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- PDB-3qd9: C72S/C353S mutant of Trypanosoma brucei QSOX containing an interd... -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 3qd9
タイトルC72S/C353S mutant of Trypanosoma brucei QSOX containing an interdomain disulfide
要素QSOX from Trypanosoma brucei (TbQSOX)
キーワードOXIDOREDUCTASE / ERV fold / thioredoxin fold / sulfhydryl oxidase / disulfide bond
機能・相同性
機能・相同性情報


flavin-dependent sulfhydryl oxidase activity / thiol oxidase / thiol oxidase activity / protein disulfide isomerase activity / protein folding / nucleotide binding / extracellular space / membrane
類似検索 - 分子機能
Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain ...Sulfhydryl oxidase / ERV/ALR sulfhydryl oxidase domain / ERV/ALR sulfhydryl oxidase domain superfamily / Erv1 / Alr family / ERV/ALR sulfhydryl oxidase domain profile. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
FLAVIN-ADENINE DINUCLEOTIDE / Sulfhydryl oxidase
類似検索 - 構成要素
生物種Trypanosoma brucei (トリパノソーマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Alon, A. / Fass, D.
引用ジャーナル: Nature / : 2012
タイトル: The dynamic disulphide relay of quiescin sulphydryl oxidase.
著者: Alon, A. / Grossman, I. / Gat, Y. / Kodali, V.K. / DiMaio, F. / Mehlman, T. / Haran, G. / Baker, D. / Thorpe, C. / Fass, D.
履歴
登録2011年1月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年5月30日Provider: repository / タイプ: Initial release
改定 1.12012年8月22日Group: Database references
改定 1.22012年8月29日Group: Database references
改定 1.32023年9月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: QSOX from Trypanosoma brucei (TbQSOX)
B: QSOX from Trypanosoma brucei (TbQSOX)
C: QSOX from Trypanosoma brucei (TbQSOX)
D: QSOX from Trypanosoma brucei (TbQSOX)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,9808
ポリマ-208,8374
非ポリマー3,1424
30617
1
A: QSOX from Trypanosoma brucei (TbQSOX)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,9952
ポリマ-52,2091
非ポリマー7861
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
2
B: QSOX from Trypanosoma brucei (TbQSOX)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,9952
ポリマ-52,2091
非ポリマー7861
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
3
C: QSOX from Trypanosoma brucei (TbQSOX)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,9952
ポリマ-52,2091
非ポリマー7861
181
タイプ名称対称操作
identity operation1_555x,y,z1
手法PISA
4
D: QSOX from Trypanosoma brucei (TbQSOX)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)52,9952
ポリマ-52,2091
非ポリマー7861
0
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)81.040, 120.310, 106.220
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain a and resseq 34:119
211chain b and resseq 34:119
311chain c and resseq 34:119
411chain d and resseq 34:119
112chain a and resseq 121:128
212chain b and resseq 121:128
312chain c and resseq 121:128
412chain d and resseq 121:128
113chain a and resseq 145:195
213chain b and resseq 145:195
313chain c and resseq 145:195
413chain d and resseq 145:195
