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- PDB-3p4s: Crystal structure of Menaquinol:fumarate oxidoreductase in comple... -

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基本情報

登録情報
データベース: PDB / ID: 3p4s
タイトルCrystal structure of Menaquinol:fumarate oxidoreductase in complex with a 3-nitropropionate adduct
要素(Fumarate reductase ...) x 4
キーワードOXIDOREDUCTASE
機能・相同性
機能・相同性情報


: / fumarate reductase complex / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...: / fumarate reductase complex / succinate dehydrogenase activity / fermentation / fumarate metabolic process / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / anaerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / bacterial-type flagellum assembly / membrane => GO:0016020 / tricarboxylic acid cycle / FAD binding / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / DNA damage response / metal ion binding / membrane / plasma membrane / cytosol
類似検索 - 分子機能
Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain ...Fumarate reductase, subunit C / Fumarate reductase subunit C / Fumarate reductase, subunit D / Fumarate reductase subunit D / Fumarate reductase, flavoprotein subunit / 4Fe-4S dicluster domain / succinate dehydrogenase protein domain / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 4Fe-4S dicluster domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Rhinovirus 14, subunit 4 / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
3-NITROPROPANOIC ACID / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Fumarate reductase subunit D / Succinate dehydrogenase iron-sulfur subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase flavoprotein subunit ...3-NITROPROPANOIC ACID / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Fumarate reductase subunit D / Succinate dehydrogenase iron-sulfur subunit / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase flavoprotein subunit / Fumarate reductase subunit C / Fumarate reductase subunit D / Fumarate reductase iron-sulfur subunit
類似検索 - 構成要素
生物種Escherichia coli 042 (大腸菌)
Escherichia coli O55:H7 str. CB9615 (大腸菌)
手法X線回折 / シンクロトロン / 解像度: 3.1 Å
データ登録者Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. ...Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankowskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
引用ジャーナル: J.Biol.Chem. / 年: 2011
タイトル: Geometric restraint drives on- and off-pathway catalysis by the Escherichia coli menaquinol:fumarate reductase.
著者: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / ...著者: Tomasiak, T.M. / Archuleta, T.L. / Andrell, J. / Luna-Chavez, C. / Davis, T.A. / Sarwar, M. / Ham, A.J. / McDonald, W.H. / Yankovskaya, V. / Stern, H.A. / Johnston, J.N. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
履歴
登録2010年10月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年12月8日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22024年2月21日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)240,37117
ポリマ－237,0348
非ポリマー3,3379
水00
1
A: Fumarate reductase flavoprotein subunit
B: Fumarate reductase iron-sulfur subunit
C: Fumarate reductase subunit C
D: Fumarate reductase subunit D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)120,2459
ポリマ－118,5174
非ポリマー1,7285
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17180 Å2
ΔGint-151 kcal/mol
Surface area41420 Å2
手法PISA
2
M: Fumarate reductase flavoprotein subunit
N: Fumarate reductase iron-sulfur subunit
O: Fumarate reductase subunit C
P: Fumarate reductase subunit D
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)120,1268
ポリマ－118,5174
非ポリマー1,6094
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17010 Å2
ΔGint-151 kcal/mol
Surface area42760 Å2
手法PISA
単位格子
Length a, b, c (Å)98.065, 139.006, 276.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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Fumarate reductase ... , 4種, 8分子 AMBNCODP

#1: タンパク質 Fumarate reductase flavoprotein subunit


分子量: 63477.707 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli 042 (大腸菌) / 株: 042/EAEC / 遺伝子: EC042_4630, frdA, SDY_4398 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D3GV56, UniProt: P00363*PLUS
#2: タンパク質 Fumarate reductase iron-sulfur subunit


分子量: 27021.885 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli 042 (大腸菌) / 株: 042/EAEC / 遺伝子: frdB, EC042_4629 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D3GV55, UniProt: P0AC47*PLUS
#3: タンパク質 Fumarate reductase subunit C


分子量: 14898.773 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli O55:H7 str. CB9615 (大腸菌)
株: CB9615/EPEC / 遺伝子: frdC, G2583_4981 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D3QL74, UniProt: P0A8Q0*PLUS
#4: タンパク質 Fumarate reductase subunit D


