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- PDB-3anz: Crystal Structure of alpha-hemolysin -

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基本情報

登録情報
データベース: PDB / ID: 3anz
タイトルCrystal Structure of alpha-hemolysin
要素Alpha-hemolysin
キーワードTOXIN / heptamer
機能・相同性
機能・相同性情報


cytolysis in another organism / toxin activity / extracellular region
類似検索 - 分子機能
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
ACETIC ACID / Alpha-hemolysin / Alpha-hemolysin
類似検索 - 構成要素
生物種Staphylococcus aureus (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.303 Å
データ登録者Yamashita, K. / Kawauchi, H. / Tanaka, Y. / Yao, M. / Tanaka, I.
引用ジャーナル: Protein Sci. / 年: 2011
タイトル: 2-Methyl-2,4-pentanediol induces spontaneous assembly of staphylococcal alpha-hemolysin into heptameric pore structure
著者: Tanaka, Y. / Hirano, N. / Kaneko, J. / Kamio, Y. / Yao, M. / Tanaka, I.
履歴
登録2010年9月16日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02011年6月22日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22011年8月10日Group: Other
改定 1.32017年10月11日Group: Refinement description / カテゴリ: software
改定 1.42023年11月1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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Alpha-hemolysin
B: Alpha-hemolysin
C: Alpha-hemolysin
D: Alpha-hemolysin
E: Alpha-hemolysin
F: Alpha-hemolysin
G: Alpha-hemolysin
H: Alpha-hemolysin
I: Alpha-hemolysin
J: Alpha-hemolysin
K: Alpha-hemolysin
L: Alpha-hemolysin
M: Alpha-hemolysin
N: Alpha-hemolysin
O: Alpha-hemolysin
P: Alpha-hemolysin
Q: Alpha-hemolysin
R: Alpha-hemolysin
S: Alpha-hemolysin
T: Alpha-hemolysin
U: Alpha-hemolysin
V: Alpha-hemolysin
W: Alpha-hemolysin
X: Alpha-hemolysin
Y: Alpha-hemolysin
Z: Alpha-hemolysin
a: Alpha-hemolysin
b: Alpha-hemolysin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)974,477112
ポリマ－966,17828
非ポリマー8,29984
水37,1832064
1
A: Alpha-hemolysin
B: Alpha-hemolysin
C: Alpha-hemolysin
D: Alpha-hemolysin
E: Alpha-hemolysin
F: Alpha-hemolysin
G: Alpha-hemolysin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,61928
ポリマ－241,5457
非ポリマー2,07521
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Alpha-hemolysin
I: Alpha-hemolysin
J: Alpha-hemolysin
K: Alpha-hemolysin
L: Alpha-hemolysin
M: Alpha-hemolysin
N: Alpha-hemolysin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,61928
ポリマ－241,5457
非ポリマー2,07521
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
3
O: Alpha-hemolysin
P: Alpha-hemolysin
Q: Alpha-hemolysin
R: Alpha-hemolysin
S: Alpha-hemolysin
T: Alpha-hemolysin
U: Alpha-hemolysin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,61928
ポリマ－241,5457
非ポリマー2,07521
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
4
V: Alpha-hemolysin
W: Alpha-hemolysin
X: Alpha-hemolysin
Y: Alpha-hemolysin
Z: Alpha-hemolysin
a: Alpha-hemolysin
b: Alpha-hemolysin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)243,61928
ポリマ－241,5457
非ポリマー2,07521
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)102.821, 293.877, 170.545
Angle α, β, γ (deg.)90.000, 92.420, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X
251Y
261Z
271a
281b

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:12 or resseq 19:64 or resseq...
211chain B and (resseq 1:12 or resseq 19:64 or resseq...
311chain C and (resseq 1:12 or resseq 19:64 or resseq...
411chain D and (resseq 1:12 or resseq 19:64 or resseq...
511chain E and (resseq 1:12 or resseq 19:64 or resseq...
611chain F and (resseq 1:12 or resseq 19:64 or resseq...
711chain G and (resseq 1:12 or resseq 19:64 or resseq...
811chain H and (resseq 1:12 or resseq 19:64 or resseq...
911chain I and (resseq 1:12 or resseq 19:64 or resseq...
1011chain J and (resseq 1:12 or resseq 19:64 or resseq...
1111chain K and (resseq 1:12 or resseq 19:64 or resseq...
1211chain L and (resseq 1:12 or resseq 19:64 or resseq...
1311chain M and (resseq 1:12 or resseq 19:64 or resseq...
1411chain N and (resseq 1:12 or resseq 19:64 or resseq...
1511chain O and (resseq 1:12 or resseq 19:64 or resseq...
1611chain P and (resseq 1:12 or resseq 19:64 or resseq...
1711chain Q and (resseq 1:12 or resseq 19:64 or resseq...
1811chain R and (resseq 1:12 or resseq 19:64 or resseq...
1911chain S and (resseq 1:12 or resseq 19:64 or resseq...
2011chain T and (resseq 1:12 or resseq 19:64 or resseq...
2111chain U and (resseq 1:12 or resseq 19:64 or resseq...
2211chain V and (resseq 1:12 or resseq 19:64 or resseq...
2311chain W and (resseq 1:12 or resseq 19:64 or resseq...
2411chain X and (resseq 1:12 or resseq 19:64 or resseq...
2511chain Y and (resseq 1:12 or resseq 19:64 or resseq...
2611chain Z and (resseq 1:12 or resseq 19:64 or resseq...
