[日本語] English
万見
- PDB-4nwr: Computationally Designed Two-Component Self-Assembling Tetrahedra... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4nwr
タイトルComputationally Designed Two-Component Self-Assembling Tetrahedral Cage T33-28
要素
  • Macrophage migration inhibitory factor-like protein
  • integron gene cassette protein
キーワードPROTEIN BINDING / two-component / self-assembling / tetrahedron / designed protein cage / computational design / computational biology / protein engineering / multimerization / nanomaterial / nanostructure / integrons / macrophage migration-inhibitory factors
機能・相同性
機能・相同性情報


phenylpyruvate tautomerase / L-dopachrome isomerase / phenylpyruvate tautomerase activity / cytokine activity / extracellular space
類似検索 - 分子機能
Macrophage migration inhibitory factor / Macrophage migration inhibitory factor (MIF) / Tautomerase/MIF superfamily
類似検索 - ドメイン・相同性
Putative integron gene cassette protein / L-dopachrome isomerase
類似検索 - 構成要素
生物種uncultured bacterium (環境試料)
Leishmania major (大形リーシュマニア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.5 Å
データ登録者McNamara, D.E. / King, N.P. / Bale, J.B. / Sheffler, W. / Baker, D. / Yeates, T.O.
引用ジャーナル: Nature / 年: 2014
タイトル: Accurate design of co-assembling multi-component protein nanomaterials.
著者: King, N.P. / Bale, J.B. / Sheffler, W. / McNamara, D.E. / Gonen, S. / Gonen, T. / Yeates, T.O. / Baker, D.
履歴
登録2013年12月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年5月28日Provider: repository / タイプ: Initial release
改定 1.12014年6月4日Group: Database references
改定 1.22014年6月11日Group: Database references
置き換え2014年12月10日ID: 1VW5, 1VW6
改定 1.32014年12月10日Group: Other
改定 1.42023年9月20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

-
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

-
集合体

登録構造単位
A: integron gene cassette protein
B: Macrophage migration inhibitory factor-like protein
D: Macrophage migration inhibitory factor-like protein
F: Macrophage migration inhibitory factor-like protein
H: Macrophage migration inhibitory factor-like protein
J: Macrophage migration inhibitory factor-like protein
L: Macrophage migration inhibitory factor-like protein
N: Macrophage migration inhibitory factor-like protein
P: Macrophage migration inhibitory factor-like protein
R: Macrophage migration inhibitory factor-like protein
T: Macrophage migration inhibitory factor-like protein
V: Macrophage migration inhibitory factor-like protein
X: Macrophage migration inhibitory factor-like protein
Z: Macrophage migration inhibitory factor-like protein
b: Macrophage migration inhibitory factor-like protein
d: Macrophage migration inhibitory factor-like protein
f: Macrophage migration inhibitory factor-like protein
h: Macrophage migration inhibitory factor-like protein
j: Macrophage migration inhibitory factor-like protein
l: Macrophage migration inhibitory factor-like protein
n: Macrophage migration inhibitory factor-like protein
p: Macrophage migration inhibitory factor-like protein
r: Macrophage migration inhibitory factor-like protein
t: Macrophage migration inhibitory factor-like protein
v: Macrophage migration inhibitory factor-like protein
x: Macrophage migration inhibitory factor-like protein
z: Macrophage migration inhibitory factor-like protein
1: Macrophage migration inhibitory factor-like protein
3: Macrophage migration inhibitory factor-like protein
5: Macrophage migration inhibitory factor-like protein
7: Macrophage migration inhibitory factor-like protein
9: Macrophage migration inhibitory factor-like protein
AB: Macrophage migration inhibitory factor-like protein
AD: Macrophage migration inhibitory factor-like protein
AF: Macrophage migration inhibitory factor-like protein
AH: Macrophage migration inhibitory factor-like protein
AJ: Macrophage migration inhibitory factor-like protein
AL: Macrophage migration inhibitory factor-like protein
AN: Macrophage migration inhibitory factor-like protein
AP: Macrophage migration inhibitory factor-like protein
AR: Macrophage migration inhibitory factor-like protein
AT: Macrophage migration inhibitory factor-like protein
AV: Macrophage migration inhibitory factor-like protein
AX: Macrophage migration inhibitory factor-like protein
AZ: Macrophage migration inhibitory factor-like protein
BB: Macrophage migration inhibitory factor-like protein
BD: Macrophage migration inhibitory factor-like protein
BF: Macrophage migration inhibitory factor-like protein
BH: Macrophage migration inhibitory factor-like protein
C: integron gene cassette protein
E: integron gene cassette protein
G: integron gene cassette protein
I: integron gene cassette protein
K: integron gene cassette protein
M: integron gene cassette protein
O: integron gene cassette protein
Q: integron gene cassette protein
S: integron gene cassette protein
U: integron gene cassette protein
W: integron gene cassette protein
Y: integron gene cassette protein
a: integron gene cassette protein
c: integron gene cassette protein
e: integron gene cassette protein
g: integron gene cassette protein
i: integron gene cassette protein
k: integron gene cassette protein
m: integron gene cassette protein
o: integron gene cassette protein
q: integron gene cassette protein
s: integron gene cassette protein
u: integron gene cassette protein
w: integron gene cassette protein
y: integron gene cassette protein
0: integron gene cassette protein
2: integron gene cassette protein
4: integron gene cassette protein
6: integron gene cassette protein
8: integron gene cassette protein
AA: integron gene cassette protein
AC: integron gene cassette protein
AE: integron gene cassette protein
AG: integron gene cassette protein
AI: integron gene cassette protein
AK: integron gene cassette protein
AM: integron gene cassette protein
AO: integron gene cassette protein
AQ: integron gene cassette protein
AS: integron gene cassette protein
AU: integron gene cassette protein
AW: integron gene cassette protein
AY: integron gene cassette protein
BA: integron gene cassette protein
BC: integron gene cassette protein
BE: integron gene cassette protein
BG: integron gene cassette protein