分子量: 13118.870 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli 042 (大腸菌) / 株: 042/EAEC / 遺伝子: frdD, EC042_4627 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: D3GV53, UniProt: P0A8Q3*PLUS

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非ポリマー , 5種, 9分子

#5: 化合物 ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / コメント: FAD*YM
#6: 化合物 ChemComp-3NP / 3-NITROPROPANOIC ACID


分子量: 119.076 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H5NO4
#7: 化合物 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe2S2
#8: 化合物 ChemComp-F3S / FE3-S4 CLUSTER


分子量: 295.795 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe3S4
#9: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe4S4

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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: 3.97 Å3/Da / 溶媒含有率: 69.06 %
結晶化温度: 298 K / 手法: 蒸気拡散法 / pH: 5.8
詳細: 10% PEG 5000 mme, 250mM MgAc, 100mM Citrate pH 5.8, 0.1% w/v DTT, 0.1mM EDTA, VAPOR DIFFUSION, temperature 298K

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データ収集

放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID13 / 波長: 1 Å
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
反射解像度: 3.1→40 Å / Num. obs: 64420

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解析

ソフトウェア
名称バージョン分類NB
REFMAC5.5.0109精密化
PDB_EXTRACT3.1データ抽出
精密化解像度: 3.1→40 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 1 / SU B: 49.281 / SU ML: 0.41 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE
Rfactor反射数%反射
Rfree0.279 1181 1.8 %
Rwork0.255 --
obs0.255 64420 93.5 %
溶媒の処理溶媒モデル: MASK
原子変位パラメータBiso mean: 93.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---1.62 Å20 Å2
3---1.72 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→40 Å
タンパク質核酸リガンド溶媒全体
原子数16642 0 150 0 16792
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02217223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.96623442
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75252130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94223.548747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.247152807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.54115109
X-RAY DIFFRACTIONr_chiral_restr0.0650.22562
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02113057
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1331.510608
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.261217044
X-RAY DIFFRACTIONr_scbond_it0.38836615
X-RAY DIFFRACTIONr_scangle_it0.684.56316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 3.1→3.18 Å
Rfactor反射数%反射
Rfree0.303 45 -
Rwork0.314 3974 -
obs--80.83 %
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)
11.78980.2702-0.22041.31210.13622.044-0.1042-0.0353-0.0864-0.05340.0818-0.06370.21340.02160.02240.03010.01180.00930.1542-0.04190.037115.813521.0157-11.8251
23.41661.0488-0.30096.10980.03372.62140.3007-0.10850.655-0.3165-0.0119-0.2357-0.54530.3304-0.28880.2552-0.05180.1670.233-0.07190.375713.041350.5774-17.2038
310.3543-3.79510.65133.6407-2.6912.755-0.03660.1953-0.13940.0011-0.3317-0.4411-0.12380.43330.36830.8086-0.26950.44730.6793-0.44590.825422.071442.8121-31.0132