2711chain a and (resseq 1:12 or resseq 19:64 or resseq...
2811chain b and (resseq 1:12 or resseq 19:64 or resseq...

NCS oper:
IDCodeMatrixベクター
1given(0.692301, -0.100461, -0.714582), (0.38006, 0.892545, 0.242728), (0.613412, -0.439625, 0.656091)40.959599, -13.9581, 19.6768
2given(0.007726, 0.158019, -0.987406), (0.749669, 0.652557, 0.110298), (0.661767, -0.74108, -0.113421)56.5956, -6.43188, 63.800999
3given(-0.538402, 0.572908, -0.61798), (0.834544, 0.464206, -0.29673), (0.116871, -0.675492, -0.728047)35.2887, 17.0133, 99.027802
4given(-0.537435, 0.834366, 0.122459), (0.571636, 0.4672, -0.674505), (-0.619997, -0.292501, -0.728044)-7.02317, 38.6105, 98.855202
5given(0.011685, 0.741736, 0.67059), (0.161237, 0.660462, -0.733344), (-0.986847, 0.116693, -0.111877)-38.395699, 41.963001, 63.6035
6given(0.696816, 0.3688, 0.61517), (-0.094497, 0.897407, -0.430964), (-0.710997, 0.242171, 0.660179)-35.155701, 24.496901, 19.450001
7given(0.999943, -0.000758, 0.010668), (0.00076, 1, -0.000196), (-0.010668, 0.000204, 0.999943)-49.829601, -1.54264, -84.665604
8given(0.700643, -0.100819, -0.706353), (0.377237, 0.892632, 0.24678), (0.605633, -0.439367, 0.663449)66.940903, -54.785, -65.824997
9given(0.017701, 0.156948, -0.987448), (0.750058, 0.650957, 0.116911), (0.661135, -0.742713, -0.106197)139.567001, -54.031799, 41.6553
10given(-0.529936, 0.573984, -0.624268), (0.839123, 0.461369, -0.288118), (0.122643, -0.676522, -0.726139)113.514, -0.262347, 155.828003
11given(-0.538536, 0.83395, 0.120444), (0.577333, 0.46932, -0.66815), (-0.613731, -0.290286, -0.734213)7.63174, 66.498199, 191.826996
12given(0.005952, 0.74036, 0.672184), (0.168136, 0.661885, -0.730505), (-0.985746, 0.117367, -0.120542)-97.1287, 94.864403, 121.817001
13given(0.691, 0.367977, 0.622183), (-0.088474, 0.897313, -0.432437), (-0.71742, 0.243767, 0.6526)-122.489998, 64.345398, -1.41786
14given(0.933699, -0.148501, 0.325812), (0.151933, -0.659643, -0.736062), (0.324226, 0.736762, -0.593346)-39.6922, 120.304001, 40.456699
15given(0.395741, -0.562585, 0.72587), (0.569771, -0.469475, -0.674503), (0.720243, 0.680508, 0.134754)-27.6294, 88.246498, -30.9778
16given(-0.289201, -0.831481, 0.474344), (0.830871, -0.464122, -0.306992), (0.475412, 0.305336, 0.825078)35.049, 47.904701, -56.123402
17given(-0.620098, -0.750711, -0.227841), (0.751571, -0.651735, 0.101894), (-0.224985, -0.108054, 0.968352)100.401001, 28.5089, -16.673901
18given(-0.341153, -0.38213, -0.858831), (0.381162, -0.891396, 0.245211), (-0.859262, -0.243699, 0.449756)119.737, 44.796501, 57.838902
19given(0.338037, -0.006767, -0.941109), (0.006213, -0.999936, 0.009422), (-0.941112, -0.009032, -0.337973)78.532799, 84.881302, 111.75
20given(0.905818, 0.100895, -0.411477), (-0.09623, -0.896846, -0.431748), (-0.412593, 0.430682, -0.802671)7.13762, 118.791, 103.702003
21given(0.929596, -0.147805, 0.337647), (0.161184, -0.660815, -0.733037), (0.331468, 0.735851, -0.590467)-113.587997, 176.029007, 73.774902
22given(0.392028, -0.562182, 0.728193), (0.574749, -0.468387, -0.671027), (0.718316, 0.681589, 0.139493)-107.982002, 118.578003, -78.613998
23given(-0.294752, -0.830737, 0.472225), (0.834105, -0.464797, -0.29704), (0.466251, 0.306332, 0.829922)10.1814, 33.410198, -150.136993
24given(-0.619082, -0.749514, -0.234451), (0.748287, -0.653586, 0.113546), (-0.238338, -0.105142, 0.965474)151.593002, -16.747101, -87.464897
25given(-0.331697, -0.38431, -0.861558), (0.37919, -0.890553, 0.251257), (-0.863824, -0.243353, 0.441121)210.063995, 6.03916, 62.473301
26given(0.348688, -0.007192, -0.937211), (0.007618, -0.999916, 0.010508), (-0.937208, -0.010803, -0.348604)141.569, 85.065002, 187.246994
27given(0.911031, 0.100971, -0.399783), (-0.090082, -0.897396, -0.431932), (-0.402377, 0.429517, -0.808461)-3.31312, 161.350006, 191.729996

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要素

#1: タンパク質 ...
Alpha-hemolysin / Alpha-HL / Alpha-toxin


分子量: 34506.363 Da / 分子数: 28 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
株: MU50 / 遺伝子: hla, hly, SAV1163 / プラスミド: pET28 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834(DE3) / 参照: UniProt: Q99UU6, UniProt: A0A0H3JRX7*PLUS
#2: 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: 56 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#3: 化合物...