分子量 (理論値)分子数
合計 (水以外)1,502,71996
ポリマ－1,502,71996
非ポリマー00
水00
1
A: integron gene cassette protein
B: Macrophage migration inhibitory factor-like protein
D: Macrophage migration inhibitory factor-like protein
F: Macrophage migration inhibitory factor-like protein
H: Macrophage migration inhibitory factor-like protein
J: Macrophage migration inhibitory factor-like protein
L: Macrophage migration inhibitory factor-like protein
N: Macrophage migration inhibitory factor-like protein
P: Macrophage migration inhibitory factor-like protein
R: Macrophage migration inhibitory factor-like protein
T: Macrophage migration inhibitory factor-like protein
V: Macrophage migration inhibitory factor-like protein
X: Macrophage migration inhibitory factor-like protein
C: integron gene cassette protein
E: integron gene cassette protein
G: integron gene cassette protein
I: integron gene cassette protein
K: integron gene cassette protein
M: integron gene cassette protein
O: integron gene cassette protein
Q: integron gene cassette protein
S: integron gene cassette protein
U: integron gene cassette protein
W: integron gene cassette protein


分子量 (理論値)分子数
合計 (水以外)375,68024
ポリマ－375,68024
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area55970 Å2
ΔGint-490 kcal/mol
Surface area116940 Å2
手法PISA
2
Z: Macrophage migration inhibitory factor-like protein
b: Macrophage migration inhibitory factor-like protein
d: Macrophage migration inhibitory factor-like protein
f: Macrophage migration inhibitory factor-like protein
h: Macrophage migration inhibitory factor-like protein
j: Macrophage migration inhibitory factor-like protein
l: Macrophage migration inhibitory factor-like protein
n: Macrophage migration inhibitory factor-like protein
p: Macrophage migration inhibitory factor-like protein
r: Macrophage migration inhibitory factor-like protein
t: Macrophage migration inhibitory factor-like protein
v: Macrophage migration inhibitory factor-like protein
Y: integron gene cassette protein
a: integron gene cassette protein
c: integron gene cassette protein
e: integron gene cassette protein
g: integron gene cassette protein
i: integron gene cassette protein
k: integron gene cassette protein
m: integron gene cassette protein
o: integron gene cassette protein
q: integron gene cassette protein
s: integron gene cassette protein
u: integron gene cassette protein


分子量 (理論値)分子数
合計 (水以外)375,68024
ポリマ－375,68024
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area55980 Å2
ΔGint-488 kcal/mol
Surface area116520 Å2
手法PISA
3
x: Macrophage migration inhibitory factor-like protein
z: Macrophage migration inhibitory factor-like protein
1: Macrophage migration inhibitory factor-like protein
3: Macrophage migration inhibitory factor-like protein
5: Macrophage migration inhibitory factor-like protein
7: Macrophage migration inhibitory factor-like protein
9: Macrophage migration inhibitory factor-like protein
AB: Macrophage migration inhibitory factor-like protein
AD: Macrophage migration inhibitory factor-like protein
AF: Macrophage migration inhibitory factor-like protein
AH: Macrophage migration inhibitory factor-like protein
AJ: Macrophage migration inhibitory factor-like protein
w: integron gene cassette protein
y: integron gene cassette protein
0: integron gene cassette protein
2: integron gene cassette protein
4: integron gene cassette protein
6: integron gene cassette protein
8: integron gene cassette protein
AA: integron gene cassette protein
AC: integron gene cassette protein
AE: integron gene cassette protein
AG: integron gene cassette protein
AI: integron gene cassette protein


分子量 (理論値)分子数
合計 (水以外)375,68024
ポリマ－375,68024
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56110 Å2
ΔGint-487 kcal/mol
Surface area116490 Å2
手法PISA
4
AL: Macrophage migration inhibitory factor-like protein
AN: Macrophage migration inhibitory factor-like protein
AP: Macrophage migration inhibitory factor-like protein
AR: Macrophage migration inhibitory factor-like protein
AT: Macrophage migration inhibitory factor-like protein
AV: Macrophage migration inhibitory factor-like protein
AX: Macrophage migration inhibitory factor-like protein
AZ: Macrophage migration inhibitory factor-like protein
BB: Macrophage migration inhibitory factor-like protein
BD: Macrophage migration inhibitory factor-like protein
BF: Macrophage migration inhibitory factor-like protein
BH: Macrophage migration inhibitory factor-like protein
AK: integron gene cassette protein
AM: integron gene cassette protein
AO: integron gene cassette protein
AQ: integron gene cassette protein
AS: integron gene cassette protein
AU: integron gene cassette protein
AW: integron gene cassette protein
AY: integron gene cassette protein
BA: integron gene cassette protein
BC: integron gene cassette protein
BE: integron gene cassette protein
BG: integron gene cassette protein


分子量 (理論値)分子数
合計 (水以外)375,68024
ポリマ－375,68024
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area56230 Å2
ΔGint-490 kcal/mol
Surface area116470 Å2
手法PISA
単位格子
Length a, b, c (Å)124.910, 189.250, 376.830
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
詳細The biological assembly is a protein cage with tetrahedral point group symmetry that comprises twenty-four subunits, where twelve each are a total of four homotrimers.