41.50470.0485-0.45992.23280.39091.5073-0.0502-0.16330.0427-0.01060.02950.12430.0493-0.19830.02070.0086-0.02440.0120.2291-0.02290.05560.604726.7553-9.7571
52.1894-0.89471.31761.92111.32783.819-0.3394-0.59140.31940.46150.05360.1325-0.115-0.22350.28580.2774-0.02680.13560.4159-0.15970.20175.216234.42027.7509
63.1578-0.6002-1.155128.99921.82375.2152-0.04530.43490.1864-0.67910.21280.83150.0089-0.6604-0.16750.0421-0.0751-0.05910.6988-0.05810.1731-9.746423.4559-40.2673
72.1485-0.6038-1.06262.0571-0.00422.55790.00220.29250.0603-0.40360.06760.12490.0823-0.399-0.06980.088-0.0541-0.02630.3496-0.02620.02190.270926.2434-36.2837
866.4334-7.60463.68342.91644.40111.57850.0067-1.12030.0027-0.43360.0916-0.0515-0.98-0.1724-0.09830.4014-0.14310.11250.12280.01280.164815.23249.25-32.4715
92.9039-0.1141.06181.08820.43432.8899-0.0944-0.12840.0765-0.3545-0.0124-0.29370.3290.22850.10680.24780.04170.15670.1699-0.03740.130627.220417.8348-30.5246
105.6323-0.94426.79550.1739-1.239913.37420.2370.079-0.1898-0.0923-0.0547-0.02780.90260.1552-0.18230.25060.03750.23850.23390.04630.352329.213812.7539-33.3248
117.4685-1.4924-2.81760.79080.86061.96990.1090.25210.4276-0.27660.07-0.41910.18480.0755-0.17890.3337-0.01860.27420.1249-0.03910.296826.311514.8146-43.855
1210.778227.3729-18.4180.7037-58.089242.95270.1392-0.4429-2.2447-3.34122.05010.15863.746-2.3953-2.18933.2289-0.2012-1.87931.88311.62593.715344.3961-0.9558-41.473
139.3566.6901-9.49545.1186-6.73714.756-0.27231.14581.0712-0.40970.86810.99071.2934-1.0238-0.59570.379-0.1129-0.04160.46790.00710.40292.27669.8573-46.7208
146.26950.0115-7.46571.80891.391710.3820.07810.2929-0.201-0.6422-0.29090.064-0.4589-0.40880.21280.4660.0450.06770.3297-0.0650.123228.922914.7976-73.1656
153.0666-0.04360.5840.9509-1.00331.8778-0.0390.01850.2523-0.3596-0.13720.01050.5684-0.31040.17620.4276-0.03360.20990.3142-0.06050.185129.231322.7927-66.5141
161.42135.9253-4.0425.7877-17.46111.83650.0331-0.1370.08870.82550.0206-0.0323-0.50090.0374-0.05370.68660.13470.15760.7939-0.29840.703435.977432.1591-41.3083
170.96861.9004-0.39415.1268-1.30920.36660.1756-0.11360.22490.2621-0.2605-0.0286-0.05180.07480.08480.4622-0.05230.23280.2703-0.10540.329840.899929.9876-64.4293
1843.7269-41.908125.580140.1683-24.516314.9645-0.56971.48383.25880.5763-1.3568-3.1428-0.36240.86821.92650.6832-0.20090.43510.5999-0.17690.838948.281429.5554-79.8045
190.55481.4585-3.25728.8655-7.621919.3033-0.09330.03910.058-0.19710.20421.57760.5412-0.1882-0.11090.6317-0.10190.11520.5472-0.21090.72221.2281-1.3191-35.8408
200.37650.0884-1.29450.8641-2.614211.09460.11850.1073-0.0575-0.3540.08450.09760.4167-0.2834-0.2030.5323-0.08470.16120.2699-0.00270.210935.153217.0593-66.7209
213.3815-1.5212-0.440312.6396-4.47266.8891-0.35730.6316-0.4536-0.0033-0.2934-0.9049-0.64360.86720.65070.5997-0.10170.37470.4132-0.02540.450948.443416.4719-81.3819
2215.38860.8114-3.10511.11860.88821.76570.022-0.3337-0.3975-0.1692-0.1384-0.08910.0258-0.12660.11640.4355-0.02310.1980.2202-0.04280.116429.36259.8277-63.6267
2317.56628.5205-9.14836.5858-5.38489.2377-0.334-0.8385-1.38190.1449-0.4417-0.1037-0.31360.03130.77560.5190.00490.22510.1493-0.0240.383826.94190.0794-63.7042
2437.836416.6544-6.07219.7187-1.93041.0199-0.18572.0830.137-1.52140.2885-1.1078-0.0411-0.3729-0.10280.70940.11040.23750.34060.03060.335743.69682.9339-75.3481