ChemComp-ACY / ACETIC ACID / 酢酸


分子量: 60.052 Da / 分子数: 28 / 由来タイプ: 合成 / 式: C2H4O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2064 / 由来タイプ: 天然 / 式: H2O

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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: 2.66 Å3/Da / 溶媒含有率: 53.84 % / Mosaicity: 0.402 °
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: HEPES, Ammonium acetate, MPD, pH 7.5, vapor diffusion, sitting drop, temperature 293K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: Photon Factory / ビームライン: BL-5A / 波長: 1 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年3月8日
放射モノクロメーター: 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: 1 Å / 相対比: 1
反射解像度: 2.3→50 Å / Num. obs: 439066 / % possible obs: 99.1 % / 冗長度: 3.4 % / Rmerge(I) obs: 0.085 / Χ2: 36.345 / Net I/σ(I): 16.3
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.343.10.399218742.604199
2.34-2.383.10.416219232.539199
2.38-2.433.20.361218362.613199.1
2.43-2.483.20.347218312.604199.1
2.48-2.533.20.31219542.686199
2.53-2.593.20.242218642.812199
2.59-2.663.30.219218953.009199
2.66-2.733.30.198218993.064199
2.73-2.813.30.165219023.253198.9
2.81-2.93.40.149219463.409199.1
2.9-33.40.128219423.711199.3
3-3.123.50.111220804.115199.7
3.12-3.263.60.098220874.737199.9
3.26-3.443.60.088221365.173199.9
3.44-3.653.70.081221176.268199.9
3.65-3.933.70.076221306.774199.8
3.93-4.333.70.068220637.003199.6
4.33-4.953.60.057220417.082199.4
4.95-6.243.70.052222086.734199.9
6.24-503.70.066213380.048195.3

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
MOLREP位相決定
PHENIX1.6.4_486精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ収集
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 7AHL

7ahl


解像度: 2.303→19.984 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7425 / SU ML: 0.28 / σ(F): 1.33 / 位相誤差: 30.92 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2262 30815 7.1 %RANDOM
Rwork0.1931 ---
obs0.2045 433754 97.85 %-
溶媒の処理減衰半径: 0.61 Å / VDWプローブ半径: 0.9 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 60.221 Å2 / ksol: 0.373 e/Å3
原子変位パラメータBiso max: 182.05 Å2 / Biso mean: 51.6053 Å2 / Biso min: 17.95 Å2
Baniso -1Baniso -2Baniso -3
1-17.7194 Å20 Å217.7253 Å2
2---14.7581 Å2-0 Å2
3----2.9613 Å2
精密化ステップサイクル: LAST / 解像度: 2.303→19.984 Å
タンパク質核酸リガンド溶媒全体
原子数65983 0 560 2064 68607
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00667915
X-RAY DIFFRACTIONf_angle_d0.91191916
X-RAY DIFFRACTIONf_dihedral_angle_d13.11124936
X-RAY DIFFRACTIONf_chiral_restr0.0589839
X-RAY DIFFRACTIONf_plane_restr0.00311782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1830X-RAY DIFFRACTIONPOSITIONAL
12B1830X-RAY DIFFRACTIONPOSITIONAL0.032
13C1830X-RAY DIFFRACTIONPOSITIONAL0.032
14D1830X-RAY DIFFRACTIONPOSITIONAL0.031
15E1830X-RAY DIFFRACTIONPOSITIONAL0.03
16F1830X-RAY DIFFRACTIONPOSITIONAL0.03
17G1830X-RAY DIFFRACTIONPOSITIONAL0.032
18H1830X-RAY DIFFRACTIONPOSITIONAL0.023
19I1830X-RAY DIFFRACTIONPOSITIONAL0.032
110J1830X-RAY DIFFRACTIONPOSITIONAL0.033
111K1830X-RAY DIFFRACTIONPOSITIONAL0.035
112L1830X-RAY DIFFRACTIONPOSITIONAL0.033
113M1830X-RAY DIFFRACTIONPOSITIONAL0.03
114N1830X-RAY DIFFRACTIONPOSITIONAL0.032
115O1830X-RAY DIFFRACTIONPOSITIONAL0.033
116P1830X-RAY DIFFRACTIONPOSITIONAL0.033
117Q1830X-RAY DIFFRACTIONPOSITIONAL0.031
118R1830X-RAY DIFFRACTIONPOSITIONAL0.032
119S1830X-RAY DIFFRACTIONPOSITIONAL0.03
120T1830X-RAY DIFFRACTIONPOSITIONAL0.028
121U1830X-RAY DIFFRACTIONPOSITIONAL0.032
122V1830X-RAY DIFFRACTIONPOSITIONAL0.032
123W1830X-RAY DIFFRACTIONPOSITIONAL0.029
124X1830X-RAY DIFFRACTIONPOSITIONAL0.029
125Y1830X-RAY DIFFRACTIONPOSITIONAL0.032
126Z1830X-RAY DIFFRACTIONPOSITIONAL0.029
127a1830X-RAY DIFFRACTIONPOSITIONAL0.026
128b1830X-RAY DIFFRACTIONPOSITIONAL0.031
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.32920.34649520.283412449X-RAY DIFFRACTION90
