and (resid 57 through 88 )
63X-RAY DIFFRACTION63chain 'P' and (resid 89 through 129 )
64X-RAY DIFFRACTION64chain 'P' and (resid 130 through 179 )
65X-RAY DIFFRACTION65chain 'P' and (resid 180 through 265 )
66X-RAY DIFFRACTION66chain 'P' and (resid 266 through 295 )
67X-RAY DIFFRACTION67chain 'P' and (resid 296 through 316 )
68X-RAY DIFFRACTION68chain 'P' and (resid 317 through 333 )
69X-RAY DIFFRACTION69chain 'Q' and (resid 1 through 33 )
70X-RAY DIFFRACTION70chain 'Q' and (resid 34 through 67 )
71X-RAY DIFFRACTION71chain 'Q' and (resid 68 through 179 )
72X-RAY DIFFRACTION72chain 'Q' and (resid 180 through 227 )
73X-RAY DIFFRACTION73chain 'Q' and (resid 228 through 303 )
74X-RAY DIFFRACTION74chain 'Q' and (resid 304 through 333 )
75X-RAY DIFFRACTION75chain 'R' and (resid 2 through 111 )
76X-RAY DIFFRACTION76chain 'R' and (resid 112 through 150 )
77X-RAY DIFFRACTION77chain 'R' and (resid 151 through 334 )
78X-RAY DIFFRACTION78chain 'S' and (resid 2 through 95 )
79X-RAY DIFFRACTION79chain 'S' and (resid 96 through 333 )
80X-RAY DIFFRACTION80chain 'T' and (resid 2 through 84 )
81X-RAY DIFFRACTION81chain 'T' and (resid 85 through 333 )
82X-RAY DIFFRACTION82chain 'U' and (resid 1 through 150 )
83X-RAY DIFFRACTION83chain 'U' and (resid 151 through 333 )
84X-RAY DIFFRACTION84chain 'V' and (resid 2 through 23 )
85X-RAY DIFFRACTION85chain 'V' and (resid 24 through 84 )
86X-RAY DIFFRACTION86chain 'V' and (resid 85 through 129 )
87X-RAY DIFFRACTION87chain 'V' and (resid 130 through 179 )
88X-RAY DIFFRACTION88chain 'V' and (resid 180 through 199 )
89X-RAY DIFFRACTION89chain 'V' and (resid 200 through 227 )
90X-RAY DIFFRACTION90chain 'V' and (resid 228 through 254 )
91X-RAY DIFFRACTION91chain 'V' and (resid 255 through 278 )
92X-RAY DIFFRACTION92chain 'V' and (resid 279 through 334 )
93X-RAY DIFFRACTION93chain 'W' and (resid 5 through 37 )
94X-RAY DIFFRACTION94chain 'W' and (resid 38 through 57 )
95X-RAY DIFFRACTION95chain 'W' and (resid 58 through 92 )
96X-RAY DIFFRACTION96chain 'W' and (resid 93 through 130 )
97X-RAY DIFFRACTION97chain 'W' and (resid 131 through 331 )
98X-RAY DIFFRACTION98chain 'X' and (resid 1 through 33 )
99X-RAY DIFFRACTION99chain 'X' and (resid 34 through 75 )
100X-RAY DIFFRACTION100chain 'X' and (resid 76 through 111 )
101X-RAY DIFFRACTION101chain 'X' and (resid 112 through 129 )
102X-RAY DIFFRACTION102chain 'X' and (resid 130 through 179 )
103X-RAY DIFFRACTION103chain 'X' and (resid 180 through 254 )
104X-RAY DIFFRACTION104chain 'X' and (resid 255 through 278 )
105X-RAY DIFFRACTION105chain 'X' and (resid 279 through 333 )

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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