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- PDB-8ti7: Crystal structure of profilin from Dermatophagoides pteronyssinus... -

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基本情報

登録情報
データベース: PDB / ID: 8ti7
タイトルCrystal structure of profilin from Dermatophagoides pteronyssinus in complex with a poly(L-proline) peptide
要素
  • Profilin
  • poly(L-proline)
キーワードALLERGEN / mite profilin / dust mite / allergy
機能・相同性
機能・相同性情報


regulation of cellular component biogenesis / regulation of cellular component organization / actin binding / cytoskeleton
類似検索 - 分子機能
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily
類似検索 - ドメイン・相同性
生物種Dermatophagoides pteronyssinus (ダニ)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.397 Å
データ登録者O'Malley, A. / Sankaran, S. / Chruszcz, M.
資金援助 米国, 1件
組織認可番号
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI077653 米国
引用ジャーナル: Biol.Chem. / : 2024
タイトル: Structural homology of mite profilins to plant profilins is not indicative of allergic cross-reactivity.
著者: O'Malley, A. / Sankaran, S. / Carriuolo, A. / Khatri, K. / Kowal, K. / Chruszcz, M.
履歴
登録2023年7月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年5月8日Provider: repository / タイプ: Initial release
改定 1.12024年6月19日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: Profilin
C: Profilin
E: Profilin
G: Profilin
I: Profilin
K: Profilin
M: Profilin
O: Profilin
B: poly(L-proline)
D: poly(L-proline)
F: poly(L-proline)
H: poly(L-proline)
J: poly(L-proline)
L: poly(L-proline)
N: poly(L-proline)
P: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)146,21128
ポリマ-145,05816
非ポリマー1,15312
2,900161
1
A: Profilin
B: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,4205
ポリマ-18,1322
非ポリマー2883
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
C: Profilin
D: poly(L-proline)


分子量 (理論値)分子数
合計 (水以外)18,1322
ポリマ-18,1322
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
3
E: Profilin
F: poly(L-proline)


分子量 (理論値)分子数
合計 (水以外)18,1322
ポリマ-18,1322
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
4
G: Profilin
H: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,2283
ポリマ-18,1322
非ポリマー961
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
5
I: Profilin
J: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3244
ポリマ-18,1322
非ポリマー1922
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
6
K: Profilin
L: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3244
ポリマ-18,1322
非ポリマー1922
362
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
7
M: Profilin
N: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3244
ポリマ-18,1322
非ポリマー1922
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
8
O: Profilin
P: poly(L-proline)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)18,3244
ポリマ-18,1322
非ポリマー1922
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)152.802, 152.802, 186.854
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDモデル要素
11I-201-

SO4

21I-312-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A
137A
147A
158A
168A
179A
189A
1910A
2010A
2111A
2211A
2312A
2412A
2513A
2613A
2714A
2814A
2915A
3015A
3116A
3216A
3317A
3417A
3518A
3618A
3719A
3819A
3920A
4020A
4121A
4221A
4322A
4422A
4523A
4623A
4724A
4824A
4925A
5025A
5126A
5226A
5327A
5427A
5528A
5628A
5729A
5829A
5930A
6030A
6131A
6231A
6332A
6432A
6533A
6633A
6734A
6834A
6935A
7035A
7136A
7236A
7337A
7437A
7538A
7638A
7739A
7839A
7940A
8040A
8141A
8241A
8342A
8442A
8543A
8643A
8744A
8844A
8945A
9045A
9146A
9246A
9347A
9447A
9548A
9648A
9749A
9849A
9950A
10050A
10151A
10251A
10352A
10452A
10553A
10653A
10754A
10854A
10955A
11055A
11156A
11256A

NCSドメイン領域:

Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111GLYGLYASNASN1 - 12925 - 153
211GLYGLYASNASN1 - 12925 - 153
322SERSERASNASN0 - 12924 - 153
422SERSERASNASN0 - 12924 - 153
533GLYGLYTYRTYR-1 - 13023 - 154
633GLYGLYTYRTYR-1 - 13023 - 154
744SERSERASNASN0 - 12924 - 153
844SERSERASNASN0 - 12924 - 153
955GLYGLYTYRTYR-1 - 13023 - 154
1055GLYGLYTYRTYR-1 - 13023 - 154
1166SERSERASNASN0 - 12924 - 153
1266SERSERASNASN0 - 12924 - 153
1377GLYGLYASNASN1 - 12925 - 153
1477GLYGLYASNASN1 - 12925 - 153
1588GLYGLYASNASN1 - 12925 - 153
1688GLYGLYASNASN1 - 12925 - 153
1799GLYGLYASNASN1 - 12925 - 153
1899GLYGLYASNASN1 - 12925 - 153
191010GLYGLYASNASN1 - 12925 - 153
201010GLYGLYASNASN1 - 12925 - 153
211111GLYGLYASNASN1 - 12925 - 153
221111GLYGLYASNASN1 - 12925 - 153
231212GLYGLYASNASN1 - 12925 - 153
241212GLYGLYASNASN1 - 12925 - 153
251313GLYGLYTYRTYR1 - 13025 - 154
261313GLYGLYTYRTYR1 - 13025 - 154
271414SERSERASNASN0 - 12924 - 153
281414SERSERASNASN0 - 12924 - 153
291515SERSERTYRTYR0 - 13024 - 154
301515SERSERTYRTYR0 - 13024 - 154
311616SERSERASNASN0 - 12924 - 153
321616SERSERASNASN0 - 12924 - 153
331717SERSERTYRTYR0 - 13024 - 154
341717SERSERTYRTYR0 - 13024 - 154
351818GLYGLYASNASN1 - 12925 - 153
361818GLYGLYASNASN1 - 12925 - 153
371919SERSERASNASN0 - 12924 - 153
381919SERSERASNASN0 - 12924 - 153
392020GLYGLYTYRTYR-1 - 13023 - 154
402020GLYGLYTYRTYR-1 - 13023 - 154
412121SERSERASNASN0 - 12924 - 153
422121SERSERASNASN0 - 12924 - 153
432222GLYGLYASNASN1 - 12925 - 153
442222GLYGLYASNASN1 - 12925 - 153
452323SERSERASNASN0 - 12924 - 153
462323SERSERASNASN0 - 12924 - 153
472424SERSERTYRTYR0 - 13024 - 154
482424SERSERTYRTYR0 - 13024 - 154
492525GLYGLYASNASN1 - 12925 - 153
502525GLYGLYASNASN1 - 12925 - 153
512626SERSERASNASN0 - 12924 - 153
522626SERSERASNASN0 - 12924 - 153
532727GLYGLYASNASN1 - 12925 - 153
542727GLYGLYASNASN1 - 12925 - 153
552828GLYGLYASNASN1 - 12925 - 153
562828GLYGLYASNASN1 - 12925 - 153
572929GLYGLYCYSCYS1 - 1225 - 36
582929GLYGLYCYSCYS1 - 1225 - 36
593030GLYGLYCYSCYS1 - 1225 - 36
603030GLYGLYCYSCYS1 - 1225 - 36
613131GLYGLYCYSCYS1 - 1225 - 36
623131GLYGLYCYSCYS1 - 1225 - 36
633232GLYGLYCYSCYS1 - 1225 - 36
643232GLYGLYCYSCYS1 - 1225 - 36
653333GLYGLYCYSCYS1 - 1225 - 36
663333GLYGLYCYSCYS1 - 1225 - 36
673434GLYGLYCYSCYS1 - 1225 - 36
683434GLYGLYCYSCYS1 - 1225 - 36
693535GLYGLYCYSCYS1 - 1225 - 36
703535GLYGLYCYSCYS1 - 1225 - 36
713636GLYGLYCYSCYS1 - 1225 - 36
723636GLYGLYCYSCYS1 - 1225 - 36
733737GLYGLYCYSCYS1 - 1225 - 36
743737GLYGLYCYSCYS1 - 1225 - 36
753838GLYGLYCYSCYS1 - 1225 - 36
763838GLYGLYCYSCYS1 - 1225 - 36
773939GLYGLYCYSCYS1 - 1225 - 36
783939GLYGLYCYSCYS1 - 1225 - 36
794040GLYGLYCYSCYS1 - 1225 - 36
804040GLYGLYCYSCYS1 - 1225 - 36
814141GLYGLYCYSCYS1 - 1225 - 36
824141GLYGLYCYSCYS1 - 1225 - 36
834242GLYGLYCYSCYS1 - 1225 - 36
844242GLYGLYCYSCYS1 - 1225 - 36
854343GLYGLYCYSCYS1 - 1225 - 36
864343GLYGLYCYSCYS1 - 1225 - 36
874444GLYGLYCYSCYS1 - 1225 - 36
884444GLYGLYCYSCYS1 - 1225 - 36
894545GLYGLYCYSCYS1 - 1225 - 36
904545GLYGLYCYSCYS1 - 1225 - 36
914646GLYGLYCYSCYS1 - 1225 - 36
924646GLYGLYCYSCYS1 - 1225 - 36
934747GLYGLYCYSCYS1 - 1225 - 36
944747GLYGLYCYSCYS1 - 1225 - 36
954848GLYGLYCYSCYS1 - 1225 - 36
964848GLYGLYCYSCYS1 - 1225 - 36
974949GLYGLYCYSCYS1 - 1225 - 36
984949GLYGLYCYSCYS1 - 1225 - 36
995050GLYGLYCYSCYS1 - 1225 - 36
1005050GLYGLYCYSCYS1 - 1225 - 36
1015151GLYGLYCYSCYS1 - 1225 - 36
1025151GLYGLYCYSCYS1 - 1225 - 36
1035252GLYGLYCYSCYS1 - 1225 - 36
1045252GLYGLYCYSCYS1 - 1225 - 36
1055353GLYGLYCYSCYS1 - 1225 - 36
1065353GLYGLYCYSCYS1 - 1225 - 36
1075454GLYGLYCYSCYS1 - 1225 - 36
1085454GLYGLYCYSCYS1 - 1225 - 36
1095555GLYGLYCYSCYS1 - 1225 - 36
1105555GLYGLYCYSCYS1 - 1225 - 36
1115656GLYGLYCYSCYS1 - 1225 - 36
1125656GLYGLYCYSCYS1 - 1225 - 36

