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- PDB-3v5i: The crystal structure of the mutant ClpP S98A (Staphylococcus aureus) -

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基本情報

登録情報
データベース: PDB / ID: 3v5i
タイトルThe crystal structure of the mutant ClpP S98A (Staphylococcus aureus)
要素ATP-dependent Clp protease proteolytic subunit
キーワードHYDROLASE / whole proteome
機能・相同性
機能・相同性情報


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / cytoplasm
類似検索 - 分子機能
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
ATP-dependent Clp protease proteolytic subunit
類似検索 - 構成要素
生物種Staphylococcus aureus subsp. 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: 2.8 Å
データ登録者List, A. / Gersch, M. / Groll, M. / Sieber, S.
引用ジャーナル: J.Biol.Chem. / 年: 2012
タイトル: Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein.
著者: Gersch, M. / List, A. / Groll, M. / Sieber, S.A.
履歴
登録2011年12月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年2月8日Provider: repository / タイプ: Initial release
改定 1.12012年7月11日Group: Database references
改定 1.22017年11月8日Group: Refinement description / カテゴリ: software / Item: _software.name
改定 1.32023年9月13日Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit


分子量 (理論値)分子数
合計 (水以外)631,75528
ポリマ－631,75528
非ポリマー00
水12,196677
1
A: ATP-dependent Clp protease proteolytic subunit
B: ATP-dependent Clp protease proteolytic subunit
C: ATP-dependent Clp protease proteolytic subunit
D: ATP-dependent Clp protease proteolytic subunit
E: ATP-dependent Clp protease proteolytic subunit
F: ATP-dependent Clp protease proteolytic subunit
G: ATP-dependent Clp protease proteolytic subunit
H: ATP-dependent Clp protease proteolytic subunit
I: ATP-dependent Clp protease proteolytic subunit
J: ATP-dependent Clp protease proteolytic subunit
K: ATP-dependent Clp protease proteolytic subunit
L: ATP-dependent Clp protease proteolytic subunit
M: ATP-dependent Clp protease proteolytic subunit
N: ATP-dependent Clp protease proteolytic subunit


分子量 (理論値)分子数
合計 (水以外)315,87814
ポリマ－315,87814
非ポリマー00
水25214
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56200 Å2
ΔGint-203 kcal/mol
Surface area91020 Å2
手法PISA
2
O: ATP-dependent Clp protease proteolytic subunit
P: ATP-dependent Clp protease proteolytic subunit
Q: ATP-dependent Clp protease proteolytic subunit
R: ATP-dependent Clp protease proteolytic subunit
S: ATP-dependent Clp protease proteolytic subunit
T: ATP-dependent Clp protease proteolytic subunit
U: ATP-dependent Clp protease proteolytic subunit
V: ATP-dependent Clp protease proteolytic subunit
W: ATP-dependent Clp protease proteolytic subunit
X: ATP-dependent Clp protease proteolytic subunit
Y: ATP-dependent Clp protease proteolytic subunit
Z: ATP-dependent Clp protease proteolytic subunit
a: ATP-dependent Clp protease proteolytic subunit
b: ATP-dependent Clp protease proteolytic subunit