114chain a and resseq 208:431
214chain b and resseq 208:431
314chain c and resseq 208:431
414chain d and resseq 208:431

NCSアンサンブル:
ID
1
2
3
4

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要素

#1: タンパク質
QSOX from Trypanosoma brucei (TbQSOX)


分子量: 52209.336 Da / 分子数: 4 / 断片: UNP residues 20-485 / 変異: C72S, C353S / 由来タイプ: 組換発現
由来: (組換発現) Trypanosoma brucei (トリパノソーマ)
遺伝子: QSOX, Tb927.6.1850 / プラスミド: pET28b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): origami 2 / 参照: UniProt: Q585M6, thiol oxidase
#2: 化合物
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 4 / 由来タイプ: 合成 / : C27H33N9O15P2 / コメント: FAD*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 17 / 由来タイプ: 天然 / : 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: 2.39 Å3/Da / 溶媒含有率: 48.54 %
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: 8
詳細: 20% w/v PEG 3350, 0.2 M sodium sulfate, 0.5% w/v polyvinylpyrrolidone K15, pH 8, 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: ESRF / ビームライン: ID23-1 / 波長: 0.9769 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2010年6月23日
放射モノクロメーター: Si 111 CHANNEL / 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: 0.9769 Å / 相対比: 1
反射解像度: 3.3→50 Å / Num. all: 29616 / Num. obs: 29261 / % possible obs: 98.8 % / Observed criterion σ(I): -5 / 冗長度: 5.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.9
反射 シェル解像度: 3.3→3.48 Å / 冗長度: 5.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5 / % possible all: 98.9

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解析

ソフトウェア
名称バージョン分類
ADSCQuantumデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.7_629)精密化
MOSFLMデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 3QCP
解像度: 3.3→38.107 Å / SU ML: 0.43 / σ(F): 0 / 位相誤差: 24.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2486 2939 10.05 %
Rwork0.1902 --
obs0.196 29236 98.59 %
all-29654 -
溶媒の処理減衰半径: 0.83 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 48.546 Å2 / ksol: 0.306 e/Å3
原子変位パラメータ
Baniso -1Baniso -2Baniso -3
1--5.3383 Å20 Å2-4.7501 Å2
2--0.0099 Å2-0 Å2
3---5.2379 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→38.107 Å
タンパク質核酸リガンド溶媒全体
原子数12306 0 212 17 12535
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.01512874
X-RAY DIFFRACTIONf_angle_d1.82817493
X-RAY DIFFRACTIONf_dihedral_angle_d19.2254623
X-RAY DIFFRACTIONf_chiral_restr0.1151890
X-RAY DIFFRACTIONf_plane_restr0.0082253
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
11A662X-RAY DIFFRACTIONPOSITIONAL
12B662X-RAY DIFFRACTIONPOSITIONAL0.107
13C662X-RAY DIFFRACTIONPOSITIONAL0.094
14D662X-RAY DIFFRACTIONPOSITIONAL0.111
21A78X-RAY DIFFRACTIONPOSITIONAL
22B78X-RAY DIFFRACTIONPOSITIONAL0.055
23C78X-RAY DIFFRACTIONPOSITIONAL0.063
24D78X-RAY DIFFRACTIONPOSITIONAL0.061
31A426X-RAY DIFFRACTIONPOSITIONAL
32B426X-RAY DIFFRACTIONPOSITIONAL0.086
33C426X-RAY DIFFRACTIONPOSITIONAL0.177
34D426X-RAY DIFFRACTIONPOSITIONAL0.187
41A1780X-RAY DIFFRACTIONPOSITIONAL
42B1780X-RAY DIFFRACTIONPOSITIONAL0.105
