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- PDB-5flj: enzyme-substrate-dioxygen complex of Ni-quercetinase -

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基本情報

登録情報
データベース: PDB / ID: 5flj
タイトルenzyme-substrate-dioxygen complex of Ni-quercetinase
要素QUERCETINASE QUED
キーワードOXIDOREDUCTASE / DIOXYGENASE / NICKEL / STREPTOMYCES / NI-QUERCETINASE / DIOXYGEN
機能・相同性
機能・相同性情報


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
NICKEL (II) ION / OXYGEN MOLECULE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / Quercetinase QueD
類似検索 - 構成要素
生物種STREPTOMYCES SP. (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.818 Å
データ登録者Jeoung, J.-H. / Nianios, D. / Fetzner, S. / Dobbek, H.
引用ジャーナル: Angew.Chem.Int.Ed.Engl. / : 2016
タイトル: Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-on O2 -Ni Complex.
著者: Jeoung, J. / Nianios, D. / Fetzner, S. / Dobbek, H.
履歴
登録2015年10月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02016年6月1日Provider: repository / タイプ: Initial release
改定 1.12024年1月10日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: QUERCETINASE QUED
B: QUERCETINASE QUED
C: QUERCETINASE QUED
D: QUERCETINASE QUED
E: QUERCETINASE QUED
F: QUERCETINASE QUED
G: QUERCETINASE QUED
H: QUERCETINASE QUED
I: QUERCETINASE QUED
J: QUERCETINASE QUED
K: QUERCETINASE QUED
L: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)258,69053
ポリマ-253,12312
非ポリマー5,56741
22,9871276
1
C: QUERCETINASE QUED
D: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,17510
ポリマ-42,1872
非ポリマー9888
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-72 kcal/mol
Surface area15870 Å2
手法PISA
2
K: QUERCETINASE QUED
L: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,0658
ポリマ-42,1872
非ポリマー8786
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-69.7 kcal/mol
Surface area15820 Å2
手法PISA
3
G: QUERCETINASE QUED
H: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,1439
ポリマ-42,1872
非ポリマー9567
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-68.7 kcal/mol
Surface area16020 Å2
手法PISA
4
E: QUERCETINASE QUED
F: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,17510
ポリマ-42,1872
非ポリマー9888
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-63.7 kcal/mol
Surface area15770 Å2
手法PISA
5
I: QUERCETINASE QUED
J: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,0658
ポリマ-42,1872
非ポリマー8786
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-69.1 kcal/mol
Surface area15490 Å2
手法PISA
6
A: QUERCETINASE QUED
B: QUERCETINASE QUED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,0658
ポリマ-42,1872
非ポリマー8786
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-66.2 kcal/mol
Surface area15820 Å2
手法PISA
単位格子
Length a, b, c (Å)102.812, 114.586, 105.990
Angle α, β, γ (deg.)90.00, 95.61, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 12分子 ABCDEFGHIJKL

#1: タンパク質
QUERCETINASE QUED / NI-QUERECETINASE


分子量: 21093.562 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) STREPTOMYCES SP. (バクテリア) / : FLA / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A2VA43, quercetin 2,3-dioxygenase

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非ポリマー , 5種, 1317分子

#2: 化合物
ChemComp-NI / NICKEL (II) ION


分子量: 58.693 Da / 分子数: 12 / 由来タイプ: 合成 / : Ni
#3: 化合物
ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN / クエルセチン


