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- PDB-3wmm: Crystal structure of the LH1-RC complex from Thermochromatium tep... -

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基本情報

登録情報
データベース: PDB / ID: 3wmm
タイトルCrystal structure of the LH1-RC complex from Thermochromatium tepidum in C2 form
要素
  • (Photosynthetic reaction center ...) x 4
  • LH1 alpha polypeptide
  • LH1 beta polypeptide
キーワードPHOTOSYNTHESIS
機能・相同性
機能・相同性情報


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / photosynthesis / endomembrane system / electron transfer activity ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / photosynthesis / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting complex / Light-harvesting Protein / Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #250 / Light-harvesting complex / Light-harvesting Protein / Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Light-harvesting complex / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Multiheme cytochrome c family profile. / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION / Ubiquinone-8 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGW / PHOSPHATE ION / Ubiquinone-8 / Reaction center protein M chain / LH1 beta polypeptide / LH1 alpha polypeptide / Reaction center protein L chain / Photosynthetic reaction center cytochrome c subunit / Photosynthetic reaction center H subunit
類似検索 - 構成要素
生物種Thermochromatium tepidum (紅色硫黄細菌)
手法X線回折 / シンクロトロン / 多重同系置換 / 解像度: 3.008 Å
データ登録者Niwa, S. / Takeda, K. / Wang-Otomo, Z.-Y. / Miki, K.
引用ジャーナル: Nature / 年: 2014
タイトル: Structure of the LH1-RC complex from Thermochromatium tepidum at 3.0 angstrom
著者: Niwa, S. / Yu, L.J. / Takeda, K. / Hirano, Y. / Kawakami, T. / Wang-Otomo, Z.Y. / Miki, K.
履歴
登録2013年11月22日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02014年4月9日Provider: repository / タイプ: Initial release
改定 1.12014年4月16日Group: Database references
改定 1.22017年6月7日Group: Other
改定 1.32024年3月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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_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_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
C: Photosynthetic reaction center C subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)392,577122
ポリマ－340,62036
非ポリマー51,95786
水905
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area207400 Å2
ΔGint-1777 kcal/mol
Surface area99770 Å2
手法PISA
単位格子
Length a, b, c (Å)227.341, 148.238, 161.792
Angle α, β, γ (deg.)90.00, 117.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDモデル要素
11H-401-

HOH

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要素

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Photosynthetic reaction center ... , 4種, 4分子 CLMH

#1: タンパク質 Photosynthetic reaction center C subunit


分子量: 43177.531 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: D2Z0P5
#2: タンパク質 Photosynthetic reaction center L subunit


分子量: 31520.771 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: D2Z0P3
#3: タンパク質 Photosynthetic reaction center M subunit


分子量: 36605.715 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: A8ASG6
#4: タンパク質 Photosynthetic reaction center H subunit


分子量: 28213.305 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: D2Z0P9

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タンパク質 / タンパク質・ペプチド , 2種, 32分子 ADFIKOQSUWY13579BEGJNPRTVXZ24680

#5: タンパク質
LH1 alpha polypeptide


分子量: 7034.442 Da / 分子数: 16 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: D2Z0P2
#6: タンパク質・ペプチド
LH1 beta polypeptide


分子量: 5534.452 Da / 分子数: 16 / 由来タイプ: 天然
由来: (天然) Thermochromatium tepidum (紅色硫黄細菌)
参照: UniProt: D2Z0P1

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非ポリマー , 12種, 91分子

#7: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#8: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 17 / 由来タイプ: 合成 / 式: Ca
#9: 化合物...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


分子量: 911.504 Da / 分子数: 36 / 由来タイプ: 合成 / 式: C55H74MgN4O6
#10: 化合物 ChemComp-BPH / BACTERIOPHEOPHYTIN A / バクテリオフェオフィチン


分子量: 889.215 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C55H76N4O6
#11: 化合物 ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione / ユビキノン8


分子量: 727.109 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C49H74O4
#12: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 4 / 由来タイプ: 合成 / 式: PO4
#13: 化合物 ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Fe
#14: 化合物 ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


分子量: 717.116 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C51H72O2
#15: 化合物
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


分子量: 596.925 Da / 分子数: 17 / 由来タイプ: 合成 / 式: C42H60O2
#16: 化合物 ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL / POPG


分子量: 749.007 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C40H77O10P / コメント: リン脂質*YM
#17: 化合物 ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / DPPE