250.17030.2970.18061.04050.10040.47110.0418-0.03820.06990.16030.11750.4791-0.1648-0.4496-0.15931.1012-0.0470.62180.80830.00691.39926.0158-39.6128-25.1938
263.8658-5.69352.1529.9056-3.02091.2139-0.10710.24110.51030.1426-0.0832-1.3294-0.05230.13490.19031.2189-0.10830.63271.02330.24051.73415.989-51.4271-40.5038
274.02885.3084-2.11513.01462.82656.52490.34390.24150.73271.45760.09991.4440.6569-0.4648-0.44381.0788-0.22430.84580.50520.20961.811112.762-41.5527-33.89
280.9971-0.11670.59370.0426-0.13960.56370.1744-0.37010.15460.057-0.05310.1074-0.1534-0.0107-0.12131.6361-0.07760.67760.8513-0.08261.298616.7167-36.2721-10.9398
290.2572-2.38030.307324.4602-2.505924.45550.01460.0772-0.03410.46350.09961.94510.1511-1.7683-0.11420.8443-0.08380.64490.60120.43921.204521.382-59.0031-30.1373
308.8837-0.64080.38726.7845-2.12387.8009-0.14690.3663-0.06990.17410.29020.4641-0.2153-0.6209-0.14320.6359-0.1420.2790.36240.06840.725819.8578-70.0269-29.8291
3114.10420.080611.22414.0053-0.140219.5439-0.35131.12430.4193-0.3160.32040.6948-0.4254-0.52850.03080.8081-0.19220.2930.56150.1410.823127.4463-55.7893-40.5591
320.1276-0.0766-0.06310.1858-0.0010.11260.0019-0.18710.22980.439-0.0256-0.1-0.08940.06180.02371.612-0.13140.4981.0183-0.0311.172817.3566-44.4567-8.6715
334.7435-0.5905-0.29920.1253-0.10461.36850.2619-0.9375-0.05540.1497-0.0301-0.0011-0.6981-0.0147-0.23181.5653-0.13780.32460.90430.1550.791116.7588-53.1389-7.1654
342.7457-0.1829-2.04676.51661.55133.3933-0.0042-0.4143-0.01580.36210.06560.28880.01940.1104-0.06140.86170.02540.44770.92140.09190.9612.3432-58.1574-6.2257
350.12650.00780.00720.1244-0.08690.0714-0.1361-0.0708-0.35330.40840.0777-0.1399-0.33980.02690.05851.9233-0.0940.13690.9023-0.00981.187346.1834-42.3656-17.4464
362.55530.7375-0.08751.3464-0.40161.52660.0652-0.45580.10081.1259-0.1648-0.18650.00710.27530.09961.5427-0.0010.23660.38140.05170.605939.3001-37.574-26.2439
3710.51465.71361.53317.2119-0.45365.796-1.06850.2340.0230.95230.68761.2885-0.29110.42040.38090.7496-0.07680.57610.471-0.13980.722419.048-23.6796-34.3003
383.2064-2.4583-0.06952.59511.13472.0829-0.0004-0.0306-0.5980.0097-0.13110.8157-0.1187-0.65930.13140.9545-0.11460.55220.51630.22560.90719.1812-33.0534-41.1665
3928.53896.56376.53326.38370.12196.2165-1.10820.482-0.3336-0.41090.90590.5148-1.6916-0.55930.20231.02490.04850.34320.26020.00440.664725.7008-25.2135-40.455
4013.56723.49093.89664.6624-3.90577.548-1.14410.2457-1.22390.40151.3861-0.3211-1.3296-1.6178-0.2420.82020.13890.37250.864-0.00451.417616.3622-21.1862-43.4849
414.2643-4.2612.84326.9597-2.83098.0154-0.25480.23520.11830.19850.24040.8891-0.0654-0.2940.01440.5406-0.13140.39670.15020.10730.726528.8858-22.7806-48.0653
424.1948-0.7169-3.79260.4482-0.65338.64770.60290.24420.38020.01260.150.0106-1.01-0.9562-0.75291.41-0.22680.44580.6302-0.00970.826842.7091-20.9134-20.2362
431.03570.9732-3.14694.8931-6.682318.44370.1416-0.1853-0.00870.3395-0.3757-0.1363-0.31910.99460.23410.35650.00920.24470.191-0.03410.402651.8641-21.3245-57.6492
440.6937-0.8939-0.19632.8295-0.82825.1247-0.05240.02420.1348-0.2234-0.0743-0.06690.32320.25910.12670.3733-0.01220.24470.0981-0.01550.272453.8634-25.374-66.2886