分子量: 302.236 Da / 分子数: 12 / 由来タイプ: 合成 / : C15H10O7
#4: 化合物
ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 15 / 由来タイプ: 合成 / : C2H6OS / コメント: DMSO, 沈殿剤*YM
#5: 化合物 ChemComp-OXY / OXYGEN MOLECULE / ペルオキシド


分子量: 31.999 Da / 分子数: 2 / 由来タイプ: 合成 / : O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1276 / 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: 2.4 Å3/Da / 溶媒含有率: 48.7 % / 解説: NONE
結晶化pH: 8
詳細: 0.1 M CACL2, 0.1 M TRIS-HCL PH 8.0, 10 - 13% PEG6000 AND 5% GLYCEROL

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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: BESSY / ビームライン: 14.1 / 波長: 0.9184
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD
放射モノクロメーター: SI-111 / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9184 Å / 相対比: 1
反射解像度: 1.82→47.91 Å / Num. obs: 210593 / % possible obs: 96.4 % / Observed criterion σ(I): 1.6 / 冗長度: 3.7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3
反射 シェル解像度: 1.82→1.96 Å / Rmerge(I) obs: 0.79 / % possible all: 91.1

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 5FLH
解像度: 1.818→38.803 Å / SU ML: 0.21 / σ(F): 1.35 / 位相誤差: 22.71 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2076 10533 5 %
Rwork0.1641 --
obs0.1662 210593 96.08 %
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
精密化ステップサイクル: LAST / 解像度: 1.818→38.803 Å
タンパク質核酸リガンド溶媒全体
原子数17667 0 340 1276 19283
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0118901
X-RAY DIFFRACTIONf_angle_d1.18125645
X-RAY DIFFRACTIONf_dihedral_angle_d16.5766846
X-RAY DIFFRACTIONf_chiral_restr0.0522506
X-RAY DIFFRACTIONf_plane_restr0.0063439
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8177-1.83840.32812890.2885496X-RAY DIFFRACTION79
1.8384-1.860.31133270.27236201X-RAY DIFFRACTION90
1.86-1.88270.32033310.27526302X-RAY DIFFRACTION91
1.8827-1.90650.30513340.24026328X-RAY DIFFRACTION91
1.9065-1.93160.23393360.21726387X-RAY DIFFRACTION92
1.9316-1.95810.26143360.21336382X-RAY DIFFRACTION93
1.9581-1.9860.25663410.21676488X-RAY DIFFRACTION94
1.986-2.01570.27043450.21116553X-RAY DIFFRACTION95
2.0157-2.04720.25823510.20886665X-RAY DIFFRACTION96
2.0472-2.08070.25253510.1986667X-RAY DIFFRACTION96
2.0807-2.11660.22693520.18246685X-RAY DIFFRACTION97
2.1166-2.15510.24083550.18386759X-RAY DIFFRACTION98
2.1551-2.19650.23953580.18016784X-RAY DIFFRACTION98
2.1965-2.24140.21753550.18216754X-RAY DIFFRACTION98
2.2414-2.29010.2393600.186850X-RAY DIFFRACTION98
2.2901-2.34340.23423550.18536742X-RAY DIFFRACTION98
2.3434-2.4020.21463610.186852X-RAY DIFFRACTION99
2.402-2.46690.24093580.18056793X-RAY DIFFRACTION98
2.4669-2.53950.26233570.19116790X-RAY DIFFRACTION98
2.5395-2.62140.22433600.17636839X-RAY DIFFRACTION98
2.6214-2.71510.21653600.17966849X-RAY DIFFRACTION98
2.7151-2.82380.21043580.16866788X-RAY DIFFRACTION98
2.8238-2.95220.21843610.16386875X-RAY DIFFRACTION99
2.9522-3.10780.21493590.16526821X-RAY DIFFRACTION98
3.1078-3.30240.23143610.15536847X-RAY DIFFRACTION99
3.3024-3.55730.18563630.15236890X-RAY DIFFRACTION99
3.5573-3.91490.18763610.14446866X-RAY DIFFRACTION99
3.9149-4.48070.17493630.12896900X-RAY DIFFRACTION99
4.4807-5.64250.15823650.12666938X-RAY DIFFRACTION99
5.6425-38.81190.17533700.16047020X-RAY DIFFRACTION99
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)