分子量: 691.959 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C37H74NO8P / コメント: リン脂質*YM
#18: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 5 / 由来タイプ: 天然 / 式: 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: 3.55 Å3/Da / 溶媒含有率: 65.32 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.4
詳細: 20mM Tris-HCl (pH 7.4), 50mM CaCl2, 0.54% DPC, 2% glycerol, 14% PEG 3000, VAPOR DIFFUSION, SITTING 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: SPring-8 / ビームライン: BL44XU / 波長: 0.9 Å
検出器タイプ: RAYONIX MX225HE / 検出器: CCD / 日付: 2010年1月25日
放射モノクロメーター: Si111 / 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: 0.9 Å / 相対比: 1
反射解像度: 3→50 Å / Num. all: 78312 / Num. obs: 78312 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.6 % / Biso Wilson estimate: 75.1 Å2 / Rsym value: 0.08 / Net I/σ(I): 16.2
反射 シェル解像度: 3→3.11 Å / 冗長度: 1.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 65.5

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
SOLVE位相決定
PHENIX(phenix.refine: 1.8.1_1168)精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 多重同系置換 / 解像度: 3.008→47.991 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.62 / σ(F): 1.52 / 位相誤差: 40.51 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3374 3926 5.02 %
Rwork0.3139 --
obs0.3151 78277 82.96 %
all-78312 -
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 119.3834 Å2
精密化ステップサイクル: LAST / 解像度: 3.008→47.991 Å
タンパク質核酸リガンド溶媒全体
原子数22183 0 3631 5 25819
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.02926929
X-RAY DIFFRACTIONf_angle_d2.05637399
X-RAY DIFFRACTIONf_dihedral_angle_d19.1019782
X-RAY DIFFRACTIONf_chiral_restr0.1023809
X-RAY DIFFRACTIONf_plane_restr0.0094345
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0081-3.04470.4397670.39731389X-RAY DIFFRACTION44
3.0447-3.08330.3728760.40082138X-RAY DIFFRACTION65
3.0833-3.12380.3682990.38872145X-RAY DIFFRACTION68
3.1238-3.16660.46161170.39362263X-RAY DIFFRACTION71
3.1666-3.21180.39411190.39632257X-RAY DIFFRACTION71
3.2118-3.25980.38711350.38982285X-RAY DIFFRACTION72
3.2598-3.31070.3841280.37942564X-RAY DIFFRACTION79
3.3107-3.3650.37731250.37722510X-RAY DIFFRACTION80
3.365-3.4230.38331330.36712567X-RAY DIFFRACTION80
3.423-3.48520.38541380.36532552X-RAY DIFFRACTION80
3.4852-3.55220.36281460.35892650X-RAY DIFFRACTION84
3.5522-3.62470.38091390.34412606X-RAY DIFFRACTION82
3.6247-3.70350.32051590.32752590X-RAY DIFFRACTION81
3.7035-3.78960.33541530.33862723X-RAY DIFFRACTION85
3.7896-3.88430.34731490.31972703X-RAY DIFFRACTION85
3.8843-3.98930.33951550.31282708X-RAY DIFFRACTION85
3.9893-4.10660.35811350.3012741X-RAY DIFFRACTION86
4.1066-4.23910.3261320.30242849X-RAY DIFFRACTION88
4.2391-4.39050.33421610.28472853X-RAY DIFFRACTION89
4.3905-4.56620.2721380.28312832X-RAY DIFFRACTION89
4.5662-4.77380.3071530.27672969X-RAY DIFFRACTION92
4.7738-5.02530.29921680.27012939X-RAY DIFFRACTION92
5.0253-5.33970.30561850.2812960X-RAY DIFFRACTION94
5.3397-5.75140.29791430.30743030X-RAY DIFFRACTION94
5.7514-6.3290.31521800.29633072X-RAY DIFFRACTION96
6.329-7.24210.31711790.29033133X-RAY DIFFRACTION97