NCSアンサンブル:
ID詳細
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24
13Local NCS retraints between domains: 25 26
14Local NCS retraints between domains: 27 28
15Local NCS retraints between domains: 29 30
16Local NCS retraints between domains: 31 32
17Local NCS retraints between domains: 33 34
18Local NCS retraints between domains: 35 36
19Local NCS retraints between domains: 37 38
20Local NCS retraints between domains: 39 40
21Local NCS retraints between domains: 41 42
22Local NCS retraints between domains: 43 44
23Local NCS retraints between domains: 45 46
24Local NCS retraints between domains: 47 48
25Local NCS retraints between domains: 49 50
26Local NCS retraints between domains: 51 52
27Local NCS retraints between domains: 53 54
28Local NCS retraints between domains: 55 56
29Local NCS retraints between domains: 57 58
30Local NCS retraints between domains: 59 60
31Local NCS retraints between domains: 61 62
32Local NCS retraints between domains: 63 64
33Local NCS retraints between domains: 65 66
34Local NCS retraints between domains: 67 68
35Local NCS retraints between domains: 69 70
36Local NCS retraints between domains: 71 72
37Local NCS retraints between domains: 73 74
38Local NCS retraints between domains: 75 76
39Local NCS retraints between domains: 77 78
40Local NCS retraints between domains: 79 80
41Local NCS retraints between domains: 81 82
42Local NCS retraints between domains: 83 84
43Local NCS retraints between domains: 85 86
44Local NCS retraints between domains: 87 88
45Local NCS retraints between domains: 89 90
46Local NCS retraints between domains: 91 92
47Local NCS retraints between domains: 93 94
48Local NCS retraints between domains: 95 96
49Local NCS retraints between domains: 97 98
50Local NCS retraints between domains: 99 100
51Local NCS retraints between domains: 101 102
52Local NCS retraints between domains: 103 104
53Local NCS retraints between domains: 105 106
54Local NCS retraints between domains: 107 108
55Local NCS retraints between domains: 109 110
56Local NCS retraints between domains: 111 112

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要素

#1: タンパク質
Profilin


分子量: 16948.895 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Dermatophagoides pteronyssinus (ダニ)
遺伝子: LOC113791125 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A2L0EBJ5
#2: タンパク質・ペプチド
poly(L-proline)