16.64813.3586-0.15837.48172.48915.7077-0.07321.0478-0.4102-0.9142-0.10130.14510.2681-0.49930.08490.40930.0527-0.02180.6828-0.04920.206167.17164.2499-11.7529
23.56120.04240.23162.075-0.09011.98820.06780.49720.1224-0.33480.02550.0708-0.1327-0.2828-0.06130.26860.0478-0.01820.34670.0710.1699163.35147.7812-2.3001
38.4685-3.16424.10435.4765-2.39164.5334-0.39170.44371.34220.192-0.0086-0.4716-1.39340.04350.45320.62090.06840.13340.37090.17890.5613166.081325.42936.0249
43.1825-0.90252.02555.2678-1.15912.6906-0.06790.01930.70840.42940.0860.1186-0.7311-0.33150.04590.37470.08210.07530.24040.04870.3378160.818422.655514.0639
51.008-0.3006-0.49891.32280.22341.46120.20840.40650.4787-0.2521-0.04520.0126-0.5447-0.1116-0.08520.36090.06510.0240.28340.12470.3345163.609818.77325.0828
61.3216-1.07971.15233.3738-0.03882.4824-0.05650.86270.8368-0.62030.0687-0.1932-0.88870.10250.04740.5471-0.01290.12450.50450.2690.6482174.67421.6115-4.5619
72.7363-0.24580.89867.16112.55446.66180.41720.29820.9369-0.06180.1615-0.6613-1.714-0.3004-0.21710.80260.0630.07330.38720.23490.7754163.959531.97083.9968
81.83120.5288-0.43311.9214-0.99382.56950.22390.18090.39390.01650.02190.497-0.3525-0.3912-0.15450.23440.13050.02010.29540.04920.3741147.536713.942715.3536
96.9862-2.2155.46182.4334-1.99244.37780.4163-0.1414-0.5511-0.64190.00530.48820.9059-1.0153-0.42690.3579-0.045-0.10560.54930.04420.3846146.8886-4.90226.5002
103.8921-0.10561.83552.9892-0.72794.01620.11490.625-0.3827-0.45790.05150.32050.3988-0.2268-0.1620.27720.0098-0.06990.3215-0.04080.2249156.0936-4.80782.5796
111.2678-0.3570.36672.1052-1.56013.34480.03240.1951-0.1597-0.30950.14930.3390.3159-0.543-0.15580.21950.006-0.06780.27710.00260.2363154.7119-3.70176.7565
120.13340.3387-0.16561.2154-0.17680.80290.09740.4860.1864-0.146-0.00210.5421-0.1343-0.5654-0.11480.26190.1095-0.07450.48780.06160.3711145.17845.92159.8856
136.22450.21270.18556.69660.95187.95160.0746-0.5584-0.55160.23420.19740.7650.1532-0.6684-0.2140.294-0.01870.03590.43720.11240.4081143.2636-0.986423.4059
141.7265-2.57022.09084.1166-2.48813.8740.37341.072-0.46250.37990.11871.61570.3328-2.0218-0.46610.4458-0.1181-0.11560.90790.1270.8875131.7931-2.05069.0505
153.4735-0.724-0.78562.38571.22754.83440.1761.3553-1.1337-0.0345-0.6380.78430.4468-0.96070.3460.4532-0.1817-0.18150.5867-0.04640.6982142.8439-7.97621.6763
163.3835-4.5209-2.14047.4836-0.41699.63450.15530.44880.89-0.8856-0.47571.3189-0.8316-0.00180.30090.51150.1581-0.17740.66940.05510.7523105.296969.89680.4075
171.94250.6608-0.76052.78460.6713.04410.01090.26230.1559-0.1830.01370.3741-0.2422-0.484-0.03420.16390.0402-0.05050.3476-0.01820.2477113.11362.245880.927
183.10531.94990.99423.94122.30445.71040.2627-0.4701-0.27150.3567-0.22820.36250.7231-0.8320.10030.2488-0.10590.04870.436-0.03710.3706113.466645.424789.4008
193.71122.04141.05452.33850.67392.89160.04490.0416-0.49640.1523-0.0977-0.02190.4291-0.41970.04890.2551-0.0959-0.00710.2796-0.05390.2668121.870743.926487.7892
202.72930.68862.79752.1230.32487.3519-0.12070.0249-0.2149-0.08610.00440.3157-0.1883-0.61460.11010.1696-0.01050.0260.2842-0.05150.2219118.124453.161187.4507
213.27921.84141.495.0561.65855.64410.1784-0.21520.26860.5258-0.15420.72510.0804-0.7597-0.03910.2180.00580.06420.4424-0.08830.3786106.879159.204393.2506