2.3292-2.35650.32410210.286813298X-RAY DIFFRACTION98
2.3565-2.38520.345510320.28613355X-RAY DIFFRACTION97
2.3852-2.41540.32710750.264713318X-RAY DIFFRACTION98
2.4154-2.44710.322410390.267313485X-RAY DIFFRACTION98
2.4471-2.48060.319110520.274413280X-RAY DIFFRACTION98
2.4806-2.51590.318810670.266813318X-RAY DIFFRACTION98
2.5159-2.55340.29789910.249913490X-RAY DIFFRACTION98
2.5534-2.59320.30139580.240313448X-RAY DIFFRACTION98
2.5932-2.63560.283210360.231213498X-RAY DIFFRACTION98
2.6356-2.6810.272710550.234113246X-RAY DIFFRACTION98
2.681-2.72960.296110370.239313340X-RAY DIFFRACTION97
2.7296-2.7820.282510000.224313522X-RAY DIFFRACTION98
2.782-2.83860.271810450.22213332X-RAY DIFFRACTION98
2.8386-2.90020.27459690.216313460X-RAY DIFFRACTION98
2.9002-2.96740.272210390.217913456X-RAY DIFFRACTION98
2.9674-3.04140.255410280.216313547X-RAY DIFFRACTION99
3.0414-3.12330.237510310.204113539X-RAY DIFFRACTION99
3.1233-3.21490.233710540.194513583X-RAY DIFFRACTION99
3.2149-3.31820.234710300.191613545X-RAY DIFFRACTION99
3.3182-3.43620.219310740.182813528X-RAY DIFFRACTION99
3.4362-3.5730.210910270.170213566X-RAY DIFFRACTION99
3.573-3.73460.19310080.165613603X-RAY DIFFRACTION99
3.7346-3.93010.190210720.167713576X-RAY DIFFRACTION99
3.9301-4.17430.1969470.167613689X-RAY DIFFRACTION99
4.1743-4.49320.16610610.151413599X-RAY DIFFRACTION99
4.4932-4.93920.162310580.144513579X-RAY DIFFRACTION99
4.9392-5.63980.18710040.169413706X-RAY DIFFRACTION100
5.6398-7.05320.225510860.202513746X-RAY DIFFRACTION100
7.0532-19.98510.18029670.172312838X-RAY DIFFRACTION92
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)
10.41840.3389-0.28760.2349-0.28270.3782-0.0182-0.0218-0.03590.0576-0.01690.04060.00020.059200.2747-0.0056-0.01930.2787-0.00770.2448-7.2691-0.679287.8853
20.25170.1339-0.1077-0.0280.0410.3344-0.00480.00380.1039-0.02420.0336-0.0666-0.03460.0554-00.2938-0.00960.00390.2980.030.313313.812114.831563.5638
30.419-0.0349-0.05910.99090.02550.02630.0672-0.04620.08810.1058-0.00920.1164-0.06350.028100.2582-0.02050.00330.215-0.02050.2319-5.324915.560485.9746
40.17980.0673-0.31910.4327-0.05360.54190.0595-0.0816-0.04460.0519-0.0929-0.08820.0460.0729-00.21650.0093-0.06560.29960.00880.279513.5124-13.264282.3971
50.1759-0.14280.28470.0873-0.27130.3346-0.06330.06360.0136-0.0505-0.0345-0.2791-0.06170.206900.3168-0.03180.04090.31010.04640.27319.0669.142155.1796
60.4727-0.0164-0.54190.7921-0.00470.83770.1497-0.14170.03950.1767-0.0823-0.0974-0.2460.146700.2877-0.0553-0.06830.3268-0.02010.281619.89221.849483.6629
70.28940.3608-0.04520.57210.06230.3726-0.0242-0.0191-0.0914-0.0643-0.003-0.13740.0087-0.0184-00.24590.01840.03240.3161-0.00810.351219.7587-24.220160.9533
80.0943-0.2520.17960.2978-0.40440.1126-0.02670.14460.0066-0.1273-0.0504-0.2089-0.05780.0837-00.4253-0.01920.03850.33350.05180.314915.44877.292544.6457
90.46720.1508-0.12020.24090.26811.001-0.0528-0.0209-0.0938-0.14280.079-0.2849-0.10470.159500.2762-0.00260.02990.3628-0.01480.42330.7415-11.650360.9455
100.085-0.06840.03730.645-0.12790.227-0.002-0.0175-0.0503-0.1424-0.0002-0.037-0.0279-0.0019-00.3673-0.03710.08290.3414-0.03670.27336.8138-25.045339.6309
11-0.108-0.2751-0.09480.42650.30430.1228-0.06130.0863-0.0472-0.1490.0818-0.1913-0.0142-0.024800.4454-0.03630.00060.34820.02860.27515.591610.635339.808
120.63370.04480.06810.28630.01170.2085-0.16120.0848-0.0296-0.29560.0985-0.1664-0.02590.007600.3932-0.06390.11210.3308-0.02520.306719.1346-15.106134.9934
130.58180.03130.43390.563400.3759-0.070.18590.0176-0.1120.02150.01420.02830.0303-00.385-0.0385-0.00370.35020.01330.2256-15.5982-15.307734.4482
140.19270.26630.10810.21870.1807-0.0664-0.10650.02340.0164-0.37550.0583-0.0543-0.1184-0.0826-00.424-0.0466-0.02340.36160.04780.3406-2.915116.614844.3512
151.4913-0.06860.60410.16920.25470.37-0.18860.55660.3504-0.26450.11360.0424-0.05330.132-00.4909-0.10820.00930.51360.0860.2837-6.1941-5.513425.1308