分子量 (理論値)分子数
合計 (水以外)315,87814
ポリマ－315,87814
非ポリマー00
水25214
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56290 Å2
ΔGint-204 kcal/mol
Surface area90990 Å2
手法PISA
単位格子
Length a, b, c (Å)97.550, 109.730, 171.410
Angle α, β, γ (deg.)73.10, 78.68, 71.46
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(1), (1), (1)
2given(0.61284, -0.278482, 0.73951), (0.239231, 0.957311, 0.162248), (-0.753124, 0.077482, 0.6533)14.22802, 12.16527, -32.80698
3given(-0.229332, -0.385553, 0.893732), (0.253107, 0.862994, 0.43724), (-0.939864, 0.326482, -0.100326)-4.793, 21.99991, -63.67568
4given(-0.894401, -0.238647, 0.378277), (0.047437, 0.79037, 0.61079), (-0.444742, 0.564236, -0.695588)-41.65689, 21.89986, -69.39188
5given(-0.892843, 0.055409, -0.446946), (-0.233287, 0.791987, 0.564211), (0.385238, 0.608019, -0.694194)-68.60879, 12.12808, -45.16394
6given(-0.197812, 0.257766, -0.945742), (-0.38596, 0.866389, 0.316866), (0.901058, 0.427699, -0.071895)-64.7825, -0.7409, -9.82493
7given(0.631455, 0.231255, -0.740126), (-0.2699, 0.960355, 0.069795), (0.726924, 0.155687, 0.668837)-34.80478, -5.32518, 9.45954
8given(0.694918, -0.151567, 0.702934), (-0.148197, -0.986736, -0.066254), (0.703652, -0.058131, -0.708163)14.73225, 3.57076, -33.04937
9given(0.988304, 0.137923, -0.065049), (0.137838, -0.990438, -0.005824), (-0.06523, -0.00321, -0.997865)-2.20293, 13.77246, -64.96279
10given(0.547341, 0.355716, -0.757551), (0.354705, -0.918456, -0.174992), (-0.758025, -0.172926, -0.628883)-38.76703, 14.38516, -72.65258
11given(-0.314699, 0.342526, -0.885235), (0.347366, -0.826365, -0.443235), (-0.883347, -0.446986, 0.141074)-67.24151, 5.09557, -50.14194
12given(-0.941938, 0.118455, -0.314198), (0.108638, -0.77788, -0.618951), (-0.317726, -0.617147, 0.719847)-65.68723, -7.62028, -14.83545
13given(-0.859687, -0.157411, 0.485964), (-0.163248, -0.816788, -0.553361), (0.484034, -0.555049, 0.676485)-37.36406, -12.89384, 6.20315
14given(-0.139601, -0.283156, 0.94886), (-0.279438, -0.90803, -0.312084), (0.949961, -0.308714, 0.047637)-1.55738, -8.22059, -1.13756
15given(-0.205489, -0.343942, 0.91623), (-0.525158, -0.75125, -0.399791), (0.825823, -0.563319, -0.02625)70.91398, -53.72794, 48.82568
16given(0.621286, -0.421777, 0.660384), (-0.423086, -0.889932, -0.170349), (0.659547, -0.173564, -0.731351)108.55198, -15.27111, -56.91235
17given(0.986522, -0.143844, -0.077991), (-0.152735, -0.980515, -0.123539), (-0.058701, 0.133786, -0.98927)43.9688, 14.05837, -152.06322
18given(0.617568, 0.279246, -0.735276), (0.081288, -0.952505, -0.293472), (-0.782306, 0.12147, -0.610936)-73.49903, 12.04142, -164.94968
19given(-0.203148, 0.524664, -0.826716), (0.101834, -0.828421, -0.55077), (-0.973838, -0.196076, 0.114864)-155.96939, -19.79066, -86.67632
20given(-0.869789, 0.409804, -0.274822), (-0.106128, -0.69931, -0.706897), (-0.481875, -0.585685, 0.651744)-140.68433, -57.97894, 25.60225
21given(-0.866108, 0.026013, 0.499179), (-0.386712, -0.667629, -0.63618), (0.316717, -0.74404, 0.588299)-39.76838, -72.5549, 85.27555
22given(0.512633, -0.527414, 0.677526), (0.496931, 0.825755, 0.266811), (-0.70019, 0.199907, 0.685398)106.12038, 44.11281, -15.31763
23given(-0.32634, -0.41212, 0.850681), (0.487097, 0.697944, 0.524987), (-0.810086, 0.585688, -0.027025)56.7673, 76.95535, -117.80689
24given(-0.927272, -0.018289, 0.373943), (0.268643, 0.663172, 0.698594), (-0.260765, 0.748243, -0.610028)-57.25275, 80.79517, -146.82852
25given(-0.842951, 0.354214, -0.404927), (-0.000278, 0.752379, 0.65873), (0.53799, 0.55539, -0.634121)-151.4467, 52.56436, -81.1407
26given(-0.126959, 0.420715, -0.898265), (-0.116204, 0.893049, 0.434696), (0.985078, 0.15957, -0.064492)-154.03682, 13.43832, 31.272
27given(0.667954, 0.133643, -0.732104), (0.016343, 0.980872, 0.193966), (0.744023, -0.141526, 0.652993)-64.40492, -6.52636, 103.99892
28given(0.95813, -0.284952, -0.02811), (0.286269, 0.951187, 0.115299), (-0.006117, -0.118518, 0.992933)52.08113, 6.26383, 84.05774

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要素

#1: タンパク質 ...
ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp


分子量: 22562.680 Da / 分子数: 28 / 変異: S98A / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus subsp. aureus (黄色ブドウ球菌)
株: NCTC 8325 / 遺伝子: clpP, SAOUHSC_00790 / プラスミド: pET301 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q2G036, endopeptidase Clp
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 677 / 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: 2.62 Å3/Da / 溶媒含有率: 53.01 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.18 M Magnesium acetate, 0.1 M Sodium cacodylate, 12% MPD, pH 7.0, VAPOR DIFFUSION, HANGING 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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2011年11月5日
放射モノクロメーター: double-crystal fixed-exit monochromator
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: 2.8→25 Å / Num. all: 157772 / Num. obs: 150830 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 5.55
反射 シェル解像度: 2.8→2.9 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 1.67 / % possible all: 96.5

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解析

ソフトウェア
名称バージョン分類
RemDAqデータ収集
REFMAC5.6.0119精密化
XDSデータ削減
XSCALEデータスケーリング
REFMAC5.6.0119位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3QWD