228.0034-0.5806-3.34982.5338-0.55042.15270.45860.3626-0.63660.3146-0.29411.91670.451-2.0322-0.06070.4999-0.17560.08410.8977-0.01310.85397.846947.739289.4942
235.3177-2.94220.43189.7027-2.10445.0505-0.1987-0.4142-0.90470.642-0.22550.20110.4879-0.62960.36650.5043-0.29360.01920.57940.03370.4949110.898738.362891.4337
242.3336-0.9314-0.12418.9362-5.98184.3150.2624-0.3193-0.56730.5167-0.00530.27280.577-0.234-0.2520.4925-0.02390.02080.3274-0.03960.3984133.737538.361371.9949
254.84340.3768-0.75684.23750.09923.4888-0.06150.3213-0.7767-0.1982-0.002-0.03990.7023-0.1766-0.04310.2828-0.05970.01010.1947-0.04460.226128.520441.069878.8915
263.413-0.1161-1.02171.9363-0.06041.4521-0.06530.282-0.0001-0.183-0.00460.09330.0673-0.28290.06340.2295-0.0484-0.02480.2744-0.04090.1682128.665651.245971.7808
273.69172.09714.89683.78850.64178.0617-0.37910.99590.6239-0.8310.17360.3177-0.61420.3430.07080.39970.0330.00660.4464-0.01760.2475128.925264.467764.8748
283.53711.17620.39884.01130.40323.51010.09140.48780.2517-0.34580.04890.1427-0.2247-0.2515-0.12890.23150.0324-0.00060.23680.01780.1882125.806365.625774.0348
299.5315-0.83216.80813.2239-1.70065.2289-0.390.23080.9486-0.47990.06150.4201-1.5582-0.79810.41710.57130.1698-0.06180.45410.05080.365120.758173.972269.3637
303.56760.82581.38711.59320.13872.23060.01670.62070.0964-0.37090.01580.042-0.1844-0.0302-0.02580.30130.0041-0.03730.26760.03240.2011127.328966.368372.418
310.8625-0.5763-0.63382.17360.42350.49370.1570.3497-0.0906-0.3584-0.18470.01710.091-0.34740.01070.2725-0.0206-0.04470.3569-0.02530.1843128.1753.405167.5857
326.1088-0.31130.38446.2842-6.66349.3627-0.14640.7658-0.1134-0.7887-0.0087-0.27860.69920.76920.15330.3715-0.06460.08830.4506-0.06310.3487143.115854.585367.217
333.11931.6129-0.02643.49160.4972.7156-0.37231.5944-0.445-1.81840.1212-0.1546-0.49250.78740.25350.6568-0.04960.04530.70350.00020.3256131.583354.933252.9546
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541.80620.2801-0.19971.33150.48082.0143-0.08470.0245-0.0903-0.17650.0433-0.28340.17030.06050.03240.27170.03590.02050.3140.03920.2692123.109951.160920.8032
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639.08335.66431.27953.78330.29514.56220.3906-0.6788-0.06450.9955-0.3255-1.1099-0.39960.6483-0.05010.3403-0.0761-0.03330.36-0.02570.3968144.193724.093959.7147
642.17521.5024-1.04614.2133-0.95172.0723-0.05690.0588-0.06640.02980.0818-0.5034-0.21170.2523-0.02330.2622-0.04680.04850.2053-0.02180.3687139.323423.345352.7615
654.5266-5.0386-0.12559.74660.34390.01490.09460.092-0.1496-0.2888-0.11560.10540.03830.07460.03070.3390.01910.0740.21940.00070.2963137.012613.50547.0417
663.1155-0.8965-1.73770.26540.51114.57230.3710.140.5018-0.275-0.0299-0.3663-0.5253-0.0194-0.34550.4055-0.00590.09710.21690.04550.3578135.562127.145236.9754
675.46794.1191-0.49785.88551.81033.1349-0.31720.40940.1289-1.20820.3757-0.91640.02520.4993-0.08830.45490.05450.19320.3634-0.01210.4665141.980814.690831.5817
687.8359-2.4469-3.43333.93661.8077.7520.60021.17251.4314-1.1071-0.1942-1.683-1.47480.9163-0.3420.6693-0.1370.25540.58070.06070.7242146.543932.072333.5036
697.88710.00243.8814.9849-1.23414.5786-0.1080.0486-0.50280.57060.0294-0.8847-1.21571.15060.06560.4248-0.07440.1190.3990.01430.7422149.123728.704748.4782
702.3681-2.86112.29149.3589-0.04647.4223-0.6728-0.26510.76620.78810.2009-0.6094-0.85450.37950.39510.4826-0.06340.02920.3619-0.06360.3905127.850727.915769.9264