160.33850.3586-0.18620.52360.00520.4050.00520.08210.0823-0.1290.09050.13110.05830.0448-00.33260.0121-0.05740.3820.04510.2794-30.4527-2.225249.4567
170.32670.19760.27170.41120.243-0.0283-0.10110.19480.0626-0.16950.11440.0222-0.0628-0.019300.3287-0.025-0.00680.3390.04020.2777-3.745920.829254.9201
180.73780.0747-0.24620.26560.36250.6306-0.00470.18510.2484-0.23950.11030.1484-0.1734-0.012-00.4361-0.028-0.07380.38680.10850.3003-25.72649.889439.0623
190.65290.3184-0.22550.37150.04670.37380.03080.03930.0454-0.01620.02310.15-0.05640.0172-00.2340.0208-0.01080.23190.0110.2441-26.88214.292673.1594
200.6251-0.1219-0.21980.1520.20750.08-0.05910.00660.0979-0.09180.06640.00940.0962-0.018200.2511-0.0032-0.02210.28540.0110.25593.684920.067463.4438
210.4617-0.12610.2140.67270.05410.34910.04510.10450.23540.04630.03080.1782-0.2920.0209-00.36630.0131-0.00020.28420.06430.3528-25.502819.265866.0363
220.20540.2407-0.26570.358-0.16790.27270.067-0.0409-0.01980.1357-0.07390.0913-0.06450.01300.37090.03250.01220.25760.00680.25340.71270.8585173.0093
230.25660.0105-0.3543-0.1042-0.02710.41550.143-0.04670.09880.1689-0.01290.0344-0.16410.0227-00.24340.0184-0.0110.17580.02580.177162.110316.3584148.9085
240.36620.066-0.05350.8071-0.17080.10720.071-0.03190.04860.1242-0.04290.0731-0.0717-0.007700.37120.02010.03820.1886-0.00760.200242.775517.2377170.9682
250.17340.1053-0.33630.5658-0.11970.53180.0817-0.0499-0.04280.0937-0.1376-0.0898-0.03080.021800.2955-0.0025-0.08390.29080.0360.260661.4959-11.7497167.721
260.196-0.22010.10190.0987-0.41460.31330.0289-0.03180.04050.1429-0.0171-0.1091-0.1283-0.009100.31980.0418-0.03080.21540.02720.23767.391610.6719140.5889
270.3212-0.0334-0.39810.84960.15660.48180.1924-0.13650.02040.2557-0.1469-0.0898-0.26750.083700.388-0.0452-0.08850.28160.01360.241267.90943.57168.8966
280.21050.25280.08260.7325-0.0260.629-0.0062-0.0061-0.0857-0.0068-0.0083-0.1105-0.01070.025-00.20760.0318-0.03440.28410.02820.300267.9932-22.6692146.2709
290.0804-0.39430.10060.537-0.72970.00670.0106-0.00140.00890.062-0.0635-0.2203-0.0152-0.0017-00.28790.0593-0.03230.23780.03530.243363.88488.8078129.9456
300.1815-0.0829-0.16440.24650.30021.12160.0123-0.0319-0.04890.01720.0197-0.209-0.23940.16100.2589-0.0019-0.0510.29360.04170.342879.0082-10.1378146.3808
310.18580.3289-0.05450.92140.04640.4288-0.07070.0535-0.0794-0.10020.0482-0.0256-0.0126-0.0662-00.21850.0255-0.00280.26570.00970.211655.3314-23.5628124.8459
32-0.1474-0.1589-0.12380.4819-0.1811-0.0182-0.00040.04-0.04050.20450.0508-0.07530.0631-0.06800.28810.0649-0.0370.26970.00950.229654.147912.1581124.9928
330.38620.00270.02340.59240.10710.5056-0.11660.03190.0018-0.2410.0508-0.1188-0.04080.0227-00.24150.01050.02880.25030.01180.263567.693-13.6425120.3255
340.18710.0516-0.12211.1392-0.09750.1353-0.04240.0198-0.0126-0.03950.03750.10830.0588-0.075800.24890.0142-0.050.38810.01010.224933.0045-13.7481119.3838
35-0.07760.07210.06550.41590.14980.0757-0.02460.10260.0193-0.04970.10180.0006-0.0974-0.0701-00.3120.0402-0.02230.31780.01290.265145.571618.1597129.5188
360.2956-0.0225-0.39150.5549-0.0940.51040.0180.07820.0749-0.14580.0706-0.0207-0.0078-0.078200.28620.0205-0.01870.34960.01150.22642.602-3.6648110.1668
370.49040.31980.25890.4891-0.04520.190.02250.080.09130.02440.05730.13150.02410.006600.22320.10450.0020.36670.08170.254317.9317-0.6652134.3267
380.49190.17110.31970.28890.2881-0.032-0.08480.14280.0315-0.06210.10080.0601-0.0916-0.074200.24720.05510.00330.27440.06560.197944.623622.3401140.0555
390.94750.122-0.08830.30610.34130.6972-0.00880.26640.185-0.14440.13990.1555-0.1632-0.074600.33280.0776-0.01370.42760.11820.335322.544711.3252124.0329
400.36280.2278-0.29270.47190.00710.36450.0886-0.00220.060.10890.01430.1637-0.0974-0.083600.31540.0960.04690.29460.04940.30821.31865.8274158.0816