3qwd


解像度: 2.8→24.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 32.93 / SU ML: 0.304 / 交差検証法: THROUGHOUT / ESU R Free: 0.371 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor反射数%反射Selection details
Rfree0.24151 7542 5 %RANDOM
Rwork0.21603 ---
obs0.2173 143288 95.62 %-
all-150830 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 86.52 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å2-1.67 Å23.05 Å2
2---1.84 Å20.41 Å2
3----2.96 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→24.8 Å
タンパク質核酸リガンド溶媒全体
原子数39788 0 0 677 40465
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01940292
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.97454376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34455096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6825.3851820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.237157392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.79615224
X-RAY DIFFRACTIONr_chiral_restr0.0950.26328
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02129820
LS精密化 シェル解像度: 2.8→2.87 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.357 544 -
Rwork0.349 10337 -
obs--96.57 %
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)
16.1222-17.40752.47951.1887-7.57161.2167-0.6714-0.44060.20950.5710.5998-1.43170.19570.07520.07161.28020.11590.31291.1052-0.15961.3624-30.6601-29.2103-56.2207
21.91950.5631-0.08032.8708-0.60512.3002-0.0960.226-0.1765-0.29090.1364-0.29850.1910.0814-0.04041.0072-0.04780.24170.8319-0.14370.9563-20.0001-14.3165-66.6817
35.31374.0075.05173.81883.95124.8422-0.0507-0.36530.0699-0.0398-0.0047-0.2840.0658-0.29460.05540.9872-0.07580.18530.9163-0.07220.9506-16.35596.7602-60.6799
42.50870.00831.03052.85610.25733.3036-0.12420.71270.1857-0.46540.143-0.3784-0.07780.1754-0.01881.0395-0.07880.28240.992-0.04780.9231-19.42014.1008-73.8097
534.259417.476423.554276.7815-14.219326.3648-1.52482.0895-2.2223-2.76622.3804-2.1484-0.30170.8943-0.85561.742-0.06610.4681.399-0.49971.1135-35.3323-12.4074-79.2478
628.112-5.5723-1.02391.11690.2010.0388-0.6064-2.0783-1.3760.1030.52530.11890.06290.04930.08112.76370.75540.15241.9081-0.48942.3815-20.8623-29.5837-55.8081
756.96626.3778-1.10924.6231-3.37958.41562.4503-2.2999-3.00680.6246-1.1160.27873.3908-0.1285-1.33433.0384-0.6148-0.09051.0464-0.10841.2424-15.6134-26.2472-54.9783
85.30580.10781.1844.16130.02454.2456-0.01010.077-0.3692-0.16580.0847-0.23030.25020.3646-0.07471.00580.04490.22640.8409-0.03841.1449-4.3259-23.1523-50.3617
90.5490.53950.36030.68140.63941.7451-0.18980.0632-0.1108-0.00720.1451-0.37410.09810.36320.04471.00740.07620.1540.9834-0.05531.23683.7805-5.9017-49.6927
1029.66785.23416.51782.0533.883210.36331.16462.412-2.1193-0.10261.0297-1.54730.98581.6477-2.19431.3781-0.11430.39151.2898-0.36491.62243.274-9.5777-66.1027
117.47881.64352.06860.5932-1.179415.2549-0.43340.8749-1.1867-0.37710.3411-0.0692.1167-0.34090.09231.30480.12260.1271.0303-0.10241.5104-12.2404-31.2236-44.419
121.945-4.7761-1.476813.4744.5745.9675-0.11460.0147-0.0309-0.407-0.0802-0.1827-0.2752-0.04890.19480.98620.118-0.00230.86710.02251.2381-8.4215-24.2897-31.6999
131.7829-0.0850.46281.95650.38332.7061-0.03310.1312-0.4683-0.2311-0.0449-0.66960.30230.27680.0780.9460.16690.04810.92760.00811.3466-0.668-26.3908-27.9681
141.8059-1.1427-2.29421.80292.94134.99760.08390.0077-0.1661-0.11780.0181-0.2131-0.21940.1433-0.1020.88910.1304-0.0370.96390.09481.1999-2.6217-9.5263-14.1497
152.0027-0.14210.62916.0221.5275.0866-0.07010.0791-0.226-0.46040.1205-0.37360.2150.7757-0.05030.85930.11050.01281.11790.01211.407111.2593-14.1183-25.6427
167.22851.595-6.067210.8112-1.89965.153-0.64530.2621-0.9577-1.7742-0.05580.41250.7168-0.05310.70111.3080.2907-0.11561.026-0.06221.3747-18.2665-36.5092-31.5465
172.76140.08710.31582.15931.2062.007-0.0748-0.1158-0.35520.00350.0452-0.47610.33140.31160.02970.95990.1317-0.06960.78930.08231.0565-21.922-31.3374-14.3536