712.5421-0.1022-1.01030.9043-0.57762.6910.0438-0.09070.13830.02870.0313-0.0856-0.25770.0426-0.05430.2859-0.0050.03170.1227-0.03110.2347125.865723.998159.906
722.6789-3.12931.43656.338-5.14095.1464-0.29820.0416-0.42640.19420.70660.9518-0.0106-0.8777-0.41010.27580.02830.0960.31130.00450.3822108.630420.783351.1828
731.4001-0.00060.18095.5129-1.1641.77850.01950.12370.0320.01820.14490.2891-0.0952-0.3339-0.15880.20460.01650.03820.22460.00790.2533114.393818.167346.0573
744.244-0.0594-0.33034.4296-0.45074.01170.0178-0.24140.32990.25670.12830.6341-0.3632-0.7062-0.10070.24550.04230.08230.2958-0.02650.2908110.795623.760464.5567
756.78434.97695.12349.05664.2074.3565-0.013-0.7125-0.3978-0.1896-0.22780.781-0.4709-1.46450.19110.41140.05520.11460.53660.04470.6683103.419924.653248.7834
766.9473-3.7506-0.61127.4153-1.68494.4412-0.2458-1.2854-0.23421.56310.1184-0.3628-0.44330.44880.11540.5378-0.1024-0.01110.71710.01190.208587.57898.813112.8393
772.72620.18090.65021.89030.48161.33370.1114-0.35170.13610.4015-0.0243-0.0521-0.16310.4492-0.04150.3353-0.1014-0.01250.5466-0.09180.184590.930911.4126103.1206
784.56942.41621.85538.34762.44214.45070.1491-0.5651.15870.104-0.43470.9817-0.854-0.1850.29050.4507-0.11450.17940.4066-0.12260.415485.411426.401991.9807
793.54761.17011.6734.54422.35272.7020.1943-0.20970.6835-0.16750.0043-0.1657-0.63220.3144-0.14260.3589-0.11950.11170.324-0.07410.317792.486523.483785.2853
805.28913.18582.92173.5822.39871.93760.1531-0.54080.5130.1483-0.20980.187-0.3002-0.01880.0510.2327-0.05340.02810.3158-0.06560.215384.743817.276188.2773
814.51151.82731.45673.0170.00921.94830.048-0.58040.7690.35090.07570.2782-0.7510.2091-0.07170.4613-0.08860.12640.4678-0.18030.361581.578522.5044103.1713
824.792-0.77022.24756.2195-4.14394.4350.273-0.2730.88650.0550.00040.7175-1.64280.3148-0.19870.5674-0.07350.08710.424-0.19680.711885.946933.432591.9081
833.3034-3.34-1.11248.2157-1.60694.99920.2918-0.27830.7239-0.28140.0106-0.4007-0.87510.3479-0.23180.4167-0.19970.12880.5307-0.1190.4714110.563821.317778.7895
845.19451.4321.49663.34172.0791.78750.16040.06670.493-0.77830.1802-0.3141-0.94530.6994-0.31420.3759-0.230.10060.4737-0.06560.3161102.025821.902581.6685
850.43230.6076-0.41983.09731.76283.46260.1208-0.51510.17540.2634-0.0838-0.2996-0.00250.7471-0.16420.1825-0.1251-0.0340.6121-0.13560.2964106.167812.462388.3969
862.24280.34832.6653.52462.56254.61820.2564-0.512-0.59750.9219-0.0497-0.77450.76351.0559-0.85280.2794-0.0376-0.21341.0874-0.07720.388109.63120.387796.6932
871.23780.84511.64041.31260.94452.54130.1317-0.47680.00260.19210.0609-0.44930.22210.6906-0.19320.2926-0.0251-0.08640.6328-0.04790.261799.94861.660296.5388
885.2944-0.45986.90840.5618-0.64368.96280.2573-1.4016-0.67770.68760.004-0.13630.84760.3447-0.48480.47090.0919-0.14211.01860.09520.3172101.0166-3.4053106.0721
891.23221.31461.20231.51.23271.94350.0581-0.3482-0.14120.24580.1448-0.37250.21470.8763-0.24810.27260.0106-0.08980.7115-0.06210.2808101.5342.019495.7018
902.99422.03023.12223.5120.93794.2230.1744-0.9155-0.0282-0.6098-0.6556-0.73110.30810.7562-0.69550.0237-0.2074-0.13420.8155-0.16870.2929111.680110.253187.2423
911.69011.46570.99494.01880.11110.80190.3351-0.5728-0.11850.2646-0.0102-1.87610.07541.3546-0.19690.38370.1054-0.14951.3191-0.14330.9661120.97263.46388.9586