410.7073-0.0254-0.13610.04430.1737-0.03680.04260.13030.13940.12650.05750.1112-0.08-0.12100.25820.0372-0.01160.21630.03090.210951.968321.5439148.6336
420.75880.0410.11680.25930.09390.58350.10050.09830.2460.17160.01260.2356-0.3494-0.0037-00.38970.10880.07780.27130.07750.352722.742620.8058150.9401
430.1107-0.10630.00150.44540.04080.09880.00690.0160.0064-0.0595-0.0264-0.07970.0207-0.045700.2948-0.01790.02980.2421-0.00660.219927.2751109.933271.4846
440.1454-0.37360.15910.2142-0.38430.20950.07690.0264-0.0223-0.1252-0.0511-0.00070.01930.0686-00.25160.01290.01420.23390.02260.281441.354278.655681.3696
450.58430.06680.02820.4464-0.09970.37370.04160.0515-0.0846-0.2158-0.0235-0.10840.0051-0.0100.3929-0.00070.03670.3003-0.01270.287830.951397.510361.2781
460.0135-0.1308-0.02210.85930.05910.41670.04650.00910.08070.0514-0.033-0.0355-0.0569-0.0074-00.2389-0.0401-0.00180.3095-0.00850.274542.9898111.173190.7985
470.31890.25-0.07320.3395-0.0637-0.14180.0266-0.0316-0.0858-0.0614-0.0387-0.16710.02510.017700.3541-0.0048-0.02230.28290.02060.322242.531375.459792.3022
480.4216-0.1711-0.38120.41250.07560.89550.0111-0.02780.0755-0.08410.0024-0.10210.07390.109200.2791-0.0030.02090.32550.02240.292151.7483100.854881.0051
490.2966-0.1552-0.02530.79090.05780.5811-0.05750.01180.05690.10670.0189-0.00380.06660.062200.25390.0063-0.04050.35090.01040.267640.2884101.7506113.6912
500.02490.21960.12260.27720.24920.022-0.0316-0.0419-0.09220.00020.0678-0.18960.04680.051600.41190.00910.0090.3313-0.00750.338535.477169.502998.8392
510.13370.2907-0.01880.9303-0.27941.0827-0.0506-0.02140.0196-0.09360.0216-0.30490.2130.2261-00.22420.0446-0.03430.35270.00370.306852.400491.7672107.9229
520.2858-0.162-0.10630.41960.0977-0.0845-0.0414-0.0152-0.01020.13520.00130.0860.0827-0.018900.34930.03870.00220.35670.03040.27921.322388.5324122.7562
53-0.04690.08080.09960.1170.06180.236-0.052-0.0347-0.08160.080.05110.01190.14190.040200.34810.00020.04450.3065-0.00520.353425.34265.196696.0557
540.9753-0.2093-0.09060.1747-0.0130.1144-0.0568-0.0759-0.13670.18880.04090.08570.0465-0.0036-00.34730.0678-0.01040.2990.03110.294632.790676.573121.9157
550.4651-0.015-0.12180.33430.23750.6076-0.0477-0.0168-0.08450.09050.03160.128-0.0099-0.05200.2925-0.01290.05160.26450.02150.33420.20481.7404111.422
560.22540.1814-0.16130.1069-0.02850.2621-0.0484-0.02410.0284-0.01760.04230.02510.106-0.020800.2966-0.02140.02370.2481-0.0170.300519.789865.786186.1975
570.6549-0.00850.18120.4645-0.00680.5963-0.07370.0316-0.3280.20830.04270.12950.19680.0536-00.37730.01220.05770.26790.02260.41447.347566.9617112.8573
580.3949-0.1904-0.04010.4088-0.10250.149-0.01020.0449-0.0556-0.0136-0.01850.07770.0027-0.0481-00.2897-0.0451-0.00520.2804-0.0320.337-7.072386.373787.9977
590.27660.0648-0.0392-0.0151-0.02240.0448-0.12760.0403-0.25280.01670.01560.14210.1152-0.040700.30010.00440.02380.2391-0.0170.323523.020570.897176.5295
600.03050.039-0.14440.68790.0060.3589-0.04770.0137-0.07070.0872-0.01330.09390.0769-0.042-00.2447-0.0630.03460.221-0.03680.344-4.350469.982186.9353
610.2461-0.1073-0.10250.57780.17630.22060.01380.0078-0.047-0.1054-0.0615-0.02490.0251-0.0132-00.326-0.023-0.020.2932-0.02670.2645.013798.882670.1991
620.4471-0.19640.2849-0.0296-0.28920.26930.11750.1235-0.1757-0.2051-0.11980.1140.08690.0194-00.32740.00660.01270.2964-0.01060.341732.595776.598974.3855
630.68790.059-0.06520.41680.06330.2180.04310.11-0.1962-0.3079-0.10030.06150.0386-0.0679-00.3754-0.0244-0.02610.3135-0.06810.31276.005183.670663.9101
640.1305-0.0129-0.03480.3721-0.1570.10720.0734-0.01250.046-0.1089-0.0266-0.1023-0.02910.0144-00.364-0.01750.06730.3024-0.01820.295275.0433111.4632157.0998
650.1528-0.1441-0.05840.1672-0.32190.26510.0629-0.01930.0157-0.18170.0081-0.1115-0.00590.121800.23070.0217-0.0140.2871-0.00950.287789.036980.158167.2098
660.4527-0.05980.00480.35610.29390.55020.09990.0359-0.0209-0.305-0.0041-0.2148-0.07320.066100.4087-0.00470.07750.2992-0.02910.302878.848199.0095146.9422