452.266-2.1077-3.01511.98322.83894.16640.0412-0.52480.07960.09280.3982-0.03070.24640.4895-0.43931.3092-0.27170.06530.76280.28481.710424.236-39.0477-56.91
461.4901-1.8025-0.00353.33980.62340.33690.39930.3403-0.5390.0063-0.27190.39890.29440.0213-0.12740.8177-0.11950.12230.4754-0.10340.744740.9029-34.216-72.947
4771.015342.635224.529926.26637.227693.7657-0.04841.55431.2703-0.19651.0120.95231.9865-0.9619-0.96360.8262-0.02780.17710.7182-0.14890.550448.2954-30.1614-86.4208
481.8034-5.1457-7.497915.287722.156932.14350.4367-0.16730.039-0.6367-0.1697-0.1879-1.1012-0.2214-0.2671.1244-0.08490.23841.41040.04641.061924.6642-11.7065-34.8064
497.5444-1.9403-5.45772.86240.01784.80790.1285-0.11810.3853-0.05370.15880.0417-0.01580.1107-0.28720.4351-0.05030.25850.342-0.01410.443543.3918-21.7722-64.5932
507.07093.37913.12077.6767-2.14363.5635-0.67890.40110.2083-0.94240.63890.18160.1036-0.04190.040.7860.06410.2430.51620.06260.380850.9564-19.9817-85.6635
512.390.35352.31193.2847-0.97835.95290.1949-0.1549-0.00350.02930.16840.0175-0.1047-0.2906-0.36340.41020.01490.350.2035-0.00820.515244.6361-15.9468-60.0107
522.89810.0136-5.37525.63048.802123.82880.3256-0.0963-0.06780.4707-0.3048-0.08040.157-0.3562-0.02070.46040.00520.30620.31680.05560.454445.3802-6.7961-55.5269
532.6986-2.87439.8369.6354-11.711136.09190.15180.6205-0.066-1.40340.1530.0810.75882.108-0.30480.6345-0.00640.15750.51710.00210.406246.219-6.8408-76.4099
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 228
2X-RAY DIFFRACTION2A229 - 316
3X-RAY DIFFRACTION3A317 - 336
4X-RAY DIFFRACTION4A337 - 536
5X-RAY DIFFRACTION5A537 - 576
6X-RAY DIFFRACTION6B1 - 27
7X-RAY DIFFRACTION7B28 - 105
8X-RAY DIFFRACTION8B106 - 115
9X-RAY DIFFRACTION9B116 - 165
10X-RAY DIFFRACTION10B166 - 192
11X-RAY DIFFRACTION11B193 - 236
12X-RAY DIFFRACTION12B237 - 243
13X-RAY DIFFRACTION13C1 - 18
14X-RAY DIFFRACTION14C19 - 60
15X-RAY DIFFRACTION15C61 - 98
16X-RAY DIFFRACTION16C99 - 107
17X-RAY DIFFRACTION17C108 - 126
18X-RAY DIFFRACTION18C127 - 130
19X-RAY DIFFRACTION19D0 - 5
20X-RAY DIFFRACTION20D6 - 46
21X-RAY DIFFRACTION21D47 - 64
22X-RAY DIFFRACTION22D65 - 91
23X-RAY DIFFRACTION23D92 - 108
24X-RAY DIFFRACTION24D109 - 118
25X-RAY DIFFRACTION25M0 - 105
26X-RAY DIFFRACTION26M106 - 120
27X-RAY DIFFRACTION27M121 - 143
28X-RAY DIFFRACTION28M144 - 230
29X-RAY DIFFRACTION29M231 - 254
30X-RAY DIFFRACTION30M255 - 317
31X-RAY DIFFRACTION31M318 - 347
32X-RAY DIFFRACTION32M348 - 500
33X-RAY DIFFRACTION33M501 - 534
34X-RAY DIFFRACTION34M535 - 576
35X-RAY DIFFRACTION35N1 - 50
36X-RAY DIFFRACTION36N51 - 108
37X-RAY DIFFRACTION37N109 - 123
38X-RAY DIFFRACTION38N124 - 162
39X-RAY DIFFRACTION39N163 - 183
40X-RAY DIFFRACTION40N184 - 195
41X-RAY DIFFRACTION41N196 - 243
42X-RAY DIFFRACTION42O1 - 12
43X-RAY DIFFRACTION43O13 - 53
44X-RAY DIFFRACTION44O54 - 92
45X-RAY DIFFRACTION45O93 - 108
46X-RAY DIFFRACTION46O109 - 126
47X-RAY DIFFRACTION47O127 - 130
48X-RAY DIFFRACTION48P0 - 5
49X-RAY DIFFRACTION49P6 - 43
50X-RAY DIFFRACTION50P44 - 62
51X-RAY DIFFRACTION51P63 - 91
52X-RAY DIFFRACTION52P92 - 109
53X-RAY DIFFRACTION53P110 - 118

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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