922.27450.0917-0.40433.79550.56840.2051-0.0807-0.9721-0.67740.9418-0.3045-0.24010.53141.1106-0.86210.34760.0828-0.46591.4884-0.15650.4828113.4412-1.9376102.2972
930.2775-0.7746-0.00541.86150.19551.2779-0.3907-0.2537-0.43830.16770.0305-0.42610.58430.64230.24090.44980.17170.16370.37040.09040.5269147.2027-9.033949.709
942.12320.3478-0.23310.6182-0.84351.7823-0.46980.349-0.66060.07710.07230.21850.5320.08860.04950.52580.09130.2370.12210.0030.5384136.2033-10.417944.7657
950.96070.93430.55112.0331-3.04651.8798-0.43930.8933-0.8312-1.19160.03780.08630.9163-0.3208-0.21570.7656-0.14160.22070.2897-0.1380.6133123.8938-11.65535.4119
960.3232-0.3879-0.19442.9954-0.32471.3417-0.24270.2096-0.5708-0.2648-0.10480.33730.6157-0.27140.22180.4594-0.080.13880.246-0.10240.5238120.5036-8.377742.9882
971.75340.51630.46324.0457-1.64791.2745-0.14660.4613-0.7247-0.47010.02640.24250.68920.13810.03870.61110.02390.20740.3336-0.11310.5737136.3899-13.519733.8313
988.7351-2.1762-1.13134.8391.01784.3709-0.43270.9963-0.8875-0.8842-0.52240.90910.4975-1.14680.7880.8706-0.14180.00010.5579-0.29290.7698119.7767-17.184932.9058
995.615-0.5647-0.02592.85342.50466.741-0.40630.5654-1.2244-0.63870.26630.4649-0.4029-0.817-0.19360.6069-0.10960.35440.36960.06150.6912110.0158-13.262360.0615
1001.1905-0.5376-0.87614.13231.33222.7164-0.28480.0191-0.5819-0.06450.03180.16190.4038-0.17440.16270.3774-0.03360.19450.19940.01750.4596116.9717-8.468258.8667
1012.1143-0.6181-0.00452.32670.17721.1432-0.4529-0.8306-0.83030.41460.0987-0.19310.75880.44910.13460.69860.05910.3576-0.1260.13650.6667124.6445-13.755857.559
1022.5093-2.49182.03253.6857-3.12652.5917-0.7325-1.2721-0.31770.88380.2986-0.6260.25930.4401-0.03020.77480.2710.28930.2730.31250.557135.5317-7.850268.7371
1030.910.81610.12944.1118-0.02021.4562-0.2746-0.3013-0.27250.67290.11190.04530.37920.26670.10550.42220.12370.10530.25080.07040.3892136.5693-1.884860.7669
1046.0146-5.23354.30246.0195-3.48163.1509-0.379-0.2635-0.10230.5803-0.1935-1.05440.37641.10370.43560.51650.2430.0440.64270.23280.6431147.1624-4.839863.5314
1050.5312-1.23530.40043.4097-1.22150.467-0.4173-0.3905-0.33750.32630.0786-0.18770.43110.44410.2570.52970.18540.14060.34430.14840.4765138.788-6.561862.4488
1060.50581.29440.40639.42240.50930.6433-0.3451-0.4212-0.48570.5980.11640.23130.47870.21180.12660.43670.08830.2030.24030.0730.494130.3703-5.351161.4858
1072.7737-1.34260.85125.67690.20490.4144-0.3785-0.5129-0.44920.59320.1145-0.08630.4653-0.06530.21480.50150.08130.1920.33070.12590.429120.3166-5.550671.2459
1088.9437-2.90120.79376.8848-0.79684.7829-0.9206-1.4455-0.90551.5906-0.0739-0.89060.92620.45360.941.10170.12330.08010.70760.25820.6028127.625-15.238779.9443
1098.38525.0516-1.17466.59030.04811.7844-0.3632-1.4434-0.70230.7602-0.1636-0.45160.4090.63240.30830.8470.29150.04590.59160.19810.6013139.6429-10.420573.8506