670.5051-0.08880.09060.67660.05720.420.07690.0460.0505-0.10380.0391-0.1526-0.12420.0564-00.2027-0.0840.0680.3443-0.07810.35490.556112.6754176.6372
680.0897-0.0352-0.09370.2440.0429-0.0792-0.0454-0.1211-0.0174-0.12980.0945-0.10350.04340.136200.3219-0.0215-0.02960.3876-0.02790.408590.153577.0139178.1136
690.70270.57950.33460.5298-0.03590.97530.0490.1044-0.0589-0.13980.1234-0.34010.11710.313300.2666-0.02260.07960.421-0.09770.430999.3231102.4428166.8817
700.37620.0267-0.24120.77390.17770.2416-0.0235-0.09110.07740.09350.1-0.07290.04060.1273-00.1981-0.0051-0.06640.4731-0.05310.330987.6753103.269199.4393
71-0.07150.07920.07920.38820.0957-0.0348-0.0746-0.0793-0.0476-0.05860.2197-0.2159-0.02670.221200.3470.0291-0.00650.3912-0.03280.370683.013271.0392184.5768
720.3745-0.0452-0.02470.71050.00850.6789-0.0426-0.1078-0.03080.01240.1266-0.30110.17840.3195-00.24960.0362-0.03130.5463-0.08330.487499.76893.2697193.8236
730.0898-0.0112-0.23820.4640.31550.1753-0.0685-0.12470.00960.13790.04380.01330.08820.1022-00.26110.0543-0.04850.38770.03570.225568.636390.1242208.3652
74-0.10350.09580.03670.14160.24130.265-0.0819-0.0584-0.05460.1290.0461-0.00820.18950.037700.34210.06030.03960.32610.00990.334872.905166.7205181.7084
750.42450.0656-0.18490.4318-0.2011.0135-0.2193-0.1859-0.26440.25680.0605-0.00380.24320.3354-00.29560.1281-0.04480.44480.04970.349580.05678.1054207.6894
760.526-0.2282-0.02230.43530.19610.7996-0.0681-0.0225-0.09570.05080.01320.0757-0.00770.044300.23860.00460.03080.24780.01350.296447.597983.2957196.762
770.15840.0753-0.1260.26290.05690.1642-0.0985-0.0166-0.05730.02640.03570.01560.1319-0.008800.28750.02420.00120.2948-0.0040.293467.468667.3208171.749
780.2804-0.150.22090.6739-0.17510.8804-0.0871-0.0746-0.19660.21970.04910.12720.27790.168600.38350.06110.03550.3170.03150.385654.899368.4191198.1987
790.6751-0.1478-0.41510.42360.09070.44350.0330.0211-0.0326-0.0574-0.08320.1215-0.0060.00200.2464-0.0239-0.04260.2577-0.03490.2940.559987.8931173.2392
800.3192-0.0012-0.11480.0190.09990.1598-0.0492-0.0117-0.2051-0.0642-0.00650.10670.06410.005-00.22570.02460.00740.2289-0.00690.260170.8272.4455162.1193
81-0.00520.0048-0.13330.8475-0.02690.5131-0.0588-0.0372-0.09610.0735-0.01510.150.12540.007900.2106-0.01570.0070.1985-0.02630.294343.348671.5269172.1994
820.4415-0.1813-0.06180.56860.17530.17050.0704-0.0202-0.0263-0.2233-0.1195-0.0438-0.07450.0387-00.3270.0107-0.02230.264-0.02020.225552.8037100.4071155.5098
830.4437-0.16590.1419-0.0062-0.02820.21990.1040.0041-0.0349-0.3075-0.0206-0.09910.05980.0164-00.30750.01180.03170.2833-0.02510.35680.37978.1352160.0621
840.7742-0.0953-0.15320.59240.12820.42410.08440.0976-0.2104-0.2997-0.11510.06230.0247-0.0092-00.34510.0287-0.05550.2713-0.04930.259953.899885.1903149.2598
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:98)A1 - 98
2X-RAY DIFFRACTION2(chain A and resid 99:167)A99 - 167
3X-RAY DIFFRACTION3(chain A and resid 168:295)A168 - 295
4X-RAY DIFFRACTION4(chain B and resid 1:98)B1 - 98
5X-RAY DIFFRACTION5(chain B and resid 99:167)B99 - 167
6X-RAY DIFFRACTION6(chain B and resid 168:295)B168 - 295
7X-RAY DIFFRACTION7(chain C and resid 1:98)C1 - 98
8X-RAY DIFFRACTION8(chain C and resid 99:167)C99 - 167
9X-RAY DIFFRACTION9(chain C and resid 168:295)C168 - 295
10X-RAY DIFFRACTION10(chain D and resid 1:98)D1 - 98
11X-RAY DIFFRACTION11(chain D and resid 99:167)D99 - 167
12X-RAY DIFFRACTION12(chain D and resid 168:295)D168 - 295
13X-RAY DIFFRACTION13(chain E and resid 1:98)E1 - 98
14X-RAY DIFFRACTION14(chain E and resid 99:167)E99 - 167
15X-RAY DIFFRACTION15(chain E and resid 168:295)E168 - 295
16X-RAY DIFFRACTION16(chain F and resid 1:98)F1 - 98
17X-RAY DIFFRACTION17(chain F and resid 99:167)F99 - 167
18X-RAY DIFFRACTION18(chain F and resid 168:295)F168 - 295