43C1780X-RAY DIFFRACTIONPOSITIONAL0.087
44D1780X-RAY DIFFRACTIONPOSITIONAL0.101
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.35420.37771200.29271234X-RAY DIFFRACTION98
3.3542-3.4120.31491500.24191244X-RAY DIFFRACTION98
3.412-3.4740.27211480.23471241X-RAY DIFFRACTION100
3.474-3.54070.3061200.22361278X-RAY DIFFRACTION97
3.5407-3.6130.31661390.22361236X-RAY DIFFRACTION100
3.613-3.69150.29761380.20961234X-RAY DIFFRACTION97
3.6915-3.77730.26441350.1981256X-RAY DIFFRACTION100
3.7773-3.87160.25941470.20471250X-RAY DIFFRACTION98
3.8716-3.97620.28591600.19861245X-RAY DIFFRACTION100
3.9762-4.09310.26521100.18381254X-RAY DIFFRACTION98
4.0931-4.2250.24871500.18331259X-RAY DIFFRACTION100
4.225-4.37580.24531450.16611240X-RAY DIFFRACTION99
4.3758-4.55080.2291370.16591241X-RAY DIFFRACTION98
4.5508-4.75750.21091410.17211274X-RAY DIFFRACTION99
4.7575-5.00780.22081440.16971269X-RAY DIFFRACTION100
5.0078-5.32080.27011480.17881243X-RAY DIFFRACTION99
5.3208-5.73030.26711460.21821261X-RAY DIFFRACTION99
5.7303-6.30470.27431330.22951262X-RAY DIFFRACTION98
6.3047-7.21160.23871390.18261279X-RAY DIFFRACTION99
7.2116-9.06560.21311450.1441259X-RAY DIFFRACTION99
9.0656-38.10910.17781440.17431238X-RAY DIFFRACTION95
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0780.07780.33571.3273-0.24571.87380.3789-0.6366-0.04721.1563-0.82310.4498-0.21380.1595-0.10170.95440.15950.3881.06180.36950.89556.965936.614215.7342
20.41780.0481-0.10220.02050.03780.18840.6637-0.0091-0.36760.4890.26950.1405-0.2998-0.6054-0.00050.78820.19650.16421.05660.24921.11782.509636.6206-0.1551
32.24960.4881-0.15951.63950.25560.06920.3955-0.6190.55890.7648-0.05620.6489-0.5369-0.08150.16520.53210.03810.20890.3101-0.08780.464515.883136.069714.0497
40.57760.15590.6540.14730.12640.75720.1534-0.1595-0.08030.03490.3185-0.4384-0.2455-0.27090.21470.57590.110.27320.24130.16820.813412.760435.37767.3701
51.1110.7139-0.90440.7825-0.66050.75560.3230.5374-0.023-0.39820.31480.74170.0928-0.13940.07330.40150.0660.09180.3124-0.03550.671515.9234.3911-1.8591
60.60620.1167-0.78960.0529-0.16221.03010.7634-0.23990.57790.36920.0827-0.4368-0.57330.34230.07080.7217-0.08560.26650.37420.03361.071523.121442.23064.3384
70.26340.1918-0.08640.1401-0.06280.0284-0.21630.14970.4052-0.30810.1749-0.0097-0.0257-0.12950.00010.84860.34320.26810.63760.20970.90256.861949.8949-0.8499
80.70990.72580.27140.76040.26940.11170.6656-0.4722-0.2620.73770.1411-0.3662-0.1298-0.04420.08050.87230.37590.28010.93750.11971.5029-0.297742.693520.4341
90.47680.1303-0.1141.20970.80561.44630.0831-0.25660.1186-0.14850.07430.426-0.870.2711-0.03020.2969-0.02350.10320.4334-0.04090.03618.970418.665530.8252
100.1832-0.13220.22410.533-0.83591.2793-0.00160.0297-0.2336-0.1416-0.14250.0120.49190.5814-0.3045-0.14890.5956-0.12090.2210.03880.293516.98885.901416.6245
110.52890.4272-0.6450.3423-0.50531.4503-0.3115-0.0936-0.6905-0.08740.30270.19020.8707-0.6461-0.0340.33780.0175-0.05030.35190.12880.3297.8953.428713.432