188.149-4.285-0.30333.95820.22611.06930.1071-0.2995-0.19570.1294-0.004-0.24580.10590.1694-0.10310.84190.0234-0.16840.79710.03050.8718-28.103-16.8766-0.9162
197.3468-3.9019-5.504811.33094.65424.4586-0.4578-0.8342-0.0460.50710.5343-0.77510.46820.6254-0.07650.88540.0857-0.22061.06680.16051.038-12.8144-20.8093-1.1468
201.3098-5.2863.066221.4403-12.36357.17961.2970.84340.4645-2.7241-2.8654-1.49422.05781.99241.56845.44811.44771.87174.526-0.04853.0278-2.8662-34.176-11.6635
2110.5659-3.2662-3.11511.02540.97530.9325-0.37470.0661-1.03660.10580.0790.24040.13720.09350.29571.30020.10890.04760.931-0.00941.1349-32.3714-37.7993-29.8392
224.453-0.4650.11713.34921.28983.7489-0.12420.1089-0.3125-0.03330.0607-0.2570.39450.30970.06350.81110.00670.01680.67660.01680.7964-44.6463-30.2981-24.7051
231.8613-2.0644-0.163.57090.27420.5366-0.0429-0.096-0.17460.1461-0.05-0.01580.1152-0.01240.09280.805-0.0301-0.02290.69070.03960.7419-50.6715-21.5887-16.2818
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342.16543.6653-1.848110.10820.88835.9331-0.58360.31810.3084-1.09460.45010.9481-0.0018-0.30080.13350.89340.0083-0.12260.9479-0.03920.7666-58.4305-2.6113-61.8064
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360.4806-1.09811.50223.5075-4.85749.61740.07910.27930.35260.0229-0.32620.1028-1.6480.61780.24711.2312-0.02360.04210.8950.13921.382-44.371538.3673-9.3148
372.84741.18640.48594.88870.02173.6692-0.0078-0.11440.21230.16530.1106-0.0921-0.35290.0434-0.10280.7456-0.0019-0.02820.71-0.02720.6726-43.32224.79740.9906
384.6387-3.94250.81655.1013-0.56340.17090.1844-0.00090.1693-0.1168-0.0957-0.3840.08580.0115-0.08870.80150.0092-0.03770.78190.01340.7214-44.80158.1750.0614
396.67483.0579-3.4081.74920.08569.59110.5571-1.0827-0.34810.3229-0.5789-0.18920.0574-0.09660.02180.86930.0077-0.08010.91080.02860.7771-49.7427.22869.7947
407.6751-6.11151.797211.4594-1.02994.78380.0427-0.5159-0.17140.66870.00161.1804-0.371-0.2846-0.04430.8068-0.06920.0720.8566-0.03210.7593-59.140311.86110.3439
4125.61054.3598-1.21748.464-14.510326.57721.3613-1.11323.79012.1401-0.86240.7015-3.44920.734-0.49891.6427-0.20580.18051.4987-0.29121.5028-35.73639.424-6.9117
4211.18172.65532.13432.01533.48167.18890.32570.52820.4292-0.0226-0.45520.0011-0.2398-0.68430.12950.9538-0.0201-0.07050.89320.13690.7216-26.561529.265-3.2235
432.39180.675-1.121.6231-1.30322.51480.2016-0.38130.05190.3677-0.0496-0.2724-0.22540.1724-0.1520.8454-0.0184-0.13120.8199-0.03210.8042-20.885824.06075.2599
444.1579-2.8002-5.52633.07023.0997.7764-0.0999-0.0768-0.24190.0142-0.0827-0.13720.17130.24180.18260.84560.0288-0.20140.86260.07241.0392-10.62054.5679-2.4654
453.6254-0.3661.54287.5390.71624.1854-0.1433-0.4579-0.24490.71660.0937-0.0728-0.07430.25770.04960.9397-0.0706-0.1410.90150.11310.7779-22.94249.176912.8203
4617.62833.6455-5.84461.40120.25245.41660.2218-0.40770.9209-0.3014-0.21180.3093-1.1284-0.4569-0.011.21540.0442-0.17920.8789-0.07490.923-18.34139.2542-8.5947
471.9849-0.136-0.2732.5509-1.03083.29830.0034-0.14450.00250.16360.0235-0.3331-0.24520.164-0.02690.8377-0.0547-0.10.8684-0.03040.9623-3.290930.5691-12.842
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5011.6416-16.7596-18.461833.40147.77567.87940.7879-0.77171.31340.26981.275-1.6374-3.18510.9617-2.0631.1738-0.2498-0.24081.4069-0.29841.4863-2.610826.98066.2424
512.8713-0.9476-0.60860.74970.07197.02970.0087-0.2460.07330.1541-0.04910.0039-0.27480.00030.04040.8576-0.0882-0.04060.78350.00790.8926-14.178440.3772-27.9704
522.65320.5927-0.76920.2187-0.22991.546-0.00470.04940.1657-0.06990.0472-0.2401-0.17860.418-0.04250.9023-0.12570.0430.8229-0.04081.0077-3.632639.2956-36.5574
535.32781.99043.01592.96452.94453.20150.1090.0010.0048-0.1958-0.0425-0.1435-0.0721-0.0695-0.06660.9649-0.09860.11870.8852-0.03570.985-7.003420.8543-51.8917
5413.5533-4.3563-2.97357.16330.23999.6299-0.39630.9343-0.0497-0.22730.1186-0.5375-0.03110.63850.27770.9053-0.13150.05920.99620.01281.01976.406831.5249-49.2092