-
要素

#1: タンパク質 ...
integron gene cassette protein


分子量: 17788.957 Da / 分子数: 48
変異: K49I, D53A, Q56I, S57F, I58L, F64D, L109E, E112L, K113A, A116V
由来タイプ: 組換発現 / 由来: (組換発現) uncultured bacterium (環境試料) / 遺伝子: ORF1 / プラスミド: pET29b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: B0BGB0
#2: タンパク質 ...
Macrophage migration inhibitory factor-like protein


分子量: 13517.698 Da / 分子数: 48 / 変異: E18L, N19L, Q22I, V23I, A26I, D30V, K87A, E88V / 由来タイプ: 組換発現
由来: (組換発現) Leishmania major (大形リーシュマニア)
株: FRIEDLIN / 遺伝子: LMJF_33_1740, MIF1 / プラスミド: pET29b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q4Q413

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.96 Å3/Da / 溶媒含有率: 58.5 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.6
詳細: 100 mM sodium citrate tribasic dihydrate pH 5.6, 200 mM ammonium acetate, 24% (v/v) (+/-)-2-methyl-2,4-pentanediol, vapor diffusion, hanging drop, temperature 298K

-
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: APS / ビームライン: 24-ID-C / 波長: 0.9793 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年8月11日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9793 Å / 相対比: 1
反射解像度: 3.5→94.207 Å / Num. all: 220615 / Num. obs: 217956 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / 冗長度: 3.71 % / Biso Wilson estimate: 90.552 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 9.02
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.593.930.6192.31199.6
3.59-3.693.860.5182.77199.6
3.69-3.83.80.453.21199.2
3.8-3.913.540.3753.76198.8
3.91-4.043.70.3144.59198.4
4.04-4.183.90.2456.01199.4
4.18-4.343.840.2017.3199.4
4.34-4.523.770.1698.37199.3
4.52-4.723.720.1499.26199.2
4.72-4.953.620.1359.9199
4.95-5.223.410.1379.24197.4
5.22-5.533.790.1379.97199.2
5.53-5.923.830.12710.66199.4
5.92-6.393.780.12210.9199.5
6.39-73.640.10911.74199
7-7.833.280.0715.8196.4
7.83-9.043.550.0424.96198.5
9.04-11.073.470.03130.13197.3
11.07-15.653.280.02929.53194
15.65-94.2073.650.02732.2195.6

-
位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation7.8 Å94.63 Å
Translation7.8 Å94.63 Å

-
解析

ソフトウェア
名称バージョン分類NB
XSCALEデータスケーリング
PHASER2.5.2位相決定
PHENIX1.8.4_1496精密化
PDB_EXTRACT3.11データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: Model of 24-mer based on 3FUY and 3FWU