7.2421-9.11410.30231470.27433198X-RAY DIFFRACTION98
9.1141-47.99670.36561670.32063125X-RAY DIFFRACTION95
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)
10.07990.0809-0.08810.1170.07650.04370.0275-0.27950.2917-1.27760.7351-0.38940.8771-0.27180-1.06560.60970.9764-0.2797-0.1659-0.8183-18.499-21.30452.8791
20.02870.0026-0.0191-0.0075-0.00830.0180.04570.04380.3248-0.08760.09140.0638-0.01180.036100.08930.41950.30050.27880.09380.7855-26.1121-1.9529-13.18
3-0.011-0.0308-0.0132-0.0190.0228-0.0232-0.0776-0.1880.2303-0.06710.1342-0.279-0.1723-0.28050-1.6950.1795-0.4522-0.7421-0.6111-0.7008-41.3111-10.7059-8.95
4-0.0036-0.07990.01910.0482-0.03670.0457-0.3068-0.26850.12350.2543-0.05180.13070.0238-0.1031-0-0.09550.19530.2981-0.1542-0.4561-0.4012-28.3909-14.88641.5517
50.0098-0.0013-0.0118-0.11520.0524-0.01050.1509-0.1260.10980.156-0.08620.06370.0447-0.057-0-1.35890.08610.06150.69030.03580.3248-73.6974-17.3016-28.208
60.0074-0.00470.00160.0043-0.00490.0022-0.04010.1081-0.0417-0.0551-0.1133-0.1198-0.04140.025600.3847-0.0413-0.18940.8690.17450.7546-80.9532-30.6423-45.3841
70.0384-0.06360.14190.14790.26980.1845-0.49040.69930.01810.309-0.23590.44580.82560.03420-0.9254-0.0994-1.31030.7035-0.2155-1.3816-59.0102-25.9969-69.4999
80.0150.1539-0.01320.0071-0.0345-0.00980.1884-0.1229-0.32040.1704-0.29490.2046-0.04660.0221-0-0.1383-0.6794-0.1140.5365-0.02220.4688-65.7868-42.1411-39.7688
90.0019-0.00080.0010.0004-0.00080.00410.0175-0.0081-0.0011-0.00570.00820.00630.0016-0.002-01.0071-0.1958-0.130.79-0.2350.8368-66.1165-34.5761-12.7134
100.00250.0085-0.00150.0107-0.00520.01230.0779-0.0388-0.04260.1245-0.0342-0.05650.00110.0121-00.6924-0.2639-0.25631.12080.26630.7011-54.1025-36.035-17.0257
110.0004-0.0006-0.00060.00180.00190.0018-0.0119-0.0186-0.0147-0.0552-0.03890.04270.0222-0.046500.982-0.0498-0.01261.0051-0.06281.0772-47.5459-47.7493-19.3265
12-0.0020.00450.0040.0001-0.0015-0.00070.0135-0.0059-0.03570.0502-0.03090.02250.0264-0.004-00.7897-0.4743-0.1370.75910.03470.6106-53.2674-43.5616-19.8549
13-0.0029-0.00280.01090.0123-0.0005-0.00210.03720.0282-0.1010.1178-0.13240.09240.0254-0.006300.4103-0.04870.07730.17610.08870.3964-57.5483-39.1165-43.492
140.00070.0030.00370.00560.00510.00560.00150.0203-0.01410.00610.0066-0.0189-0.00720.008300.4695-0.1185-0.15040.4146-0.14980.5407-54.9565-31.0701-53.1193
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530.06490.0061-0.04550.0067-0.04510.0132-0.0238-0.03960.1206-0.0470.0783-0.1343-0.20110.0391-00.3675-0.01950.24671.2768-0.1984-0.4091-5.571-21.2033-51.1809
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580.0002-0.055-0.03610.0997-0.0620.03550.10330.14570.26450.3522-0.3117-0.3246-0.13420.074-01.11130.5465-0.34660.1818-0.16361.215-37.2663-55.2755-37.5967
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640.0069-0.0107-0.0465-0.00330.03340.0479-0.2012-0.0554-0.2268-0.0734-0.12610.15430.1499-0.128200.59860.169-0.21940.3807-0.04180.3334-24.0795-15.88332.4522
650.0089-0.02510.0380.00640.00360.00470.2455-0.08520.2034-0.2820.15880.0778-0.1407-0.08-0-0.64610.8323-0.6823-0.64790.7353-0.4248-51.912-16.8992-30.0187