121.06570.3239-0.74060.29940.08451.0009-0.12210.1580.0276-0.08930.30910.4782-0.1819-0.56780.09630.42820.0411-0.00270.25620.0190.32082.865810.002517.9201
130.7516-0.1658-0.54010.5890.07170.64360.1777-0.1140.8911-0.6146-0.320.2685-0.48540.5508-0.01650.3046-0.0636-0.02060.3966-0.06290.58.735623.139628.8653
142.77612.29571.4412.29010.99151.152-0.045-0.0869-0.7931-0.26320.5859-0.71310.51740.64320.68820.23590.03360.16950.71260.06160.242821.17785.104630.0158
150.2754-0.23520.26620.7654-0.0970.2903-0.17070.18180.1563-0.26180.3335-0.5586-0.12890.8362-0.03310.41450.07160.00570.8478-0.12440.256522.783714.154218.4663
160.0968-0.0175-0.16890.3373-0.03350.3047-0.18240.2560.3198-0.3352-0.0105-0.94110.25210.6322-00.52560.00640.02141.26190.16990.43830.366612.913726.2956
170.9192-0.89080.42941.74740.19280.6205-0.23190.19520.2909-0.29630.0147-0.3146-0.44190.5938-0.08840.3342-0.16-0.04351.0543-0.0360.198427.888915.339235.0999
180.06740.0260.0770.09910.07510.1128-0.1882-0.74690.45410.10770.4563-0.3697-0.96210.42020.00010.772-0.2503-0.00711.0479-0.12360.65722.411428.086536.7486
190.0577-0.0640.00490.2711-0.04970.01180.1029-0.3394-0.30740.3021-0.35390.49550.0891-0.0157-0.00740.88790.0497-0.02371.8224-0.09710.641227.216117.771450.808
200.44220.24060.27421.47640.22850.1822-0.176-0.63340.035-0.01710.05230.10490.05290.1709-0.13060.4424-0.0122-0.04611.07750.0428-0.002819.9239.57642.3941
210.5473-0.43660.71220.5985-0.41391.0216-0.73240.50920.0376-0.7364-0.39860.2949-0.44010.2878-0.17890.6496-0.0357-0.0271.1607-0.20710.622342.416226.1513-14.9233
220.00930.00710.01440.2766-0.16030.1342-0.10030.40970.0631-0.50270.1954-1.2408-0.21180.53590.00150.64210.12650.08860.83790.01810.682338.31218.0747-15.0387
230.31630.1791-0.13170.42-0.16840.1132-0.39081.25910.2968-0.6942-0.1046-0.0891-0.7049-0.4522-0.01151.07950.1214-0.23370.73040.00020.531723.643122.0544-19.325
241.0015-0.0355-0.02810.6679-0.01640.4176-0.03450.0057-0.06-0.34-0.1243-0.13980.18360.1449-0.08880.25710.4167-0.1479-0.14570.07920.19836.160221.1943-5.6975
250.6491-0.227-0.10.13380.09830.505-0.05050.21440.24570.5390.0930.32760.09890.0730.20790.51290.25590.0516-0.08540.20340.428529.503222.0621-9.3152
261.0035-0.0857-0.05790.0396-0.00270.6208-0.2143-0.28250.5497-0.24510.09380.4782-0.5856-0.5460.08280.26820.25280.06110.21850.16930.47921.119323.5886-5.9661
270.30090.0308-0.13180.30220.1110.4572-0.2207-0.3106-0.29110.75050.140.3060.0155-0.019-0.0420.23640.018-0.0270.11350.01660.40825.44115.01660.6705
280.3993-0.35080.3130.3065-0.27480.2465-0.02490.1491-0.2899-0.22780.34820.12070.1667-0.07210.15860.6863-0.1527-0.27020.5868-0.27080.690520.32257.8372-15.3234
290.0096-0.01030.03240.022-0.05590.3330.41250.6948-0.8554-0.555-0.1858-0.54570.25130.62280.00450.7435-0.06430.12771.0497-0.20340.723445.007216.4872-19.9245
300.12150.01440.06540.0832-0.1170.22690.05030.0993-0.0478-0.1024-0.1701-0.2431-0.11190.38640.08010.3840.17090.11140.33110.38680.25450.907941.3525-11.7569