3fuy

3fwu


解像度: 3.5→94.207 Å / SU ML: 0.55 / σ(F): 1.35 / 位相誤差: 31.62 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2983 21784 10 %
Rwork0.2616 --
obs0.2653 217862 98.76 %
all-220615 -
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 89.5853431813 Å2
精密化ステップサイクル: LAST / 解像度: 3.5→94.207 Å
タンパク質核酸リガンド溶媒全体
原子数88858 0 0 0 88858
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00290704
X-RAY DIFFRACTIONf_angle_d0.489124361
X-RAY DIFFRACTIONf_dihedral_angle_d10.45929072
X-RAY DIFFRACTIONf_chiral_restr0.01915010
X-RAY DIFFRACTIONf_plane_restr0.00316369
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.53980.36547320.32026573X-RAY DIFFRACTION100
3.5398-3.58140.37227300.31296570X-RAY DIFFRACTION100
3.5814-3.62510.35637260.30026535X-RAY DIFFRACTION99
3.6251-3.6710.35237320.29866585X-RAY DIFFRACTION100
3.671-3.71930.34167270.29016547X-RAY DIFFRACTION99
3.7193-3.77020.34957310.28946580X-RAY DIFFRACTION99
3.7702-3.82410.3437220.29096500X-RAY DIFFRACTION99
3.8241-3.88120.33337220.27666492X-RAY DIFFRACTION99
3.8812-3.94180.32647150.28026437X-RAY DIFFRACTION97
3.9418-4.00650.33277250.28256530X-RAY DIFFRACTION99
4.0065-4.07550.30727290.26676553X-RAY DIFFRACTION100
4.0755-4.14970.30677310.25776586X-RAY DIFFRACTION99
4.1497-4.22950.30247240.25496515X-RAY DIFFRACTION99
4.2295-4.31580.29417320.24916587X-RAY DIFFRACTION99
4.3158-4.40960.28297280.23846563X-RAY DIFFRACTION99
4.4096-4.51220.25617280.23616545X-RAY DIFFRACTION99
4.5122-4.62510.28317370.24436634X-RAY DIFFRACTION99
4.6251-4.75010.27837170.24866453X-RAY DIFFRACTION99
4.7501-4.88990.28127260.25196546X-RAY DIFFRACTION99
4.8899-5.04770.30167310.25846577X-RAY DIFFRACTION99
5.0477-5.22810.3047100.26486392X-RAY DIFFRACTION97
5.2281-5.43740.30327300.26946563X-RAY DIFFRACTION99
5.4374-5.68480.30727310.27536579X-RAY DIFFRACTION99
5.6848-5.98450.3187290.27986565X-RAY DIFFRACTION99
5.9845-6.35940.30057320.28826590X-RAY DIFFRACTION99
6.3594-6.85020.33047320.29666592X-RAY DIFFRACTION99
6.8502-7.53940.32397270.29076544X-RAY DIFFRACTION98
7.5394-8.62970.25157140.22556417X-RAY DIFFRACTION97
8.6297-10.86990.20237230.19086514X-RAY DIFFRACTION97
10.8699-94.24160.30357110.26446414X-RAY DIFFRACTION94
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)
12.64910.74151.07918.0123-2.01445.2077-0.21750.11680.0260.31570.3433-0.4401-0.7151-0.4113-0.12230.46580.0033-0.0540.62940.20570.509413.607215.354131.0469
22.09020.9391-0.5224-0.43020.67945.19020.09960.50730.46-0.22940.0022-0.03760.1619-0.0649-0.19430.9834-0.0293-0.14880.52970.18080.596333.749131.392727.6824
31.30431.3672-0.66132.0426-0.65725.632-0.2399-0.3633-0.0821.0465-0.0044-0.2672-0.9168-0.48430.22340.85550.2194-0.20930.71520.120.762710.23951.607661.0299
44.0212.31441.97683.73621.45624.14530.38080.05260.132-0.541-0.1856-0.1633-0.1625-0.0428-0.25430.68720.23090.12610.48120.00630.477928.0013-0.175880.4827
51.7997-0.3322-1.27754.92432.40416.1384-0.1510.2409-1.18830.10020.21850.05240.62380.0578-0.09650.4438-0.0263-0.11810.5417-0.02460.968314.776-17.376534.3277
67.27450.2242-0.72254.0545-2.84034.71630.33590.59030.2817-0.17440.21960.189-0.58730.7858-0.5780.7137-0.27120.03260.698-0.14510.621336.7401-29.775127.0638
75.9296-0.77-2.4472.43920.11252.46290.118-0.14220.18950.003-0.27270.2605-0.04790.27120.17350.3262-0.017-0.00380.3735-0.00811.088188.1252-26.814274.1887
80.2824-0.4090.62423.1135-0.67637.32090.11630.3521-0.6851-0.06370.1172-0.6238-0.1041-0.0561-0.29980.324-0.03650.05090.5678-0.12741.052198.3258-7.999459.081
94.58881.6859-0.13922.3562-0.03713.5875-0.42750.7733-0.5928-0.24790.19740.13030.1723-0.33430.19140.3823-0.0662-0.00350.5158-0.23891.219464.2472-45.470360.9832
104.6796-2.5013-1.16170.5298-1.00912.9058-0.18980.23810.0716-0.35460.5381-0.63790.03420.3236-0.33220.6569-0.17310.03930.602-0.36580.969949.7389-40.143939.6554
113.1039-1.0235-1.33311.53071.81835.92720.3826-0.1316-0.60680.0092-0.15580.21280.0128-0.1442-0.21060.4420.00510.03190.28860.0770.879258.3571-28.033988.4959
127.1291-0.014-0.1122.7857-0.13472.2209-0.0947-0.2964-0.2506-0.1410.3046-0.4593-0.0768-0.0444-0.21310.79970.027-0.00550.339-0.00220.453245.6196-5.320590.206
132.65581.35580.81521.18520.00842.1208-0.21030.3944-0.2861-0.21140.114-0.12260.2118-0.38830.15450.9545-0.34660.20441.2604-0.17740.576795.3734-0.072717.8431
143.9082-4.8799-0.52678.7503-1.21144.7769-0.36080.1124-0.29-0.4079-0.07240.0767-0.44890.1520.4130.4923-0.2249-0.06440.57390.05090.7462100.34065.074543.1004
15-0.32480.6918-1.1621.37941.07521.9253-0.26710.0109-0.0401-0.35430.5691-0.11030.4694-0.2907-0.20711.3242-0.84520.30482.1138-0.37160.947170.3055-17.41825.1374