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 12 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 13 THROUGH 60 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 61 THROUGH 74 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 75 THROUGH 102 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 103 THROUGH 148 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 149 THROUGH 170 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 171 THROUGH 184 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 60 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 61 THROUGH 74 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 75 THROUGH 102 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 103 THROUGH 123 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 124 THROUGH 148 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 149 THROUGH 161 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 162 THROUGH 170 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 171 THROUGH 185 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 3 THROUGH 12 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 13 THROUGH 60 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 61 THROUGH 75 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 76 THROUGH 119 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 120 THROUGH 137 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 138 THROUGH 161 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 162 THROUGH 171 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 172 THROUGH 185 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 3 THROUGH 12 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 13 THROUGH 30 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 31 THROUGH 60 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 61 THROUGH 74 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 75 THROUGH 90 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 91 THROUGH 102 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 103 THROUGH 123 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 124 THROUGH 148 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 149 THROUGH 161 )
33X-RAY DIFFRACTION33CHAIN 'D' AND (RESID 162 THROUGH 171 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID 172 THROUGH 185 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 3 THROUGH 12 )
36X-RAY DIFFRACTION36CHAIN 'E' AND (RESID 13 THROUGH 30 )
37X-RAY DIFFRACTION37CHAIN 'E' AND (RESID 31 THROUGH 44 )
38X-RAY DIFFRACTION38CHAIN 'E' AND (RESID 45 THROUGH 60 )
39X-RAY DIFFRACTION39CHAIN 'E' AND (RESID 61 THROUGH 74 )
40X-RAY DIFFRACTION40CHAIN 'E' AND (RESID 75 THROUGH 90 )
41X-RAY DIFFRACTION41CHAIN 'E' AND (RESID 91 THROUGH 102 )
42X-RAY DIFFRACTION42CHAIN 'E' AND (RESID 103 THROUGH 119 )
43X-RAY DIFFRACTION43CHAIN 'E' AND (RESID 120 THROUGH 148 )
44X-RAY DIFFRACTION44CHAIN 'E' AND (RESID 149 THROUGH 161 )
45X-RAY DIFFRACTION45CHAIN 'E' AND (RESID 162 THROUGH 171 )
46X-RAY DIFFRACTION46CHAIN 'E' AND (RESID 172 THROUGH 185 )
47X-RAY DIFFRACTION47CHAIN 'F' AND (RESID 3 THROUGH 12 )
48X-RAY DIFFRACTION48CHAIN 'F' AND (RESID 13 THROUGH 30 )
49X-RAY DIFFRACTION49CHAIN 'F' AND (RESID 31 THROUGH 60 )
50X-RAY DIFFRACTION50CHAIN 'F' AND (RESID 61 THROUGH 74 )
51X-RAY DIFFRACTION51CHAIN 'F' AND (RESID 75 THROUGH 90 )
52X-RAY DIFFRACTION52CHAIN 'F' AND (RESID 91 THROUGH 102 )
53X-RAY DIFFRACTION53CHAIN 'F' AND (RESID 103 THROUGH 119 )
54X-RAY DIFFRACTION54CHAIN 'F' AND (RESID 120 THROUGH 148 )
55X-RAY DIFFRACTION55CHAIN 'F' AND (RESID 149 THROUGH 161 )
56X-RAY DIFFRACTION56CHAIN 'F' AND (RESID 162 THROUGH 171 )
57X-RAY DIFFRACTION57CHAIN 'F' AND (RESID 172 THROUGH 185 )
58X-RAY DIFFRACTION58CHAIN 'G' AND (RESID 3 THROUGH 12 )