19X-RAY DIFFRACTION19(chain G and resid 1:98)G1 - 98
20X-RAY DIFFRACTION20(chain G and resid 99:167)G99 - 167
21X-RAY DIFFRACTION21(chain G and resid 168:295)G168 - 295
22X-RAY DIFFRACTION22(chain H and resid 1:98)H1 - 98
23X-RAY DIFFRACTION23(chain H and resid 99:167)H99 - 167
24X-RAY DIFFRACTION24(chain H and resid 168:295)H168 - 295
25X-RAY DIFFRACTION25(chain I and resid 1:98)I1 - 98
26X-RAY DIFFRACTION26(chain I and resid 99:167)I99 - 167
27X-RAY DIFFRACTION27(chain I and resid 168:295)I168 - 295
28X-RAY DIFFRACTION28(chain J and resid 1:98)J1 - 98
29X-RAY DIFFRACTION29(chain J and resid 99:167)J99 - 167
30X-RAY DIFFRACTION30(chain J and resid 168:295)J168 - 295
31X-RAY DIFFRACTION31(chain K and resid 1:98)K1 - 98
32X-RAY DIFFRACTION32(chain K and resid 99:167)K99 - 167
33X-RAY DIFFRACTION33(chain K and resid 168:295)K168 - 295
34X-RAY DIFFRACTION34(chain L and resid 1:98)L1 - 98
35X-RAY DIFFRACTION35(chain L and resid 99:167)L99 - 167
36X-RAY DIFFRACTION36(chain L and resid 168:295)L168 - 295
37X-RAY DIFFRACTION37(chain M and resid 1:98)M1 - 98
38X-RAY DIFFRACTION38(chain M and resid 99:167)M99 - 167
39X-RAY DIFFRACTION39(chain M and resid 168:295)M168 - 295
40X-RAY DIFFRACTION40(chain N and resid 1:98)N1 - 98
41X-RAY DIFFRACTION41(chain N and resid 99:167)N99 - 167
42X-RAY DIFFRACTION42(chain N and resid 168:295)N168 - 295
43X-RAY DIFFRACTION43(chain O and resid 1:98)O1 - 98
44X-RAY DIFFRACTION44(chain O and resid 99:167)O99 - 167
45X-RAY DIFFRACTION45(chain O and resid 168:295)O168 - 295
46X-RAY DIFFRACTION46(chain P and resid 1:98)P1 - 98
47X-RAY DIFFRACTION47(chain P and resid 99:167)P99 - 167
48X-RAY DIFFRACTION48(chain P and resid 168:295)P168 - 295
49X-RAY DIFFRACTION49(chain Q and resid 1:98)Q1 - 98
50X-RAY DIFFRACTION50(chain Q and resid 99:167)Q99 - 167
51X-RAY DIFFRACTION51(chain Q and resid 168:295)Q168 - 295
52X-RAY DIFFRACTION52(chain R and resid 1:98)R1 - 98
53X-RAY DIFFRACTION53(chain R and resid 99:167)R99 - 167
54X-RAY DIFFRACTION54(chain R and resid 168:295)R168 - 295
55X-RAY DIFFRACTION55(chain S and resid 1:98)S1 - 98
56X-RAY DIFFRACTION56(chain S and resid 99:167)S99 - 167
57X-RAY DIFFRACTION57(chain S and resid 168:295)S168 - 295
58X-RAY DIFFRACTION58(chain T and resid 1:98)T1 - 98
59X-RAY DIFFRACTION59(chain T and resid 99:167)T99 - 167
60X-RAY DIFFRACTION60(chain T and resid 168:295)T168 - 295
61X-RAY DIFFRACTION61(chain U and resid 1:98)U1 - 98
62X-RAY DIFFRACTION62(chain U and resid 99:167)U99 - 167
63X-RAY DIFFRACTION63(chain U and resid 168:295)U168 - 295
64X-RAY DIFFRACTION64(chain V and resid 1:98)V1 - 98
65X-RAY DIFFRACTION65(chain V and resid 99:167)V99 - 167
66X-RAY DIFFRACTION66(chain V and resid 168:295)V168 - 295
67X-RAY DIFFRACTION67(chain W and resid 1:98)W1 - 98
68X-RAY DIFFRACTION68(chain W and resid 99:167)W99 - 167
69X-RAY DIFFRACTION69(chain W and resid 168:295)W168 - 295
70X-RAY DIFFRACTION70(chain X and resid 1:98)X1 - 98
71X-RAY DIFFRACTION71(chain X and resid 99:167)X99 - 167
72X-RAY DIFFRACTION72(chain X and resid 168:295)X168 - 295
73X-RAY DIFFRACTION73(chain Y and resid 1:98)Y1 - 98
74X-RAY DIFFRACTION74(chain Y and resid 99:167)Y99 - 167
75X-RAY DIFFRACTION75(chain Y and resid 168:295)Y168 - 295
76X-RAY DIFFRACTION76(chain Z and resid 1:98)Z1 - 98
77X-RAY DIFFRACTION77(chain Z and resid 99:167)Z99 - 167
78X-RAY DIFFRACTION78(chain Z and resid 168:295)Z168 - 295
79X-RAY DIFFRACTION79(chain a and resid 1:98)a1 - 98
80X-RAY DIFFRACTION80(chain a and resid 99:167)a99 - 167
81X-RAY DIFFRACTION81(chain a and resid 168:295)a168 - 295
82X-RAY DIFFRACTION82(chain b and resid 1:98)b1 - 98
83X-RAY DIFFRACTION83(chain b and resid 99:167)b99 - 167
84X-RAY DIFFRACTION84(chain b and resid 168:295)b168 - 295

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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