分子量: 1183.393 Da / 分子数: 8 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 12 / 由来タイプ: 合成 / : SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 161 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.89 Å3/Da / 溶媒含有率: 57.5 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M BIS-TRIS pH 6.5, 2 M ammonium sulfate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年4月13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: 1 Å / 相対比: 1
Reflection twin
タイプCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.2356
pseudo-merohedral22K, H, -L20.0842
pseudo-merohedral33-1/3H-2/3K-2/3L, -2/3H-1/3K+2/3L, -2/3H+2/3K-1/3L30.1611
pseudo-merohedral44-2/3H-1/3K+2/3L, -1/3H-2/3K-2/3L, 2/3H-2/3K+1/3L40.1219
pseudo-merohedral551/3H-1/3K+2/3L, -H, -2/3H-4/3K-1/3L50.0759
pseudo-merohedral66-K, -1/3H+1/3K-2/3L, 4/3H+2/3K-1/3L60.0686
pseudo-merohedral77-1/3H+1/3K-2/3L, -K, -4/3H-2/3K+1/3L70.1329
pseudo-merohedral88-H, 1/3H-1/3K+2/3L, 2/3H+4/3K+1/3L80.1198
反射解像度: 2.397→40 Å / Num. obs: 63158 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / 冗長度: 4.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.036 / Rrim(I) all: 0.078 / Rsym value: 0.069 / Net I/σ(I): 30.4
反射 シェル解像度: 2.4→2.44 Å / 冗長度: 5.2 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3136 / CC1/2: 0.687 / CC star: 0.902 / Rpim(I) all: 0.318 / Rrim(I) all: 0.735 / Rsym value: 0.662 / % possible all: 99.7