552.93711.40940.06177.11222.83878.2004-0.076-0.2170.32150.00080.0959-0.6861-0.31290.5901-0.01990.7714-0.04170.01281.03340.01451.24118.5528.5534-36.3935
5633.217210.1111-36.45273.0806-11.10240.03032.2146-3.21992.37590.454-0.36060.7242-1.86153.3805-1.8542.69910.3752-1.52271.9189-0.27283.2387-20.024545.602-26.959
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6113.78559.75950.17257.120.10626.94420.1907-0.53460.57110.3024-0.1816-0.012-1.07920.1409-0.0091.08790.0082-0.16630.774-0.10061.0728-35.672346.5669-31.6815
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631.79682.01330.79452.6201-0.00162.702-0.15580.21630.1224-0.20290.16870.1368-0.26210.0075-0.01290.93010.0821-0.0960.7410.05880.7304-51.319934.1105-46.1384
641.16131.1242-0.95716.1785-2.92464.0873-0.10070.17360.1063-0.14920.06160.0593-0.2228-0.22050.03910.77770.0598-0.11630.88040.00760.732-60.56619.6502-48.7057
6510.64241.49450.98075.91152.57364.7203-0.46590.78230.8647-0.73670.25250.4792-0.92630.15020.21351.07050.039-0.09030.89130.1010.7171-48.204136.8023-58.3197
668.73225.3831-7.1247.4144-3.12686.240.5602-0.39841.39780.19830.693-0.075-0.60770.6669-1.25321.14030.0514-0.21310.8769-0.0891.2677-46.807442.9173-22.4936
671.82190.640.25231.9073-0.27641.4983-0.0050.04890.22380.1260.00410.2011-0.2786-0.02180.00090.83380.0918-0.03550.7349-0.01920.7288-59.235927.8981-20.049
686.6466-5.87023.117910.9388-4.15583.148-0.0054-0.33010.05820.31770.23480.3803-0.0741-0.4241-0.22940.7360.0419-0.00260.8435-0.02090.6922-65.14788.8491-16.3195
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7073.850867.4554-2.116462.4164-4.792110.31084.1330.4417.91415.0760.04468.2411-4.11830.1382-4.17762.74230.50991.4680.89070.23912.8476-68.33637.4851-34.4529
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723.99960.18550.26442.9091-0.41123.84960.11060.12540.45860.35760.18890.0627-0.487-0.0409-0.29940.80940.16150.03670.92510.08210.9681-93.506768.244-95.1818
730.82321.2203-0.31584.1757-0.70460.4716-0.02360.09880.24090.21990.26130.6737-0.068-0.4108-0.23770.75510.17660.0141.10490.13221.1354-105.466656.5999-97.8819
745.35232.912-1.01688.4561-3.5412.2753-0.18590.48430.37220.05310.31211.3115-0.1107-0.4655-0.12620.72430.2333-0.07211.33870.20951.3247-113.442558.6285-107.5117
7529.66164.788321.87880.79763.514416.1529-0.9919-0.52942.3161-0.0032-0.36850.6053-0.6673-0.29791.36041.560.14620.78391.5904-0.07642.9055-105.652477.6706-110.4796
769.20950.6074-4.9558.2266-7.74499.39120.0538-0.41171.33431.1756-0.088-0.7496-1.0990.33520.03421.15750.0866-0.09010.9627-0.0011.1241-81.309969.6164-88.887
772.79691.71460.83445.15520.31742.2342-0.0202-0.03850.35740.5380.09050.1468-0.38680.1506-0.07030.99630.14170.04190.86010.01360.7636-84.341655.3999-77.38
782.9064-2.89580.94438.8114-0.36610.60740.1161-0.0944-0.0742-0.1815-0.02930.5005-0.0413-0.3287-0.08680.82020.12990.13660.9770.07930.8935-95.374647.1943-80.883
790.90310.0835-0.5263.1790.07581.5958-0.2012-0.2665-0.05730.70730.26390.4759-0.0088-0.3118-0.06270.92130.11170.11331.01360.06530.8789-94.123734.6011-76.9029
804.5808-4.75425.48977.323-11.288719.799-0.7281-0.82740.53161.53140.76-0.0773-2.3394-0.6926-0.03191.41280.13050.67151.1321-0.18221.6803-104.480754.6074-76.468
8111.1313-5.10546.21082.4248-3.24286.29470.20830.52482.27970.0509-0.3528-0.8385-0.9125-0.22370.14451.59350.04550.19371.10440.0431.2485-70.402962.6245-80.3081
823.7923-1.7732-1.8334.61810.08915.97750.0647-0.14210.29690.33080.1745-0.0782-0.59210.3843-0.23921.0116-0.0277-0.07040.92650.00360.8227-61.728952.2016-78.3626
832.3128-1.3643-1.70821.9921.30724.18490.0253-0.25380.00360.45620.0814-0.1928-0.16730.4906-0.10670.98330.0056-0.10770.89660.04090.7222-65.350943.2438-73.7273
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8519.5577-21.69384.07133.27990.48473.972-1.575-2.43480.94473.15032.0847-1.22410.2984-0.3852-0.50971.4283-0.08270.15351.5032-0.29341.0221-74.005940.9843-63.7468
868.5613-3.44221.15586.1514-7.701311.15910.1871-1.2530.32321.76710.0906-0.0496-2.92440.313-0.27762.0911-0.29880.32271.5588-0.08771.2785-62.292765.4991-85.5238