311.9650.05240.14840.31870.15740.773-0.11470.1620.6536-0.0680.1170.1223-0.5742-0.2531-0.27290.57750.2771-0.05180.08870.43570.341239.390151.1019-3.445
320.84660.97480.02731.50170.65511.0442-0.36470.27430.7687-0.5179-0.1318-0.054-0.70090.1224-2.31220.88910.0373-0.18960.54550.45840.990336.476754.2335-12.4234
331.4101-0.08680.13690.7846-0.65110.75290.01390.57430.0947-0.56150.04890.09730.04540.04640.07170.1491-0.21030.3957-0.12540.7837-0.189849.420141.0178-11.2265
340.3310.12540.09041.01270.4410.1982-0.1429-0.17390.08720.03050.13790.4643-0.3848-0.2407-0.21080.42430.42040.16980.01830.37470.470443.179645.63892.7528
350.9183-0.1358-0.67460.3256-0.32871.09490.13110.00340.4055-0.0124-0.0396-0.0854-0.38470.07770.34990.2793-0.02310.1547-0.18510.56920.406548.985443.10199.4217
363.4506-3.1751.942.9199-1.7831.091-0.465-0.38840.56820.6940.0058-0.7275-0.37290.4272-0.25140.36190.04880.02410.22370.09420.233657.113839.67497.387
372.23611.55720.22491.10150.11340.1199-0.2993-0.0016-0.297-0.3380.264-0.3108-0.1478-0.0301-0.06320.39160.11420.00510.09750.02680.30658.510827.80320.9198
380.04640.0425-0.03820.19280.08620.1279-0.13790.8724-0.21470.0909-0.3223-0.1744-0.28440.2049-0.00050.52290.16150.08661.12070.06411.093773.104537.44945.9347
390.6434-0.1905-1.23970.05660.36682.3918-0.3536-0.86140.04950.1048-0.2678-0.2371-0.15250.8072-0.14880.2299-0.1663-0.12120.61230.11040.735968.474842.33238.7977
400.0682-0.01690.05020.0757-0.00270.03610.4170.44670.2638-0.426-0.3-0.3057-0.21230.2733-0.00280.7363-0.07970.08590.55550.22560.832962.65747.9465-6.2237
410.07620.03860.03210.1573-0.14560.26680.0676-0.1467-0.0274-0.70820.3469-0.4488-0.5404-0.48410.00521.2363-0.40970.03531.43670.30091.027969.863914.979248.9891
420.1284-0.0688-0.0350.1092-0.05790.0929-0.2137-0.5152-0.20370.4018-0.114-0.77590.28370.57390.00081.10950.1351-0.26341.67090.50211.249373.6724-0.430754.8673
431.84720.72780.5840.34650.20810.2020.1143-1.08691.1210.6702-0.098-0.0244-1.19920.08740.09320.740.06380.03371.1624-0.0060.573460.651312.417849.5837
440.526-0.2356-0.44540.6487-0.13290.56890.2857-0.73630.32440.0102-0.67350.05590.7738-0.7857-0.04930.5551-0.11710.01911.2178-0.07620.460564.04775.456951.7021
450.1333-0.08970.15110.2313-0.02150.2161-0.3198-0.1854-0.5343-0.2801-0.15440.06040.7675-0.1969-0.0680.63390.05340.02171.20710.43010.690660.4839-3.271553.7684
461.60891.06431.05410.81110.64220.71580.1768-0.2690.7810.0922-0.56920.6025-0.30110.0483-0.14290.5069-0.12890.13661.3301-0.08280.375252.97496.106558.7488
470.1164-0.2851-0.12611.01180.37710.15-0.5622-0.43280.06160.39130.07630.5224-0.09250.2015-0.07771.1416-0.0791-0.34781.4260.1780.722668.65161.701267.5067
480.06020.02910.01790.0889-0.01130.20010.1894-0.38940.164-0.09140.3435-0.0216-0.2263-0.18350.01330.8476-0.3185-0.17631.2047-0.08940.734474.965222.50149.9633
491.1017-0.1509-0.37770.1622-0.02160.1682-0.1136-0.62570.18970.6772-0.026-0.3163-0.22860.0953-0.1360.37730.02-0.08210.2037-0.0080.263967.858917.622725.7064