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0415精密化
HKL-3000データ削減
HKL-3000データスケーリング
MOLREP位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.397→34.161 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 8.1 / SU ML: 0.134 / 交差検証法: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.039 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.1948 3203 5.073 %
Rwork0.1657 59930 -
all0.167 --
obs-63133 98.846 %
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 BULK SOLVENT
原子変位パラメータBiso mean: 74.893 Å2
Baniso -1Baniso -2Baniso -3
1--16.148 Å2-0 Å2-0 Å2
2---16.148 Å2-0 Å2
3---32.297 Å2
精密化ステップサイクル: LAST / 解像度: 2.397→34.161 Å
タンパク質核酸リガンド溶媒全体
原子数8608 0 60 161 8829
拘束条件
Refine-IDタイプDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128864
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168201
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.66412137
X-RAY DIFFRACTIONr_angle_other_deg1.0571.57418964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60951129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.959540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.676101310
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.94710374
X-RAY DIFFRACTIONr_chiral_restr0.0680.21352
X-RAY DIFFRACTIONr_chiral_restr_other1.5370.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210567
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021873
X-RAY DIFFRACTIONr_nbd_refined0.2070.21616
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2290.27329
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24297
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.24666
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2308
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.213
X-RAY DIFFRACTIONr_nbd_other0.2250.248
X-RAY DIFFRACTIONr_mcbond_it6.3165.1994564
X-RAY DIFFRACTIONr_mcbond_other6.3145.1994564
X-RAY DIFFRACTIONr_mcangle_it8.7159.3325677
X-RAY DIFFRACTIONr_mcangle_other8.7149.3335678
X-RAY DIFFRACTIONr_scbond_it6.2215.3994300
X-RAY DIFFRACTIONr_scbond_other6.1795.3994253
X-RAY DIFFRACTIONr_scangle_it8.5989.8236460
X-RAY DIFFRACTIONr_scangle_other8.6069.8286389
X-RAY DIFFRACTIONr_lrange_it10.97747.1769311
X-RAY DIFFRACTIONr_lrange_other10.97647.1799312
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.053822
X-RAY DIFFRACTIONr_ncsr_local_group_20.1020.053834
X-RAY DIFFRACTIONr_ncsr_local_group_30.1020.053846
X-RAY DIFFRACTIONr_ncsr_local_group_40.1080.053800
X-RAY DIFFRACTIONr_ncsr_local_group_50.1090.053872
X-RAY DIFFRACTIONr_ncsr_local_group_60.1030.053816
X-RAY DIFFRACTIONr_ncsr_local_group_70.1060.053756
X-RAY DIFFRACTIONr_ncsr_local_group_80.0960.053842
X-RAY DIFFRACTIONr_ncsr_local_group_90.0940.053772
X-RAY DIFFRACTIONr_ncsr_local_group_100.0930.053825
X-RAY DIFFRACTIONr_ncsr_local_group_110.0960.053837
X-RAY DIFFRACTIONr_ncsr_local_group_120.0910.053838
X-RAY DIFFRACTIONr_ncsr_local_group_130.0950.053878
X-RAY DIFFRACTIONr_ncsr_local_group_140.0960.053765
X-RAY DIFFRACTIONr_ncsr_local_group_150.1090.053862
X-RAY DIFFRACTIONr_ncsr_local_group_160.0950.053843
X-RAY DIFFRACTIONr_ncsr_local_group_170.0970.053906
X-RAY DIFFRACTIONr_ncsr_local_group_180.0990.053792
X-RAY DIFFRACTIONr_ncsr_local_group_190.1040.053764
X-RAY DIFFRACTIONr_ncsr_local_group_200.0960.053876
X-RAY DIFFRACTIONr_ncsr_local_group_210.10.053736
X-RAY DIFFRACTIONr_ncsr_local_group_220.1020.053759
X-RAY DIFFRACTIONr_ncsr_local_group_230.1020.053842
X-RAY DIFFRACTIONr_ncsr_local_group_240.1060.053875
X-RAY DIFFRACTIONr_ncsr_local_group_250.0990.053812