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890.79660.38550.44211.90161.87132.0444-0.0703-0.1636-0.15190.13830.1515-0.4224-0.04540.4539-0.08120.7596-0.0022-0.15361.2920.08411.1873-39.563633.4041-97.9303
900.7286-3.5512.938248.468829.113974.0870.0948-0.1381-0.27640.91685.3541-0.68690.4326.2804-5.44881.10630.1466-0.57552.6472-0.482.1785-45.433344.3961-73.2356
910.37081.38021.942147.892210.56510.626-0.29130.0440.06630.66680.36140.6349-1.6390.266-0.07011.1826-0.04910.10071.3201-0.06221.3118-56.391668.0523-94.6477
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972.3476-1.96480.25632.89592.13264.8661-0.09440.03630.23620.1110.10530.0765-0.29070.1412-0.01090.88590.00470.11530.92190.03180.9808-67.995972.3523-123.1467
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10120.0433-2.2543.55282.6543-2.44052.378-0.0604-1.29751.11971.1666-0.2331-0.3244-1.00460.17710.29351.22460.01020.09381.12620.01561.1816-73.315677.9349-108.7095
1021.33060.6367-0.30862.06390.57634.26080.02810.03930.2748-0.23040.14020.2248-0.5083-0.103-0.16830.85690.146-0.03290.97430.13981.0125-88.661874.1069-117.9021
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1041.834-2.54830.96688.2271-1.29690.51340.04640.02980.09160.1579-0.06460.4617-0.0058-0.02680.01820.9740.1086-0.12541.26980.24011.1974-102.583364.0927-128.9125
1059.10380.83660.14076.5693-4.81113.715-0.39240.43110.7182-0.54240.74720.66060.0806-0.2387-0.35471.309-0.0497-0.0841.32640.18730.9861-86.7674.4175-135.0377
10632.7372-0.45519.87541.57333.237510.40040.69750.6561-2.55760.3612-0.57110.50631.1231-1.0524-0.12641.3405-0.1452-0.01850.99740.00241.2394-75.33743.9619-140.2295
1071.75110.52180.30834.69271.00733.4161-0.15440.0408-0.2143-0.30420.1685-0.00830.3534-0.0481-0.01420.9683-0.01950.0960.9013-0.09680.8579-59.49037.0508-134.1844
1081.55160.43251.42260.21620.68483.8599-0.21770.0240.1133-0.26040.1043-0.12960.01020.2850.11341.0984-0.05660.22480.9553-0.06420.9706-52.602514.3851-138.3954
1091.7542-0.1293-2.38421.21493.105510.8645-0.161-0.0537-0.169-0.13590.0218-0.26910.17750.36410.13910.85530.11680.08031.0168-0.04561.1215-42.534620.7206-123.4916
1106.2561-1.33512.78762.72930.40844.8572-0.25790.3841-0.1335-0.48340.2698-0.26310.29540.4282-0.01191.0754-0.08420.21740.9832-0.020.9109-47.88222.7491-143.4529
1117.7333-1.9033-0.11621.63063.268210.4516-0.2369-0.429-1.47640.18630.09310.60561.0714-1.14120.14381.6054-0.25050.0261.26810.01971.4182-73.0461-1.9827-131.7838
1123.2194-1.30021.64055.5598-0.24373.462-0.11810.0836-0.1576-0.40910.1206-0.29620.81540.1534-0.00251.07060.01110.16410.981-0.05740.9855-65.2165-3.9703-117.8913
1132.5132-0.3306-1.01230.50690.77234.4896-0.2159-0.0695-0.1826-0.10540.1032-0.18880.28540.24130.11270.86290.12080.07810.90580.00521.0121-55.43012.9188-110.9929
1140.7998-1.1978-0.62723.21581.72072.8078-0.2953-0.1474-0.38510.21540.0362-0.29280.51250.61010.25920.88190.24160.04211.07490.08471.1791-49.38548.4691-101.0818
11574.864516.830839.59523.8219.603234.54561.28062.35831.87720.58580.50180.24855.66563.1361-1.78243.98051.0188-1.26361.0881-0.49712.432-44.6686-1.7912-126.3352
11652.803337.101120.032827.075917.139720.3286-0.33221.1482-1.4711-0.19030.0415-0.30451.0229-1.13750.29081.5936-0.0627-0.06261.481-0.36071.6103-78.015-6.2366-123.1221
1175.4219-0.4811-3.17052.6265-1.65594.4582-0.48680.2757-0.4254-0.23110.20550.11170.6765-0.17210.28130.9618-0.05050.03620.9582-0.03640.9756-82.9819-4.1637-107.9823
1180.9093-0.8363-0.22842.8935-0.14032.2753-0.1125-0.039-0.45540.2220.00920.01060.5332-0.07190.10331.00060.05550.08280.88230.01990.9665-78.1431-3.4908-97.2023
1195.3138-5.1474-0.15278.43061.42782.1561-0.0660.05820.0136-0.0646-0.08540.15570.0577-0.09990.15140.86540.04070.02730.88080.0330.8477-83.840116.4873-86.2386
1204.22710.424-0.81132.2311-0.53313.9108-0.1823-0.1649-0.55220.41670.1438-0.15710.74220.2790.03851.0160.1152-0.02530.96140.11580.9523-71.780.0193-85.9542