163.85421.22441.93420.71530.65683.1554-0.43270.9023-0.2167-0.20490.36740.0627-0.21090.75660.17780.6767-0.25850.20581.1731-0.45261.055856.6098-32.534421.5355
175.5601-1.47943.61335.8862-0.8612.9249-0.55290.43050.3352-0.970.03760.54550.1227-0.94730.63811.0911-0.48860.05951.7214-0.25360.750770.050915.70783.515
181.4177-0.1462-1.52355.6831.51752.5411-0.26670.44920.2693-0.1063-0.15110.0823-0.53280.50750.43520.7877-0.2958-0.25881.1550.06770.606450.305128.2615.1774
196.1876-0.29212.62320.26712.33894.3166-0.3259-0.06320.12350.3257-0.0421-0.30770.38850.40540.27871.08570.0797-0.03650.39520.10350.815187.036835.43368.5596
206.9462.8901-3.26314.6697-0.20374.8352-0.21820.30290.3370.04230.35470.1636-0.1123-0.0331-0.13520.6153-0.0134-0.08880.34420.08570.639597.387212.532662.3149
213.2063-0.8087-2.6965-0.879-0.93261.72520.0535-0.58350.01880.4959-0.0305-0.15910.3224-0.14120.01241.5160.0034-0.20910.3883-0.13561.089258.233834.321484.6835
223.86171.35681.63053.2315-1.17132.5454-0.3870.23640.77850.50990.14790.3703-0.751-0.02290.31141.01530.22790.03040.45260.05290.577741.18114.575686.468
232.68382.396-2.65323.9354-3.88335.5773-0.21320.33740.4422-0.33050.42320.0525-0.1464-0.4379-0.26040.9687-0.1144-0.24090.40190.0320.768360.096449.074755.2851
246.7827-0.4456-2.18293.78392.37712.6019-0.29810.31750.30790.06430.09670.3463-0.15030.43690.24820.6521-0.1411-0.09910.60840.18810.479751.829840.62131.8486
250.23092.0442-0.18736.5412-3.36.0891-0.3385-0.1324-0.1082-0.34660.40780.49610.528-0.49210.00580.38710.03980.01290.60650.170.764713.5169-100.6741157.3335
263.9806-1.7249-1.15590.43581.92955.51050.0799-0.4892-0.28460.0004-0.2339-0.30460.05270.21320.11030.9260.01260.08180.54960.24350.660833.6786-116.7169160.7753
271.4622-1.54552.88031.0715-1.14837.19230.1640.0763-0.1545-0.3459-0.08990.18860.6978-0.3016-0.17290.649-0.1963-0.00280.57510.19560.730110.2425-86.9669127.3728
283.8446-2.8321-0.32466.40831.63863.97360.3186-0.15770.14180.4859-0.5328-0.32610.0323-0.14940.16560.7026-0.225-0.16490.46090.05510.569527.9202-85.0489108.0223
290.2920.2536-0.19674.65452.17396.3039-0.1514-0.1230.69760.07980.19910.3067-0.42320.10710.01520.3770.0805-0.01540.5319-0.02240.931814.753-67.9929154.0793
309.1241-1.20750.6343.9107-4.0657.28540.4825-0.725-0.48790.12050.374-0.26390.56650.9126-0.85780.65680.1892-0.11790.726-0.21360.765436.7273-55.5717161.3258
315.80050.54790.6392.98150.16821.90680.31680.215-0.3810.0765-0.1803-0.29790.29860.354-0.1730.37530.0714-0.17810.380.00261.040388.1066-58.5484114.2449
321.6850.11321.07322.6877-0.27467.16630.1269-0.24220.06370.06920.1301-0.69950.2884-0.0337-0.23440.36640.0921-0.12620.533-0.07461.001898.3436-77.3955129.3186
333.1624-2.4507-0.52892.47581.14083.1793-0.1819-0.76310.8840.11580.08730.198-0.1357-0.03480.12320.3714-0.0083-0.090.5829-0.2661.241964.228-39.8783127.5429
341.90352.67710.35643.10220.68684.5714-0.1124-0.24780.30560.38760.3398-0.18980.03250.2826-0.2480.42320.1526-0.08930.6303-0.28340.897949.7386-45.2464148.8357
353.3056-0.06681.1566-0.00061.34975.96660.2355-0.10840.078-0.0172-0.0403-0.01890.3451-0.2137-0.2120.4425-0.0772-0.08340.26010.07230.789758.3749-57.2574100.0006
362.9886-1.2115-0.47043.89410.47190.3-0.397-0.12430.29470.59980.3087-0.62330.3303-0.120.06920.7039-0.067-0.15940.4442-0.0260.439345.4383-79.812498.2477
374.0249-2.241-1.95742.7386-0.56963.7726-0.4347-0.53850.53540.48160.4542-0.497-0.3487-0.8270.02620.85460.3449-0.19511.3449-0.17470.53795.3746-85.2576170.5635
382.08390.4062-1.45735.8439-1.94592.9813-0.4117-0.45140.20860.07610.0515-0.15520.29380.1050.29070.5620.1694-0.15870.58440.04460.5872100.2254-90.4788145.432
391.7243-1.5373-1.40592.38942.07271.496-0.0918-0.89140.59170.60710.0838-0.0253-0.6497-0.26490.02291.23660.8058-0.47262.0325-0.40990.844870.2728-67.9536183.3313
404.0630.4411-1.76970.8125-0.3268.2961-0.4341-1.30020.76390.27460.2945-0.33690.19090.67650.19430.61250.2647-0.18191.0431-0.33660.937756.5522-52.9083166.9867
412.14542.1622-1.41264.7154-0.60752.0132-0.2564-0.1298-0.42961.00620.1564-0.3473-0.1405-0.6740.1561.060.5205-0.2531.8598-0.220.848869.9911-101.0365184.9088
422.6226-0.3219-0.05725.48552.73863.773-0.2867-0.48950.1030.1298-0.42960.38940.51070.44580.76170.74510.25430.10020.97140.1220.580750.2483-113.5404173.2151
437.58520.7595-1.16970.62842.0614.4289-0.17820.0533-0.4297-0.3752-0.0428-0.3359-0.70290.45080.09220.9908-0.03010.08870.38190.06550.764286.9767-120.7401119.8759
440.67111.139-0.60935.0607-0.31462.5746-0.5822-0.20220.08320.0180.33380.14590.14070.10060.2460.56310.1083-0.08020.4513-0.04360.671797.4072-97.8488126.2449
454.2550.48961.5283-0.77460.23872.40680.19730.4525-0.22660.0907-0.2828-0.3071-0.1567-0.11280.05961.23390.0946-0.14080.4229-0.08730.960358.1959-119.5865103.7037