59X-RAY DIFFRACTION59CHAIN 'G' AND (RESID 13 THROUGH 30 )
60X-RAY DIFFRACTION60CHAIN 'G' AND (RESID 31 THROUGH 60 )
61X-RAY DIFFRACTION61CHAIN 'G' AND (RESID 61 THROUGH 74 )
62X-RAY DIFFRACTION62CHAIN 'G' AND (RESID 75 THROUGH 90 )
63X-RAY DIFFRACTION63CHAIN 'G' AND (RESID 91 THROUGH 102 )
64X-RAY DIFFRACTION64CHAIN 'G' AND (RESID 103 THROUGH 119 )
65X-RAY DIFFRACTION65CHAIN 'G' AND (RESID 120 THROUGH 131 )
66X-RAY DIFFRACTION66CHAIN 'G' AND (RESID 132 THROUGH 148 )
67X-RAY DIFFRACTION67CHAIN 'G' AND (RESID 149 THROUGH 161 )
68X-RAY DIFFRACTION68CHAIN 'G' AND (RESID 162 THROUGH 171 )
69X-RAY DIFFRACTION69CHAIN 'G' AND (RESID 172 THROUGH 185 )
70X-RAY DIFFRACTION70CHAIN 'H' AND (RESID 3 THROUGH 12 )
71X-RAY DIFFRACTION71CHAIN 'H' AND (RESID 13 THROUGH 60 )
72X-RAY DIFFRACTION72CHAIN 'H' AND (RESID 61 THROUGH 74 )
73X-RAY DIFFRACTION73CHAIN 'H' AND (RESID 75 THROUGH 137 )
74X-RAY DIFFRACTION74CHAIN 'H' AND (RESID 138 THROUGH 170 )
75X-RAY DIFFRACTION75CHAIN 'H' AND (RESID 171 THROUGH 185 )
76X-RAY DIFFRACTION76CHAIN 'I' AND (RESID 3 THROUGH 12 )
77X-RAY DIFFRACTION77CHAIN 'I' AND (RESID 13 THROUGH 60 )
78X-RAY DIFFRACTION78CHAIN 'I' AND (RESID 61 THROUGH 74 )
79X-RAY DIFFRACTION79CHAIN 'I' AND (RESID 75 THROUGH 114 )
80X-RAY DIFFRACTION80CHAIN 'I' AND (RESID 115 THROUGH 131 )
81X-RAY DIFFRACTION81CHAIN 'I' AND (RESID 132 THROUGH 170 )
82X-RAY DIFFRACTION82CHAIN 'I' AND (RESID 171 THROUGH 185 )
83X-RAY DIFFRACTION83CHAIN 'J' AND (RESID 3 THROUGH 12 )
84X-RAY DIFFRACTION84CHAIN 'J' AND (RESID 13 THROUGH 30 )
85X-RAY DIFFRACTION85CHAIN 'J' AND (RESID 31 THROUGH 60 )
86X-RAY DIFFRACTION86CHAIN 'J' AND (RESID 61 THROUGH 74 )
87X-RAY DIFFRACTION87CHAIN 'J' AND (RESID 75 THROUGH 90 )
88X-RAY DIFFRACTION88CHAIN 'J' AND (RESID 91 THROUGH 102 )
89X-RAY DIFFRACTION89CHAIN 'J' AND (RESID 103 THROUGH 131 )
90X-RAY DIFFRACTION90CHAIN 'J' AND (RESID 132 THROUGH 154 )
91X-RAY DIFFRACTION91CHAIN 'J' AND (RESID 155 THROUGH 171 )
92X-RAY DIFFRACTION92CHAIN 'J' AND (RESID 172 THROUGH 185 )
93X-RAY DIFFRACTION93CHAIN 'K' AND (RESID 3 THROUGH 30 )
94X-RAY DIFFRACTION94CHAIN 'K' AND (RESID 31 THROUGH 60 )
95X-RAY DIFFRACTION95CHAIN 'K' AND (RESID 61 THROUGH 73 )
96X-RAY DIFFRACTION96CHAIN 'K' AND (RESID 74 THROUGH 132 )
97X-RAY DIFFRACTION97CHAIN 'K' AND (RESID 133 THROUGH 171 )
98X-RAY DIFFRACTION98CHAIN 'K' AND (RESID 172 THROUGH 185 )
99X-RAY DIFFRACTION99CHAIN 'L' AND (RESID 2 THROUGH 11 )
100X-RAY DIFFRACTION100CHAIN 'L' AND (RESID 12 THROUGH 44 )
101X-RAY DIFFRACTION101CHAIN 'L' AND (RESID 45 THROUGH 60 )
102X-RAY DIFFRACTION102CHAIN 'L' AND (RESID 61 THROUGH 75 )
103X-RAY DIFFRACTION103CHAIN 'L' AND (RESID 76 THROUGH 90 )
104X-RAY DIFFRACTION104CHAIN 'L' AND (RESID 91 THROUGH 102 )
105X-RAY DIFFRACTION105CHAIN 'L' AND (RESID 103 THROUGH 119 )
106X-RAY DIFFRACTION106CHAIN 'L' AND (RESID 120 THROUGH 137 )
107X-RAY DIFFRACTION107CHAIN 'L' AND (RESID 138 THROUGH 161 )
108X-RAY DIFFRACTION108CHAIN 'L' AND (RESID 162 THROUGH 170 )
109X-RAY DIFFRACTION109CHAIN 'L' AND (RESID 171 THROUGH 185 )

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月:コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか? / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例:em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る