1216.2468-2.27152.92651.0788-1.3111.63070.2610.5714-0.4323-0.8399-0.04430.24730.8562-0.0662-0.21672.2293-0.4052-0.01161.656-0.27341.4163-88.3722-4.8487-118.616
1224.5269-1.00411.96761.1842-0.63123.8935-0.08220.0073-0.4042-0.19060.24530.28040.4406-0.0783-0.16311.0182-0.15550.07891.0932-0.04651.0909-101.27431.6772-111.7176
1231.2077-1.02530.16673.4592-1.19530.4975-0.22060.0286-0.2145-0.08480.26260.45130.2347-0.2489-0.0420.9083-0.1830.11721.15230.02191.0593-103.64016.0823-101.0004
1240.4156-1.790.446812.1442-3.91083.8509-0.21090.13890.19120.23580.17680.4350.0486-0.31410.03410.6826-0.058-0.0271.16740.07121.0964-107.701425.2902-97.8549
1255.6033-1.04850.1941.260.07763.197-0.2129-0.1212-0.57160.23570.25810.72740.6711-0.3323-0.04520.87-0.0480.14481.11830.10341.0929-103.72559.0388-87.7957
12623.8371-9.962.38614.1732-1.02340.33261.65470.2953-2.9199-1.1142-0.70321.21470.5996-0.3325-0.95152.5482-0.6128-0.01192.4165-0.08751.825-96.4871-0.5617-121.3645
1274.1953-0.86025.37660.3707-1.11637.10670.60650.3399-0.8195-0.14210.2277-0.11231.44160.2272-0.83421.9911-0.67310.26351.3707-0.20931.607-102.68593.1099-125.6188
1280.1019-0.4946-0.23413.79452.32363.4928-0.09740.1044-0.0874-0.2551-0.00990.39250.4998-0.2370.10731.015-0.2503-0.14821.37080.06591.1948-107.799316.9723-127.8546
1290.47610.685-0.39173.6435-0.87770.4215-0.24910.15270.0171-0.2430.26170.47270.1342-0.3853-0.01260.848-0.127-0.16711.42360.13361.307-115.337829.1139-120.4479
13090.8943-35.3892-66.831115.861724.845349.80122.1762-2.15393.3306-2.31780.63780.1842-0.32161.962-2.8142.2506-0.9976-1.80692.72950.75083.8826-120.91969.1946-110.7556
1318.88264.45972.534638.4537-1.43380.93670.43070.175-1.2078-1.1393-0.0160.33390.34440.0744-0.41471.5524-0.41280.00171.4798-0.01191.2334-97.10816.0871-133.807
1323.4781-2.52662.16382.2506-2.28625.2053-0.17140.2731-0.009-0.01030.14680.54680.868-0.51310.02461.1531-0.3246-0.07671.26530.04621.2349-95.559316.7904-144.885
1332.89132.60810.5522.60690.76771.3613-0.16960.46330.134-0.22220.14630.45470.3262-0.72240.02331.0572-0.2275-0.25741.32910.10081.057-100.011927.5413-145.7016
1342.55630.74210.3222.01560.04761.0962-0.07240.19780.1453-0.32620.21240.3865-0.0128-0.3833-0.140.9374-0.0546-0.19751.24570.10741.0532-92.885144.0746-145.8942
1356.69017.3196-0.971416.6929-2.06343.5056-0.12740.68260.34740.2223-0.09451.43720.7915-0.56660.22190.9819-0.1538-0.22511.53130.11911.2483-110.461135.4409-142.1652
13610.6334-2.4383-7.00183.75712.9525.2657-0.17090.0179-1.1832.288-0.79610.26421.2692-0.20150.96712.0948-0.1997-0.08031.3701-0.00621.1538-87.79887.5724-141.3248
1377.0420.55941.28356.79791.1145.6993-0.33610.2868-0.3876-0.66120.36820.24750.2126-0.2644-0.03221.1202-0.1449-0.05680.86540.03380.7355-75.413513.4439-148.171
1381.78290.72241.65252.2850.09673.374-0.0670.23250.0838-0.45440.22860.11650.3475-0.2072-0.16161.0625-0.1914-0.04610.92570.01120.7688-73.297426.1346-151.3707
1393.56270.97393.93941.02850.35316.3213-0.09020.14830.0116-0.10340.1847-0.1640.51460.3194-0.09440.9856-0.04060.01290.891-0.04320.8366-58.616536.4012-147.0006
1404.85610.29950.26755.68691.80135.2298-0.27320.48910.0904-0.68840.180.72950.1173-0.33720.09321.0903-0.1422-0.12851.05410.0830.8271-76.918236.4432-156.9065
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 20
2X-RAY DIFFRACTION2A21 - 113
3X-RAY DIFFRACTION3A114 - 142
4X-RAY DIFFRACTION4A143 - 187
5X-RAY DIFFRACTION5A188 - 193
6X-RAY DIFFRACTION6B4 - 16
7X-RAY DIFFRACTION7B17 - 24
8X-RAY DIFFRACTION8B25 - 61
9X-RAY DIFFRACTION9B62 - 181
10X-RAY DIFFRACTION10B182 - 193
11X-RAY DIFFRACTION11C4 - 25
12X-RAY DIFFRACTION12C26 - 42
13X-RAY DIFFRACTION13C43 - 116
14X-RAY DIFFRACTION14C117 - 155
15X-RAY DIFFRACTION15C156 - 193
16X-RAY DIFFRACTION16D4 - 29
17X-RAY DIFFRACTION17D30 - 118
18X-RAY DIFFRACTION18D119 - 164
19X-RAY DIFFRACTION19D165 - 187
20X-RAY DIFFRACTION20D188 - 193
21X-RAY DIFFRACTION21E4 - 29
22X-RAY DIFFRACTION22E30 - 73
23X-RAY DIFFRACTION23E74 - 147