463.3598-0.7544-1.40442.11951.12553.5543-0.1202-0.1683-0.3071-0.31680.33460.27520.9507-0.0485-0.1750.9785-0.1684-0.15340.44950.05340.474441.1459-99.8658101.8946
472.4954-1.95472.00183.9071-5.42547.4771-0.0473-0.167-0.27870.17730.2979-0.00840.1584-0.3779-0.32060.84850.11070.16140.3570.04490.875460.0667-134.4153133.2253
483.4595-0.6777-1.11161.06990.86241.2919-0.3592-0.703-0.65260.3470.28040.15640.39830.33670.06420.6860.20750.02890.72850.30520.830451.7451-125.9752156.636
490.4384-1.40311.62824.441-2.10166.2709-0.1851-0.63010.4519-0.6861-0.10590.5390.0062-0.95850.1830.68160.35120.05651.5344-0.07561.0326-51.33179.7169129.0154
502.20220.6884-0.18450.53031.92341.64650.17680.13280.3167-0.6493-0.45540.6953-0.6115-0.61380.25640.96120.4192-0.17940.85950.02580.8727-33.64212.2666110.0275
511.0111-0.246-0.69251.77521.4132.63660.326-0.51891.0304-0.2287-0.36870.2239-0.4993-0.78960.07930.67720.2780.13641.6565-0.20481.5147-45.385527.1379156.4508
522.96-0.11762.1026.4793-4.97315.5620.82520.3674-0.1343-0.1110.04450.3033-0.3662-0.0699-1.04550.83360.13280.23730.756-0.15431.0277-22.972438.4388164.4867
531.66441.61921.06383.9697-0.29351.79770.1661-0.1603-0.27690.2678-0.9090.56040.2707-0.83820.79610.6198-0.05940.21291.712-0.12371.2728-48.7056-5.6113158.2172
541.8366-1.07510.65551.31551.19875.48770.1547-1.0623-0.45550.4253-0.34390.26590.1267-0.91380.11650.9207-0.4140.15831.17940.05420.725-29.6117-22.664160.5023
555.4293-2.8629-2.30483.4616-0.95582.58850.1473-0.37660.5930.4866-0.0947-0.4558-0.07630.443-0.08550.6849-0.133-0.10141.0502-0.11690.489633.33114.5755172.2255
562.8609-0.7122-1.87685.1613-1.64995.9107-0.0256-0.5640.06090.0929-0.0184-0.6463-0.53520.5694-0.02090.366-0.0153-0.0220.5947-0.11830.67337.97730.8445146.7529
574.54781.6535-1.07195.00021.28581.4730.1051-0.5970.07670.9898-0.0674-0.03930.40120.4438-0.01180.8751-0.1269-0.16160.9811-0.08570.48587.0784-10.58185.6235
584.7143-2.82870.52814.08110.56254.4316-0.2861-0.93460.53390.76770.29790.34010.7317-0.30120.03120.8554-0.18550.07750.8037-0.1310.6347-13.198-21.2484172.879
592.39590.5095-0.64775.80391.29890.66340.0228-0.85490.74950.4038-0.14480.3939-0.41990.41040.12320.8355-0.0725-0.10291.1379-0.28310.68339.189122.4508185.8988
605.02030.7139-0.66893.0885-2.34422.26120.2703-0.68640.3404-0.40220.1132-0.0718-0.50820.24-0.33410.9542-0.02830.00980.8581-0.5181.1281-3.097239.6644170.454
615.13753.3275-1.88913.62131.05943.70820.0907-0.3313-0.8495-0.2612-0.1091-1.0716-0.21550.2861-0.07240.3403-0.00910.00930.4313-0.14741.136423.5178-26.8727119.1396
623.3991-0.80452.11024.57660.1096.5461-0.2159-0.2203-0.0683-0.14090.4739-0.2252-0.53530.4166-0.30040.3145-0.04650.06960.4638-0.20531.011134.7158-4.985127.0095
632.416-1.29691.59593.7075-3.98645.27120.0952-0.35510.02540.3574-0.05330.23110.1406-0.617-0.18110.5311-0.0679-0.00430.4037-0.15790.7054-4.463-39.6422131.157
645.2682-1.88220.43711.0710.557.65180.3456-0.859-0.22780.7335-0.39360.53680.5721-0.16320.06030.7083-0.23580.06750.6480.02340.5461-12.1108-32.5892155.3441
656.82910.65911.60743.2145-1.36753.7901-0.17590.52170.3663-0.34720.0042-0.1304-0.4849-0.07270.15470.6551-0.0493-0.06110.2988-0.07580.5519-5.0126-22.8053102.7531
662.5449-0.1581-2.02273.86560.02993.9603-0.15370.06260.0497-0.66540.35070.5202-0.5264-0.241-0.11380.8310.0322-0.20510.79270.19040.5176-20.8637-2.3619102.5341
675.56761.48210.86342.6905-0.3769-0.81270.30840.0616-0.324-0.9495-0.0534-0.15150.31480.0859-0.29471.6826-0.2650.34980.5979-0.02741.026927.401835.4435117.6227
681.1443-1.18050.74221.04570.99062.5256-0.7535-0.6676-0.56720.16441.0506-0.8895-3.9812-1.8452-0.01140.554-1.00530.2596-0.1149-0.59381.435536.801715.0709131.5529
692.4509-4.7825-0.44395.43141.89353.86580.0296-0.47610.4611-0.51730.17740.49870.37250.2598-0.2921.4163-0.30010.20510.7451-0.28451.14295.199755.1369132.0891
704.7622.70713.84961.2685-0.85375.27560.13010.1447-0.1443-0.1830.3174-0.3646-0.63260.4658-0.41060.8495-0.03910.2540.6178-0.26891.0089-9.406149.079152.9172
712.40981.1069-1.1189-0.4632-0.11452.75780.4760.12850.463-1.25-0.33670.0762-0.72270.0015-0.09042.0054-0.23230.050.71830.09590.8825-2.410339.4623104.0616
725.57591.1117-0.49763.5-0.01710.3782-0.23240.27550.19830.11190.311-0.2577-0.5301-0.4722-0.09861.42460.122-0.07740.60920.11060.5301-15.862417.6723100.7485
734.41561.3603-1.30684.3083-2.64534.7645-0.04660.21670.1934-0.68530.00810.4325-0.3781-0.44820.03140.56740.1398-0.15230.3631-0.13940.6061-4.4448-45.718657.2276
742.9842-0.9122-2.1344.00881.60034.30460.29080.8176-0.1064-0.5414-0.21390.5365-0.45270.1151-0.12330.96080.2706-0.17590.7704-0.06580.506-12.1481-52.767533.0744