660.00030.01920.0074-0.0042-0.0087-0.00120.0904-0.05750.1294-0.02040.0894-0.0277-0.2461-0.0892-00.3597-0.05930.1410.5427-0.01730.4331-54.3214-16.5004-38.1758
670.00630.0070.00810.00520.0140.0063-0.0618-0.0170.0088-0.0801-0.01610.0298-0.05210.028800.8446-0.0725-0.18520.8461-0.14570.8432-45.61384.4825-29.7755
68-0.0134-0.0094-0.0199-0.0008-0.0015-0.00180.0507-0.0735-0.0622-0.03550.05660.0001-0.0113-0.0188-00.2960.13880.34190.0664-0.23880.1436-68.6701-28.5824-38.5733
690.00080.0011-0.0030.00330.00450.0005-0.0010.00050.059-0.03650.00480.0388-0.07740.0032-01.01750.078-0.08140.90390.0621.0478-47.6657-14.4058-47.3318
700.00230.0013-0.002-0.00290.0049-0.00160.07060.074-0.0711-0.0873-0.02930.050.04930.0209-0.00021.25710.03690.05581.26650.10411.1878-74.7958-57.5592-36.763
710.00880.01890.02990.02830.04330.0769-0.01340.0051-0.0327-0.0037-0.0010.01010.0171-0.003-0.00011.58650.01860.15941.55980.10111.4448-87.2127-46.3127-32.4983
720.04840.04470.07390.02570.06870.0994-0.0364-0.07180.00040.0583-0.0043-0.0036-0.01970.0382-0.00012.13050.09970.06282.0944-0.11942.0573-94.2563-30.7349-29.8976
730.0001-0.0030.0001-0.00350.0063-0.00110.0034-0.04650.01390.04360.070.02770.00260.0224-01.70880.04190.04161.717-0.11721.6451-95.2308-13.1863-30.1357
740.05570.00580.04960.0010.01740.0413-0.00970.01120.0044-0.04290.03630.0370.0237-0.0157-0.00011.7053-0.00470.03421.6319-0.19971.6078-89.45942.1892-32.1191
750.0464-0.00010.04420.00070.00590.0440.0007-0.02040.00920.03360.01930.0181-0.00450.0198-0.00011.85070.0168-0.10431.8893-0.06041.8208-79.409415.5753-36.8823
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790.0048-0.01870.02160.0192-0.0530.09160.02410.01090.0052-0.01930.0017-0.018-0.02230.00030.00020.7470.0722-0.09130.9930.05850.9877-19.589711.162-53.7231
800.0005-0.00790.00480.0289-0.0340.105-0.0572-0.04990.00060.00960.03730.01380.01080.02-0.00011.73530.18570.09541.44-0.01831.5903-13.1344-3.6984-55.1067
810.00510.00420.0032-0.0051-0.00050.00040.0434-0.06090.0256-0.0486-0.0101-0.0389-0.001-0.0264-00.9378-0.0571-0.10630.9784-0.09520.8479-12.1777-21.0127-54.5269
820.0078-0.00030.00160.0022-0.0004-0-0.02420.03690.0154-0.10440.0322-0.027-0.02020.0086-01.28110.0133-0.04811.4058-0.01881.4237-18.2207-37.1051-51.8469
830.0099-0.0025-0.01170.0040.00120.053-0.0353-0.00060.0385-0.0182-0.0016-0.0334-0.0039-0.000101.33310.0439-0.19771.39810.01541.165-27.9511-49.9259-48.8164
84-0.00460.0089-0.00650.00020.00140.00770.00950.0577-0.0462-0.01420.0503-0.0099-0.00630.014201.3812-0.00430.0021.43050.12671.4634-42.0931-59.1596-45.8083
85-0.00650.0018-0.02320.0210.0670.15780.02140.0659-0.0708-0.0709-0.0261-0.01310.02720.02020.00011.7522-0.16510.09091.72460.15641.685-58.5613-63.1183-42.2179
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN C AND RESID 17:157)C17 - 157
2X-RAY DIFFRACTION2(CHAIN C AND RESID 158:188)C158 - 188
3X-RAY DIFFRACTION3(CHAIN C AND RESID 189:254)C189 - 254
4X-RAY DIFFRACTION4(CHAIN C AND RESID 255:333)C255 - 333
5X-RAY DIFFRACTION5(CHAIN H AND RESID 2:36)H2 - 36
6X-RAY DIFFRACTION6(CHAIN H AND RESID 37:62)H37 - 62