500.374-0.42130.3141.1657-0.21740.84810.1007-0.0933-0.458-0.46120.21180.72330.2487-0.27691.1260.2172-0.0157-0.13580.25340.0780.560359.6763.143221.313
511.15860.6731-0.12180.3947-0.06220.01310.11810.1588-0.8158-0.1611-0.0336-0.87540.22770.59860.00320.45890.05930.02650.2725-0.04860.366468.7025-0.878320.138
520.2589-0.1372-0.11990.4812-0.24630.2936-0.1266-0.2119-0.08680.1811-0.0021-0.3465-0.11180.25740.00160.40590.0016-0.09060.11150.13360.372973.87445.740124.3861
531.92630.220.68730.4609-0.15360.3663-0.1704-1.0981-0.25640.33750.2581-0.46850.0082-0.25430.03170.30230.0278-0.09220.3689-0.01230.363368.330320.966232.399
540.46140.34670.1981.4322-0.39810.34580.35070.0786-0.5392-0.1479-0.11060.91860.2956-0.22790.64830.1314-0.02790.02720.1568-0.07270.480955.461315.095515.8098
550.61910.16310.25410.1162-0.14910.75650.1982-0.4109-0.44660.61620.21020.2745-0.4394-0.60950.53950.44390.02490.04890.4170.44910.630653.08978.730430.2578
560.23550.1592-0.00720.4611-0.04120.0039-0.2502-0.7622-0.34570.4150.40151.06990.4483-1.03930.00590.4073-0.09880.13020.64610.15230.881245.319415.999321.1515
572.34441.87081.68865.01942.20011.5310.1409-0.83920.14690.5350.05880.48460.0802-0.44130.2896-0.0190.09910.10050.33290.10630.479149.054423.97323.118
580.7096-0.23590.28780.6261-0.65280.6962-0.4192-1.08840.12911.01110.087-0.1126-0.80870.0846-0.08841.01230.23810.18720.6824-0.03840.560654.645229.760834.6745
592.177-1.23991.09841.0916-1.24671.5617-0.1005-0.396-0.26480.06630.38890.5428-0.28030.13870.34860.71850.08620.16380.2862-0.15570.599650.7139.498919.8665
600.9485-0.1523-0.0510.03350.01690.89080.0699-0.13780.1714-0.51350.3371-0.3435-0.22160.13040.14430.3215-0.0412-0.05080.11880.10250.577757.455228.176714.7669
610.0249-0.04270.01320.0855-0.04150.03750.2812-0.2368-0.0571-0.03450.2759-0.14110.6058-0.56180.00910.8704-0.23290.04231.21830.25671.597938.7959-20.630244.5152
620.2683-0.1087-0.11810.2106-0.09550.1769-0.570.1559-0.65480.087-0.3448-0.74920.3386-0.1132-0.00071.23770.23340.12321.550.77091.706353.8116-24.777848.6445
630.4274-0.02960.2540.0032-0.03170.5132-0.3466-0.421-0.4574-0.15240.31090.44060.8454-0.5027-0.29610.7029-0.0766-0.14340.89290.56510.833240.6658-12.094243.1056
640.019-0.0107-0.00240.01040.01050.0178-0.27010.0867-0.2745-0.29270.0792-0.08270.25160.3850.00551.6055-0.0144-0.12870.9614-0.04471.287649.8552-22.179728.7608
651.7113-0.5015-0.3620.66370.11280.0817-0.1855-1.4312-0.60930.4854-0.1328-0.52060.07050.25530.02110.8827-0.0879-0.22511.08710.52310.840448.0557-11.765449.894
660.62760.1959-0.3130.2428-0.2570.29590.16470.02390.0851-0.15350.1569-0.16810.1588-0.03670.03571.4222-0.03030.14071.0616-0.14531.145862.4743-16.360447.3541
670.21260.0561-0.04940.0885-0.08160.1636-0.20510.4827-0.0094-0.62010.11260.1937-0.339-0.49840.00110.8999-0.0368-0.010.59910.21490.716250.4315-7.194636.4526
680.71970.99160.6422.67582.55932.70250.48290.359-0.4765-0.39850.6264-0.52950.15220.64820.50141.10350.2367-0.32960.87280.06191.246255.9515-24.607435.3628