757.7385-1.83943.62571.96830.31394.54020.26330.46170.58190.2139-0.2655-0.91120.22220.2319-0.05210.46560.0332-0.01690.4023-0.09631.06623.4988-58.505969.2971
761.87851.41830.21482.3945-0.55557.24060.0853-0.03330.6823-0.21480.4590.35240.84060.4785-0.53120.41170.0834-0.12120.3915-0.17021.15134.7245-80.348261.4687
775.5597-1.6213-1.9434.6379-1.20095.1252-0.2755-0.51130.34980.90130.1552-0.58310.2622-0.10370.19760.6227-0.0088-0.06360.3663-0.08350.7061-4.9912-62.459885.6796
783.29950.41670.3744.6942-1.34691.6113-0.342-0.10610.06920.80020.150.17860.4982-0.29490.24580.76140.07770.16090.6749-0.04730.4862-20.955-82.916785.8521
797.12694.00420.59923.8291.39823.94680.25061.1675-1.0164-0.08540.06540.1485-0.07230.0936-0.34651.5570.3544-0.44760.8051-0.20290.93695.1541-140.446956.2235
805.9836-4.1946-2.70571.479-0.27434.23230.0816-0.043-0.22680.01750.3879-0.46260.6720.1812-0.46570.9190.0486-0.25070.6979-0.3260.9393-9.2972-134.411935.5176
812.5867-1.23640.0632-0.15710.99212.33710.3197-0.3106-0.76871.13320.02910.11910.798-0.0382-0.37582.13110.3132-0.00530.73420.04040.7897-2.3509-124.778384.4378
824.82640.0304-0.26242.92880.5359-0.00830.0721-0.082-0.21040.61080.35360.20410.7695-0.591-0.50011.407-0.14660.10760.68740.19340.5939-15.779-102.866487.6989
834.60990.2999-0.95372.9845-0.6921-0.5905-0.1162-0.0045-0.01031.1173-0.0864-0.432-0.1272-0.00780.22741.94150.3847-0.56530.595-0.02990.977227.4535-120.747170.7569
841.09540.71990.28991.7235-0.08362.79380.5320.2279-0.16710.06920.3024-0.36261.2280.4471-0.77760.9680.3657-0.31790.598-0.23481.155936.8614-100.392456.8731
851.2547-2.4413-1.28671.44341.09751.97310.02031.0062-0.52030.1085-0.43030.27470.5368-1.17570.54380.7443-0.2694-0.10381.5719-0.30951.2103-45.4197-112.552631.9072
861.1283-0.4402-0.61835.652-1.84952.52540.80850.077-0.58090.1187-0.15490.6540.6528-0.3119-0.67450.931-0.25-0.3230.8921-0.09930.9285-22.9324-123.787223.8548
873.63070.3061-1.05094.4109-0.48514.1511-0.32160.14190.02970.6251-0.55120.77620.2924-1.08990.76760.8259-0.43640.0241.6123-0.09440.919-51.2423-95.098759.2584
881.353-0.16112.31981.69511.73422.08310.0308-0.096-0.26730.519-0.55411.02240.9004-0.66570.41441.0228-0.28380.23690.7475-0.08040.9333-33.6209-97.462178.4624
891.6597-2.7695-1.64133.1074-0.36251.992-0.06610.97720.2864-0.4172-0.56620.4451-0.4829-0.77130.66870.6796-0.0124-0.23081.80430.13661.0944-48.6488-79.840330.1409
902.13251.01190.19011.12971.84345.72390.49770.7089-0.0853-0.369-0.20390.09210.3401-1.0153-0.20180.96760.3016-0.22531.0689-0.00570.6946-29.5555-62.677228.05
910.97240.63820.54028.19182.28062.1693-0.28220.6883-0.561-0.4977-0.15340.97910.50630.46680.38210.96360.05740.08821.1797-0.40210.8629.2136-107.79162.473
924.9805-1.2610.70342.4649-2.25421.6491-0.45670.5737-0.10250.16030.116-0.14950.14150.08270.31070.97990.0722-0.16640.7886-0.41440.9356-3.0642-125.04217.9799
934.03762.13951.80641.945-1.62011.7237-0.23570.4941-0.0933-0.58960.2423-0.15970.22930.40540.02540.81110.08960.10931.1648-0.07610.445933.3772-89.902316.1312
941.8075-0.4620.8013.99931.02196.41430.36190.3839-0.21110.07760.0304-0.75910.53890.7651-0.36870.36490.1104-0.01850.5836-0.0940.857438.046-86.199641.6484
951.7138-1.8853-0.58675.6240.47670.45670.31720.673-0.0835-0.5416-0.51620.5179-0.06490.21410.23140.83160.175-0.04361.1402-0.15840.47237.1088-74.73572.8121
961.18721.2579-2.62033.31951.00183.9395-0.1250.6484-0.091-0.66390.30780.14-0.7803-0.9144-0.20340.98120.2401-0.22070.9504-0.07270.5554-13.0263-63.972415.4847
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 158 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 113 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 158 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 113 )
5X-RAY DIFFRACTION5chain 'E' and (resid 3 through 158 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 113 )
7X-RAY DIFFRACTION7chain 'G' and (resid 3 through 158 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 113 )
9X-RAY DIFFRACTION9chain 'I' and (resid 3 through 158 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 113 )
11X-RAY DIFFRACTION11chain 'K' and (resid 3 through 158 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 113 )
13X-RAY DIFFRACTION13chain 'M' and (resid 3 through 158 )
14X-RAY DIFFRACTION14chain 'N' and (resid 1 through 113 )
15X-RAY DIFFRACTION15chain 'O' and (resid 3 through 158 )
16X-RAY DIFFRACTION16chain 'P' and (resid 1 through 113 )
17X-RAY DIFFRACTION17chain 'Q' and (resid 3 through 158 )
18X-RAY DIFFRACTION18chain 'R' and (resid 1 through 113 )
19X-RAY DIFFRACTION19chain 'S' and (resid 3 through 158 )
20X-RAY DIFFRACTION20chain 'T' and (resid 1 through 113 )
21X-RAY DIFFRACTION21chain 'U' and (resid 3 through 158 )