24X-RAY DIFFRACTION24E148 - 164
25X-RAY DIFFRACTION25E165 - 193
26X-RAY DIFFRACTION26F4 - 16
27X-RAY DIFFRACTION27F17 - 23
28X-RAY DIFFRACTION28F24 - 63
29X-RAY DIFFRACTION29F64 - 153
30X-RAY DIFFRACTION30F154 - 193
31X-RAY DIFFRACTION31G4 - 56
32X-RAY DIFFRACTION32G57 - 129
33X-RAY DIFFRACTION33G130 - 166
34X-RAY DIFFRACTION34G167 - 187
35X-RAY DIFFRACTION35G188 - 193
36X-RAY DIFFRACTION36H4 - 29
37X-RAY DIFFRACTION37H30 - 94
38X-RAY DIFFRACTION38H95 - 147
39X-RAY DIFFRACTION39H148 - 165
40X-RAY DIFFRACTION40H166 - 193
41X-RAY DIFFRACTION41I4 - 16
42X-RAY DIFFRACTION42I17 - 42
43X-RAY DIFFRACTION43I43 - 118
44X-RAY DIFFRACTION44I119 - 153
45X-RAY DIFFRACTION45I154 - 193
46X-RAY DIFFRACTION46J4 - 30
47X-RAY DIFFRACTION47J31 - 118
48X-RAY DIFFRACTION48J119 - 157
49X-RAY DIFFRACTION49J158 - 187
50X-RAY DIFFRACTION50J188 - 193
51X-RAY DIFFRACTION51K4 - 49
52X-RAY DIFFRACTION52K50 - 118
53X-RAY DIFFRACTION53K119 - 150
54X-RAY DIFFRACTION54K151 - 165
55X-RAY DIFFRACTION55K166 - 193
56X-RAY DIFFRACTION56L4 - 9
57X-RAY DIFFRACTION57L16 - 28
58X-RAY DIFFRACTION58L29 - 70
59X-RAY DIFFRACTION59L71 - 146
60X-RAY DIFFRACTION60L147 - 193
61X-RAY DIFFRACTION61M4 - 26
62X-RAY DIFFRACTION62M27 - 63
63X-RAY DIFFRACTION63M64 - 128
64X-RAY DIFFRACTION64M129 - 171
65X-RAY DIFFRACTION65M172 - 193
66X-RAY DIFFRACTION66N4 - 29
67X-RAY DIFFRACTION67N30 - 129
68X-RAY DIFFRACTION68N130 - 165
69X-RAY DIFFRACTION69N166 - 187
70X-RAY DIFFRACTION70N188 - 193
71X-RAY DIFFRACTION71O4 - 23
72X-RAY DIFFRACTION72O24 - 68
73X-RAY DIFFRACTION73O69 - 161
74X-RAY DIFFRACTION74O162 - 187
75X-RAY DIFFRACTION75O188 - 193
76X-RAY DIFFRACTION76P4 - 24
77X-RAY DIFFRACTION77P25 - 90
78X-RAY DIFFRACTION78P91 - 130
79X-RAY DIFFRACTION79P131 - 180
80X-RAY DIFFRACTION80P181 - 193
81X-RAY DIFFRACTION81Q4 - 30
82X-RAY DIFFRACTION82Q31 - 62
83X-RAY DIFFRACTION83Q63 - 118
84X-RAY DIFFRACTION84Q119 - 181
85X-RAY DIFFRACTION85Q182 - 193
86X-RAY DIFFRACTION86R4 - 18
87X-RAY DIFFRACTION87R19 - 64
88X-RAY DIFFRACTION88R65 - 130
89X-RAY DIFFRACTION89R131 - 187
90X-RAY DIFFRACTION90R188 - 193
91X-RAY DIFFRACTION91S4 - 19
92X-RAY DIFFRACTION92S20 - 45
93X-RAY DIFFRACTION93S46 - 97
94X-RAY DIFFRACTION94S98 - 148
95X-RAY DIFFRACTION95S149 - 193
96X-RAY DIFFRACTION96T4 - 30
97X-RAY DIFFRACTION97T31 - 82
98X-RAY DIFFRACTION98T83 - 113
99X-RAY DIFFRACTION99T114 - 159
100X-RAY DIFFRACTION100T160 - 193
101X-RAY DIFFRACTION101U4 - 29
102X-RAY DIFFRACTION102U30 - 117
103X-RAY DIFFRACTION103U118 - 137
104X-RAY DIFFRACTION104U138 - 171
105X-RAY DIFFRACTION105U172 - 193
106X-RAY DIFFRACTION106V4 - 25
107X-RAY DIFFRACTION107V26 - 79
108X-RAY DIFFRACTION108V80 - 128
109X-RAY DIFFRACTION109V129 - 164
110X-RAY DIFFRACTION110V165 - 193
111X-RAY DIFFRACTION111W4 - 20
112X-RAY DIFFRACTION112W21 - 63
113X-RAY DIFFRACTION113W64 - 130
114X-RAY DIFFRACTION114W131 - 187
115X-RAY DIFFRACTION115W188 - 193
116X-RAY DIFFRACTION116X4 - 18
117X-RAY DIFFRACTION117X19 - 57
118X-RAY DIFFRACTION118X58 - 118
119X-RAY DIFFRACTION119X119 - 148
120X-RAY DIFFRACTION120X149 - 193
121X-RAY DIFFRACTION121Y4 - 20
122X-RAY DIFFRACTION122Y21 - 61
123X-RAY DIFFRACTION123Y62 - 118
124X-RAY DIFFRACTION124Y119 - 156
125X-RAY DIFFRACTION125Y157 - 193
126X-RAY DIFFRACTION126Z4 - 9
127X-RAY DIFFRACTION127Z16 - 29
128X-RAY DIFFRACTION128Z30 - 80
129X-RAY DIFFRACTION129Z81 - 187
130X-RAY DIFFRACTION130Z188 - 193
131X-RAY DIFFRACTION131a4 - 21
132X-RAY DIFFRACTION132a22 - 61
133X-RAY DIFFRACTION133a62 - 117
134X-RAY DIFFRACTION134a118 - 169
135X-RAY DIFFRACTION135a170 - 193
136X-RAY DIFFRACTION136b4 - 22
137X-RAY DIFFRACTION137b23 - 61
138X-RAY DIFFRACTION138b62 - 127
139X-RAY DIFFRACTION139b128 - 164
140X-RAY DIFFRACTION140b165 - 193

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万見について

-
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

-
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

+
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