690.1830.0829-0.08630.22970.01530.04240.17850.0650.9064-0.0433-0.1018-0.17220.15490.1260.00761.1871-0.24480.06711.14670.50731.301329.2753-26.557244.6027
700.1804-0.18360.21230.1907-0.22860.2280.1141-0.6154-0.19350.5130.33810.4097-0.0326-0.96993.43330.83270.0428-0.15492.03420.76340.208432.7343-4.264867.4476
710.00240-0.00970.06340.07760.1290.0114-0.044-0.00220.11980.32680.33490.182-0.43210.7341.0220.28060.1331.98260.76390.738639.0905-6.013376.8425
720.13380.24240.20890.44260.34190.63060.2647-0.2491-0.30840.30930.41150.53620.4522-0.86241.96950.7806-0.0028-0.07761.87440.72651.079637.334-13.641471.9454
731.9306-0.0319-0.59960.94950.49731.46820.0093-0.7602-0.7640.4613-0.2379-0.20820.53350.2871-0.36240.7816-0.1541-0.03921.48351.14520.90525.66-13.985457.57
740.48720.16060.15521.9464-0.65640.31650.0248-0.61660.06610.86240.01930.1235-0.2965-0.6325-0.42680.7297-0.0138-0.11942.10910.12420.270127.85214.888966.7269
750.0426-0.0836-0.05080.2162-0.07250.5441-0.00910.03780.03930.2822-0.04810.0241-0.274-0.27271.2690.6519-0.0752-0.06521.81780.35520.256530.52597.402557.5417
760.7985-0.1710.00770.13450.11410.2856-0.3964-0.52680.28810.41240.1923-0.10750.1613-0.3311-0.0060.5355-0.0664-0.07741.35590.2090.345419.71066.780556.3525
774.42280.6744-2.5270.1081-0.31712.0672-0.3965-0.2629-0.88950.24410.3510.38940.2115-0.6704-0.19360.5034-0.1744-0.05141.32390.60660.589518.2789-3.569547.0533
780.00820.11570.08811.69521.30060.99730.238-0.3041-0.28340.54030.20240.06090.16090.0391-0.00340.52730.0046-0.09311.87650.31761.21143.8034.735554.3268
790.27810.2680.60920.260.58791.334-0.3564-0.37370.40770.1438-0.24030.636-0.58190.4807-0.05970.84210.34170.06462.01240.23330.81489.44896.48960.5416
800.0288-0.1074-0.0640.38510.2290.13590.16020.24920.240.0217-0.24720.1265-0.1894-0.4511-0.12021.03540.32270.03152.13450.60350.939315.9037-5.440370.8312
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 31:44)
2X-RAY DIFFRACTION2(chain A and resid 45:57)
3X-RAY DIFFRACTION3(chain A and resid 58:85)
4X-RAY DIFFRACTION4(chain A and resid 86:121)
5X-RAY DIFFRACTION5(chain A and resid 122:148)
6X-RAY DIFFRACTION6(chain A and resid 149:170)
7X-RAY DIFFRACTION7(chain A and resid 171:186)
8X-RAY DIFFRACTION8(chain A and resid 187:206)
9X-RAY DIFFRACTION9(chain A and resid 207:230)
10X-RAY DIFFRACTION10(chain A and resid 231:256)
11X-RAY DIFFRACTION11(chain A and resid 257:279)
12X-RAY DIFFRACTION12(chain A and resid 280:293)
13X-RAY DIFFRACTION13(chain A and resid 294:320)
14X-RAY DIFFRACTION14(chain A and resid 321:339)
15X-RAY DIFFRACTION15(chain A and resid 340:351)
16X-RAY DIFFRACTION16(chain A and resid 352:368)
17X-RAY DIFFRACTION17(chain A and resid 369:379)
18X-RAY DIFFRACTION18(chain A and resid 380:403)
19X-RAY DIFFRACTION19(chain A and resid 404:414)
20X-RAY DIFFRACTION20(chain A and resid 415:432)
21X-RAY DIFFRACTION21(chain B and resid 29:34)
22X-RAY DIFFRACTION22(chain B and resid 35:42)
23X-RAY DIFFRACTION23(chain B and resid 43:57)