X-RAY DIFFRACTIONr_ncsr_local_group_260.1020.053817
X-RAY DIFFRACTIONr_ncsr_local_group_270.0950.053803
X-RAY DIFFRACTIONr_ncsr_local_group_280.0970.053781
X-RAY DIFFRACTIONr_ncsr_local_group_290.0720.05247
X-RAY DIFFRACTIONr_ncsr_local_group_300.0660.05247
X-RAY DIFFRACTIONr_ncsr_local_group_310.060.05248
X-RAY DIFFRACTIONr_ncsr_local_group_320.0160.05250
X-RAY DIFFRACTIONr_ncsr_local_group_330.0360.05252
X-RAY DIFFRACTIONr_ncsr_local_group_340.0230.05250
X-RAY DIFFRACTIONr_ncsr_local_group_350.1320.05248
X-RAY DIFFRACTIONr_ncsr_local_group_360.0720.05246
X-RAY DIFFRACTIONr_ncsr_local_group_370.10.05244
X-RAY DIFFRACTIONr_ncsr_local_group_380.070.05248
X-RAY DIFFRACTIONr_ncsr_local_group_390.0710.05248
X-RAY DIFFRACTIONr_ncsr_local_group_400.070.05247
X-RAY DIFFRACTIONr_ncsr_local_group_410.1480.05246
X-RAY DIFFRACTIONr_ncsr_local_group_420.0890.05244
X-RAY DIFFRACTIONr_ncsr_local_group_430.0630.05245
X-RAY DIFFRACTIONr_ncsr_local_group_440.0660.05248
X-RAY DIFFRACTIONr_ncsr_local_group_450.0580.05246
X-RAY DIFFRACTIONr_ncsr_local_group_460.140.05246
X-RAY DIFFRACTIONr_ncsr_local_group_470.0620.05248
X-RAY DIFFRACTIONr_ncsr_local_group_480.0660.05248
X-RAY DIFFRACTIONr_ncsr_local_group_490.0630.05247
X-RAY DIFFRACTIONr_ncsr_local_group_500.1450.05247
X-RAY DIFFRACTIONr_ncsr_local_group_510.0240.05252
X-RAY DIFFRACTIONr_ncsr_local_group_520.0230.05251
X-RAY DIFFRACTIONr_ncsr_local_group_530.130.05252
X-RAY DIFFRACTIONr_ncsr_local_group_540.0320.05252
X-RAY DIFFRACTIONr_ncsr_local_group_550.1330.05251
X-RAY DIFFRACTIONr_ncsr_local_group_560.1320.05249
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098650.0501
12AX-RAY DIFFRACTIONLocal ncs0.098650.0501
23AX-RAY DIFFRACTIONLocal ncs0.101680.05009
24AX-RAY DIFFRACTIONLocal ncs0.101680.05009
35AX-RAY DIFFRACTIONLocal ncs0.102440.05009
36AX-RAY DIFFRACTIONLocal ncs0.102440.05009
47AX-RAY DIFFRACTIONLocal ncs0.107730.05009
48AX-RAY DIFFRACTIONLocal ncs0.107730.05009
59AX-RAY DIFFRACTIONLocal ncs0.10870.05009
510AX-RAY DIFFRACTIONLocal ncs0.10870.05009
611AX-RAY DIFFRACTIONLocal ncs0.103470.05009
612AX-RAY DIFFRACTIONLocal ncs0.103470.05009
713AX-RAY DIFFRACTIONLocal ncs0.106090.05009
714AX-RAY DIFFRACTIONLocal ncs0.106090.05009
815AX-RAY DIFFRACTIONLocal ncs0.096070.0501
816AX-RAY DIFFRACTIONLocal ncs0.096070.0501
917AX-RAY DIFFRACTIONLocal ncs0.094180.0501
918AX-RAY DIFFRACTIONLocal ncs0.094180.0501
1019AX-RAY DIFFRACTIONLocal ncs0.093170.0501
1020AX-RAY DIFFRACTIONLocal ncs0.093170.0501
1121AX-RAY DIFFRACTIONLocal ncs0.096450.05009
1122AX-RAY DIFFRACTIONLocal ncs0.096450.05009
1223AX-RAY DIFFRACTIONLocal ncs0.090660.05009
1224AX-RAY DIFFRACTIONLocal ncs0.090660.05009
1325AX-RAY DIFFRACTIONLocal ncs0.095150.0501
1326AX-RAY DIFFRACTIONLocal ncs0.095150.0501
1427AX-RAY DIFFRACTIONLocal ncs0.095740.05009
1428AX-RAY DIFFRACTIONLocal ncs0.095740.05009
1529AX-RAY DIFFRACTIONLocal ncs0.108740.05009
1530AX-RAY DIFFRACTIONLocal ncs0.108740.05009
1631AX-RAY DIFFRACTIONLocal ncs0.095370.05009
1632AX-RAY DIFFRACTIONLocal ncs0.095370.05009
1733AX-RAY DIFFRACTIONLocal ncs0.096570.05009
1734AX-RAY DIFFRACTIONLocal ncs0.096570.05009
1835AX-RAY DIFFRACTIONLocal ncs0.099240.05009
1836AX-RAY DIFFRACTIONLocal ncs0.099240.05009
1937AX-RAY DIFFRACTIONLocal ncs0.104330.05009
1938AX-RAY DIFFRACTIONLocal ncs0.104330.05009
2039AX-RAY DIFFRACTIONLocal ncs0.096450.05009
2040AX-RAY DIFFRACTIONLocal ncs0.096450.05009
2141AX-RAY DIFFRACTIONLocal ncs0.100430.05009
2142AX-RAY DIFFRACTIONLocal ncs0.100430.05009