22X-RAY DIFFRACTION22chain 'V' and (resid 1 through 113 )
23X-RAY DIFFRACTION23chain 'W' and (resid 3 through 158 )
24X-RAY DIFFRACTION24chain 'X' and (resid 1 through 113 )
25X-RAY DIFFRACTION25chain 'Y' and (resid 3 through 158 )
26X-RAY DIFFRACTION26chain 'Z' and (resid 1 through 113 )
27X-RAY DIFFRACTION27chain 'a' and (resid 3 through 158 )
28X-RAY DIFFRACTION28chain 'b' and (resid 1 through 113 )
29X-RAY DIFFRACTION29chain 'c' and (resid 3 through 158 )
30X-RAY DIFFRACTION30chain 'd' and (resid 1 through 113 )
31X-RAY DIFFRACTION31chain 'e' and (resid 3 through 158 )
32X-RAY DIFFRACTION32chain 'f' and (resid 1 through 113 )
33X-RAY DIFFRACTION33chain 'g' and (resid 3 through 158 )
34X-RAY DIFFRACTION34chain 'h' and (resid 1 through 113 )
35X-RAY DIFFRACTION35chain 'i' and (resid 3 through 158 )
36X-RAY DIFFRACTION36chain 'j' and (resid 1 through 113 )
37X-RAY DIFFRACTION37chain 'k' and (resid 3 through 158 )
38X-RAY DIFFRACTION38chain 'l' and (resid 1 through 113 )
39X-RAY DIFFRACTION39chain 'm' and (resid 3 through 158 )
40X-RAY DIFFRACTION40chain 'n' and (resid 1 through 113 )
41X-RAY DIFFRACTION41chain 'o' and (resid 3 through 158 )
42X-RAY DIFFRACTION42chain 'p' and (resid 1 through 113 )
43X-RAY DIFFRACTION43chain 'q' and (resid 3 through 158 )
44X-RAY DIFFRACTION44chain 'r' and (resid 1 through 113 )
45X-RAY DIFFRACTION45chain 's' and (resid 3 through 158 )
46X-RAY DIFFRACTION46chain 't' and (resid 1 through 113 )
47X-RAY DIFFRACTION47chain 'u' and (resid 3 through 158 )
48X-RAY DIFFRACTION48chain 'v' and (resid 1 through 113 )
49X-RAY DIFFRACTION49chain 'w' and (resid 3 through 158 )
50X-RAY DIFFRACTION50chain 'x' and (resid 1 through 113 )
51X-RAY DIFFRACTION51chain 'y' and (resid 3 through 158 )
52X-RAY DIFFRACTION52chain 'z' and (resid 1 through 113 )
53X-RAY DIFFRACTION53chain '0' and (resid 3 through 158 )
54X-RAY DIFFRACTION54chain '1' and (resid 1 through 113 )
55X-RAY DIFFRACTION55chain '2' and (resid 3 through 158 )
56X-RAY DIFFRACTION56chain '3' and (resid 1 through 113 )
57X-RAY DIFFRACTION57chain '4' and (resid 3 through 158 )
58X-RAY DIFFRACTION58chain '5' and (resid 1 through 113 )
59X-RAY DIFFRACTION59chain '6' and (resid 3 through 158 )
60X-RAY DIFFRACTION60chain '7' and (resid 1 through 113 )
61X-RAY DIFFRACTION61chain '8' and (resid 3 through 158 )
62X-RAY DIFFRACTION62chain '9' and (resid 1 through 113 )
63X-RAY DIFFRACTION63chain 'AA' and (resid 3 through 158 )
64X-RAY DIFFRACTION64chain 'AB' and (resid 1 through 113 )
65X-RAY DIFFRACTION65chain 'AC' and (resid 3 through 158 )
66X-RAY DIFFRACTION66chain 'AD' and (resid 1 through 113 )
67X-RAY DIFFRACTION67chain 'AE' and (resid 3 through 158 )
68X-RAY DIFFRACTION68chain 'AF' and (resid 1 through 113 )
69X-RAY DIFFRACTION69chain 'AG' and (resid 3 through 158 )
70X-RAY DIFFRACTION70chain 'AH' and (resid 1 through 113 )
71X-RAY DIFFRACTION71chain 'AI' and (resid 3 through 158 )
72X-RAY DIFFRACTION72chain 'AJ' and (resid 1 through 113 )
73X-RAY DIFFRACTION73chain 'AK' and (resid 3 through 158 )
74X-RAY DIFFRACTION74chain 'AL' and (resid 1 through 113 )
75X-RAY DIFFRACTION75chain 'AM' and (resid 3 through 158 )
76X-RAY DIFFRACTION76chain 'AN' and (resid 1 through 113 )
77X-RAY DIFFRACTION77chain 'AO' and (resid 3 through 158 )
78X-RAY DIFFRACTION78chain 'AP' and (resid 1 through 113 )
79X-RAY DIFFRACTION79chain 'AQ' and (resid 3 through 158 )
80X-RAY DIFFRACTION80chain 'AR' and (resid 1 through 113 )
81X-RAY DIFFRACTION81chain 'AS' and (resid 3 through 158 )
82X-RAY DIFFRACTION82chain 'AT' and (resid 1 through 113 )
83X-RAY DIFFRACTION83chain 'AU' and (resid 3 through 158 )
84X-RAY DIFFRACTION84chain 'AV' and (resid 1 through 113 )
85X-RAY DIFFRACTION85chain 'AW' and (resid 3 through 158 )
86X-RAY DIFFRACTION86chain 'AX' and (resid 1 through 113 )
87X-RAY DIFFRACTION87chain 'AY' and (resid 3 through 158 )
88X-RAY DIFFRACTION88chain 'AZ' and (resid 1 through 113 )
89X-RAY DIFFRACTION89chain 'BA' and (resid 3 through 158 )
90X-RAY DIFFRACTION90chain 'BB' and (resid 1 through 113 )
91X-RAY DIFFRACTION91chain 'BC' and (resid 3 through 158 )
92X-RAY DIFFRACTION92chain 'BD' and (resid 1 through 113 )
93X-RAY DIFFRACTION93chain 'BE' and (resid 3 through 158 )
94X-RAY DIFFRACTION94chain 'BF' and (resid 1 through 113 )
95X-RAY DIFFRACTION95chain 'BG' and (resid 3 through 158 )
96X-RAY DIFFRACTION96chain 'BH' and (resid 1 through 113 )

+
万見について

-
お知らせ

-
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

+
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

+
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。

-
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