24X-RAY DIFFRACTION24(chain B and resid 58:85)
25X-RAY DIFFRACTION25(chain B and resid 86:120)
26X-RAY DIFFRACTION26(chain B and resid 121:148)
27X-RAY DIFFRACTION27(chain B and resid 149:171)
28X-RAY DIFFRACTION28(chain B and resid 172:184)
29X-RAY DIFFRACTION29(chain B and resid 185:210)
30X-RAY DIFFRACTION30(chain B and resid 211:230)
31X-RAY DIFFRACTION31(chain B and resid 231:256)
32X-RAY DIFFRACTION32(chain B and resid 257:279)
33X-RAY DIFFRACTION33(chain B and resid 280:333)
34X-RAY DIFFRACTION34(chain B and resid 334:351)
35X-RAY DIFFRACTION35(chain B and resid 352:369)
36X-RAY DIFFRACTION36(chain B and resid 370:379)
37X-RAY DIFFRACTION37(chain B and resid 380:403)
38X-RAY DIFFRACTION38(chain B and resid 404:413)
39X-RAY DIFFRACTION39(chain B and resid 414:421)
40X-RAY DIFFRACTION40(chain B and resid 422:434)
41X-RAY DIFFRACTION41(chain C and resid 30:42)
42X-RAY DIFFRACTION42(chain C and resid 43:58)
43X-RAY DIFFRACTION43(chain C and resid 59:85)
44X-RAY DIFFRACTION44(chain C and resid 86:121)
45X-RAY DIFFRACTION45(chain C and resid 122:148)
46X-RAY DIFFRACTION46(chain C and resid 149:168)
47X-RAY DIFFRACTION47(chain C and resid 169:186)
48X-RAY DIFFRACTION48(chain C and resid 187:210)
49X-RAY DIFFRACTION49(chain C and resid 211:230)
50X-RAY DIFFRACTION50(chain C and resid 231:256)
51X-RAY DIFFRACTION51(chain C and resid 257:279)
52X-RAY DIFFRACTION52(chain C and resid 280:293)
53X-RAY DIFFRACTION53(chain C and resid 294:320)
54X-RAY DIFFRACTION54(chain C and resid 321:340)
55X-RAY DIFFRACTION55(chain C and resid 341:355)
56X-RAY DIFFRACTION56(chain C and resid 356:368)
57X-RAY DIFFRACTION57(chain C and resid 369:379)
58X-RAY DIFFRACTION58(chain C and resid 380:402)
59X-RAY DIFFRACTION59(chain C and resid 403:414)
60X-RAY DIFFRACTION60(chain C and resid 415:433)
61X-RAY DIFFRACTION61(chain D and resid 33:43)
62X-RAY DIFFRACTION62(chain D and resid 44:57)
63X-RAY DIFFRACTION63(chain D and resid 58:85)
64X-RAY DIFFRACTION64(chain D and resid 86:95)
65X-RAY DIFFRACTION65(chain D and resid 96:128)
66X-RAY DIFFRACTION66(chain D and resid 129:144)
67X-RAY DIFFRACTION67(chain D and resid 145:168)
68X-RAY DIFFRACTION68(chain D and resid 169:187)
69X-RAY DIFFRACTION69(chain D and resid 188:210)
70X-RAY DIFFRACTION70(chain D and resid 211:255)
71X-RAY DIFFRACTION71(chain D and resid 256:277)
72X-RAY DIFFRACTION72(chain D and resid 278:293)
73X-RAY DIFFRACTION73(chain D and resid 294:320)
74X-RAY DIFFRACTION74(chain D and resid 321:346)
75X-RAY DIFFRACTION75(chain D and resid 347:368)
76X-RAY DIFFRACTION76(chain D and resid 369:379)
77X-RAY DIFFRACTION77(chain D and resid 380:403)
78X-RAY DIFFRACTION78(chain D and resid 404:413)
79X-RAY DIFFRACTION79(chain D and resid 414:426)
80X-RAY DIFFRACTION80(chain D and resid 427:433)

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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://pdbjlvh1.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