2243AX-RAY DIFFRACTIONLocal ncs0.102360.05009
2244AX-RAY DIFFRACTIONLocal ncs0.102360.05009
2345AX-RAY DIFFRACTIONLocal ncs0.101740.05009
2346AX-RAY DIFFRACTIONLocal ncs0.101740.05009
2447AX-RAY DIFFRACTIONLocal ncs0.105810.05009
2448AX-RAY DIFFRACTIONLocal ncs0.105810.05009
2549AX-RAY DIFFRACTIONLocal ncs0.099340.05009
2550AX-RAY DIFFRACTIONLocal ncs0.099340.05009
2651AX-RAY DIFFRACTIONLocal ncs0.102260.05009
2652AX-RAY DIFFRACTIONLocal ncs0.102260.05009
2753AX-RAY DIFFRACTIONLocal ncs0.095370.05009
2754AX-RAY DIFFRACTIONLocal ncs0.095370.05009
2855AX-RAY DIFFRACTIONLocal ncs0.09660.05009
2856AX-RAY DIFFRACTIONLocal ncs0.09660.05009
2957AX-RAY DIFFRACTIONLocal ncs0.072180.05005
2958AX-RAY DIFFRACTIONLocal ncs0.072180.05005
3059AX-RAY DIFFRACTIONLocal ncs0.066260.05005
3060AX-RAY DIFFRACTIONLocal ncs0.066260.05005
3161AX-RAY DIFFRACTIONLocal ncs0.060280.05004
3162AX-RAY DIFFRACTIONLocal ncs0.060280.05004
3263AX-RAY DIFFRACTIONLocal ncs0.016210.05005
3264AX-RAY DIFFRACTIONLocal ncs0.016210.05005
3365AX-RAY DIFFRACTIONLocal ncs0.03630.05006
3366AX-RAY DIFFRACTIONLocal ncs0.03630.05006
3467AX-RAY DIFFRACTIONLocal ncs0.022560.05005
3468AX-RAY DIFFRACTIONLocal ncs0.022560.05005
3569AX-RAY DIFFRACTIONLocal ncs0.131940.05005
3570AX-RAY DIFFRACTIONLocal ncs0.131940.05005
3671AX-RAY DIFFRACTIONLocal ncs0.072060.05005
3672AX-RAY DIFFRACTIONLocal ncs0.072060.05005
3773AX-RAY DIFFRACTIONLocal ncs0.099520.05004
3774AX-RAY DIFFRACTIONLocal ncs0.099520.05004
3875AX-RAY DIFFRACTIONLocal ncs0.070260.05006
3876AX-RAY DIFFRACTIONLocal ncs0.070260.05006
3977AX-RAY DIFFRACTIONLocal ncs0.071030.05006
3978AX-RAY DIFFRACTIONLocal ncs0.071030.05006
4079AX-RAY DIFFRACTIONLocal ncs0.06970.05006
4080AX-RAY DIFFRACTIONLocal ncs0.06970.05006
4181AX-RAY DIFFRACTIONLocal ncs0.148420.05006
4182AX-RAY DIFFRACTIONLocal ncs0.148420.05006
4283AX-RAY DIFFRACTIONLocal ncs0.089290.05004
4284AX-RAY DIFFRACTIONLocal ncs0.089290.05004
4385AX-RAY DIFFRACTIONLocal ncs0.062870.05004
4386AX-RAY DIFFRACTIONLocal ncs0.062870.05004
4487AX-RAY DIFFRACTIONLocal ncs0.066210.05005
4488AX-RAY DIFFRACTIONLocal ncs0.066210.05005
4589AX-RAY DIFFRACTIONLocal ncs0.057530.05005
4590AX-RAY DIFFRACTIONLocal ncs0.057530.05005
4691AX-RAY DIFFRACTIONLocal ncs0.140450.05005
4692AX-RAY DIFFRACTIONLocal ncs0.140450.05005
4793AX-RAY DIFFRACTIONLocal ncs0.061630.05005
4794AX-RAY DIFFRACTIONLocal ncs0.061630.05005
4895AX-RAY DIFFRACTIONLocal ncs0.065620.05005
4896AX-RAY DIFFRACTIONLocal ncs0.065620.05005
4997AX-RAY DIFFRACTIONLocal ncs0.063460.05004
4998AX-RAY DIFFRACTIONLocal ncs0.063460.05004
5099AX-RAY DIFFRACTIONLocal ncs0.145040.05005
50100AX-RAY DIFFRACTIONLocal ncs0.145040.05005
51101AX-RAY DIFFRACTIONLocal ncs0.023830.05006
51102AX-RAY DIFFRACTIONLocal ncs0.023830.05006
52103AX-RAY DIFFRACTIONLocal ncs0.023210.05006
52104AX-RAY DIFFRACTIONLocal ncs0.023210.05006
53105AX-RAY DIFFRACTIONLocal ncs0.129820.05007
53106AX-RAY DIFFRACTIONLocal ncs0.129820.05007
54107AX-RAY DIFFRACTIONLocal ncs0.032140.05007
54108AX-RAY DIFFRACTIONLocal ncs0.032140.05007
55109AX-RAY DIFFRACTIONLocal ncs0.133250.05006
55110AX-RAY DIFFRACTIONLocal ncs0.133250.05006
56111AX-RAY DIFFRACTIONLocal ncs0.132480.05006
56112AX-RAY DIFFRACTIONLocal ncs0.132480.05006
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.397-2.4590.4821730.3024187X-RAY DIFFRACTION91.8862
2.459-2.5260.3812060.2534325X-RAY DIFFRACTION99.2335
2.526-2.5990.272520.2364253X-RAY DIFFRACTION100.7379
2.599-2.6790.2192270.2364106X-RAY DIFFRACTION99.7697
2.679-2.7660.2362480.1983953X-RAY DIFFRACTION99.4084
2.766-2.8630.2851840.1913840X-RAY DIFFRACTION100.1493
2.863-2.970.1942160.1823701X-RAY DIFFRACTION99.1897
2.97-3.0910.2091890.1853571X-RAY DIFFRACTION100.0798
3.091-3.2270.1862360.1833453X-RAY DIFFRACTION100.6548
3.227-3.3840.2481600.173258X-RAY DIFFRACTION99.4183
3.384-3.5650.2412260.1753038X-RAY DIFFRACTION99.6337
3.565-3.780.1331490.162892X-RAY DIFFRACTION96.5703
3.78-4.0380.1641610.1572660X-RAY DIFFRACTION97.2759
4.038-4.3580.1531630.1332539X-RAY DIFFRACTION98.9019
4.358-4.7680.102680.1342449X-RAY DIFFRACTION99.2899
4.768-5.3210.2631280.1252140X-RAY DIFFRACTION100.0441
5.321-6.1270.182680.1811941X-RAY DIFFRACTION100
6.127-7.460.303330.1451659X-RAY DIFFRACTION99.588
7.46-10.3710.118640.1341251X-RAY DIFFRACTION97.6969
10.371-34.1610.145520.179714X-RAY DIFFRACTION98.4576
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.64660.1818-0.88272.5105-0.68111.84230.06130.06660.0138-0.3124-0.16310.41540.1221-0.31380.10170.0606-0.0137-0.09880.1888-0.0690.473920.49537.4920.684
24.1424-2.3823.03913.713-5.69328.91750.40270.1471-0.39950.0117-0.19690.2027-0.16530.2955-0.20580.15540.0279-0.04910.0364-0.04340.233730.78530.694-10.365
30.7166-0.18710.07430.49420.00352.1533-0.01360.0471-0.1233-0.17310.1167-0.10120.2870.5642-0.10310.15420.06860.03090.2274-0.07990.598617.31276.716-27.265
46.7057-5.06851.57395.3562-2.90462.33480.51610.27880.0564-0.4542-0.22120.15040.13220.0456-0.2950.3845-0.02560.02860.147-0.03640.36256.54268.991-37.372
51.03650.10860.51882.7132-0.46322.902-0.3187-0.30450.03960.17110.15150.1095-0.1445-0.35870.16730.14620.09660.1170.1159-0.04280.45044.44841.687-31.707
60.69110.1211-0.23883.13555.616215.2729-0.18250.0497-0.0766-0.09320.04180.2882-0.304-0.08640.14070.08470.01540.00080.07930.05480.26953.78656.753-40.004
72.5163-0.38860.03151.0341-0.37911.84220.03060.2662-0.2735-0.02650.13120.21860.1852-0.0756-0.16180.1264-0.0873-0.03670.1516-0.08650.50824.28920.927-60.74
88.561810.4810.454415.56071.67560.4931-0.20850.22620.0722-0.34750.13790.3244-0.0699-0.03060.07070.076-0.02770.00630.12780.03560.2177-8.96426.136-51.739
90.5374-0.72710.90832.511-0.59952.1329-0.0006-0.0911-0.2880.25920.21510.18910.1642-0.0761-0.21440.2012-0.04050.06060.05310.06720.55615.61413.67-35.576
102.65053.94720.060614.4873-0.01420.01540.2564-0.1512-0.11770.4928-0.25480.44490.00520.0491-0.00160.1843-0.0071-0.03050.22260.05260.291626.9215.553-44.373
111.6215-0.0563-0.25990.68150.51022.1813-0.1391-0.182-0.14720.10070.04910.05360.62620.04690.09010.24450.0183-0.02750.03160.08130.53940.15467.517-6.129
122.7823-5.5098-0.805711.65240.51532.5677-0.2814-0.3090.15650.42580.4756-0.2615-0.07310.4232-0.19430.21770.0349-0.00170.202-0.01110.228812.7372.3443.844
130.7671-0.2850.73571.55-0.01212.3886-0.3081-0.03870.24140.12570.155-0.1989-0.30030.18440.15310.1835-0.0496-0.09140.1127-0.07240.50832.85144.977-33.87
146.0232.10492.61571.55263.837311.6794-0.4949-0.24970.6363-0.3682-0.1540.3323-0.7697-0.44180.64890.3236-0.0867-0.08620.21460.07510.493133.53332.332-22.936
151.7604-0.53840.15411.60090.64020.4499-0.0063-0.0360.2695-0.4228-0.12380.0748-0.2369-0.04480.130.1660.07370.00750.14440.12170.521436.8260.727-1.761
162.769-0.43953.09821.2792-2.849913.68410.21040.18350.31350.0057-0.2550.0523-0.34260.04670.04470.12450.10180.04860.1460.020.331224.83268.3736.867
精密化 TLSグループSelection: ALL

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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

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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