7X-RAY DIFFRACTION7(CHAIN H AND RESID 63:259)H63 - 259
8X-RAY DIFFRACTION8(CHAIN L AND RESID 2:64)L2 - 64
9X-RAY DIFFRACTION9(CHAIN L AND RESID 65:69)L65 - 69
10X-RAY DIFFRACTION10(CHAIN L AND RESID 70:83)L70 - 83
11X-RAY DIFFRACTION11(CHAIN L AND RESID 84:89)L84 - 89
12X-RAY DIFFRACTION12(CHAIN L AND RESID 90:97)L90 - 97
13X-RAY DIFFRACTION13(CHAIN L AND RESID 98:121)L98 - 121
14X-RAY DIFFRACTION14(CHAIN L AND RESID 122:126)L122 - 126
15X-RAY DIFFRACTION15(CHAIN L AND RESID 127:161)L127 - 161
16X-RAY DIFFRACTION16(CHAIN L AND RESID 162:215)L162 - 215
17X-RAY DIFFRACTION17(CHAIN L AND RESID 216:265)L216 - 265
18X-RAY DIFFRACTION18(CHAIN L AND RESID 270:281)L270 - 281
19X-RAY DIFFRACTION19(CHAIN M AND RESID 2:14)M2 - 14
20X-RAY DIFFRACTION20(CHAIN M AND RESID 15:25)M15 - 25
21X-RAY DIFFRACTION21(CHAIN M AND RESID 26:33)M26 - 33
22X-RAY DIFFRACTION22(CHAIN M AND RESID 34:49)M34 - 49
23X-RAY DIFFRACTION23(CHAIN M AND RESID 50:55)M50 - 55
24X-RAY DIFFRACTION24(CHAIN M AND RESID 56:81)M56 - 81
25X-RAY DIFFRACTION25(CHAIN M AND RESID 82:87)M82 - 87
26X-RAY DIFFRACTION26(CHAIN M AND RESID 88:100)M88 - 100
27X-RAY DIFFRACTION27(CHAIN M AND RESID 101:109)M101 - 109
28X-RAY DIFFRACTION28(CHAIN M AND RESID 110:123)M110 - 123
29X-RAY DIFFRACTION29(CHAIN M AND RESID 124:133)M124 - 133
30X-RAY DIFFRACTION30(CHAIN M AND RESID 134:148)M134 - 148
31X-RAY DIFFRACTION31(CHAIN M AND RESID 149:320)M149 - 320
32X-RAY DIFFRACTION32(CHAIN A AND (RESID 2:61 OR RESID 102:102))A2 - 61
33X-RAY DIFFRACTION32(CHAIN A AND (RESID 2:61 OR RESID 102:102))A102
34X-RAY DIFFRACTION33(CHAIN B AND (RESID 7:46 OR RESID 101:101))B7 - 46
35X-RAY DIFFRACTION33(CHAIN B AND (RESID 7:46 OR RESID 101:101))B101
36X-RAY DIFFRACTION34(CHAIN D AND (RESID 2:61 OR RESID 102:102))D2 - 61
37X-RAY DIFFRACTION34(CHAIN D AND (RESID 2:61 OR RESID 102:102))D102
38X-RAY DIFFRACTION35(CHAIN E AND (RESID 7:46 OR RESID 101:101))E7 - 46
39X-RAY DIFFRACTION35(CHAIN E AND (RESID 7:46 OR RESID 101:101))E101
40X-RAY DIFFRACTION36(CHAIN F AND (RESID 2:61 OR RESID 102:102))F2 - 61
41X-RAY DIFFRACTION36(CHAIN F AND (RESID 2:61 OR RESID 102:102))F102
42X-RAY DIFFRACTION37(CHAIN G AND (RESID 7:46 OR RESID 101:101))G7 - 46
43X-RAY DIFFRACTION37(CHAIN G AND (RESID 7:46 OR RESID 101:101))G101
44X-RAY DIFFRACTION38(CHAIN I AND (RESID 2:61 OR RESID 102:102))I2 - 61
45X-RAY DIFFRACTION38(CHAIN I AND (RESID 2:61 OR RESID 102:102))I102
46X-RAY DIFFRACTION39(CHAIN I AND RESID 103:103) OR (CHAIN J AND RESID 7:46)I103
47X-RAY DIFFRACTION39(CHAIN I AND RESID 103:103) OR (CHAIN J AND RESID 7:46)J7 - 46
48X-RAY DIFFRACTION40(CHAIN K AND (RESID 2:61 OR RESID 102:102))K2 - 61
49X-RAY DIFFRACTION40(CHAIN K AND (RESID 2:61 OR RESID 102:102))K102
50X-RAY DIFFRACTION41(CHAIN N AND (RESID 7:46 OR RESID 101:101))N7 - 46
51X-RAY DIFFRACTION41(CHAIN N AND (RESID 7:46 OR RESID 101:101))N101
52X-RAY DIFFRACTION42(CHAIN O AND (RESID 2:61 OR RESID 102:102))O2 - 61
53X-RAY DIFFRACTION42(CHAIN O AND (RESID 2:61 OR RESID 102:102))O102
54X-RAY DIFFRACTION43(CHAIN P AND (RESID 7:46 OR RESID 101:101))P7 - 46
55X-RAY DIFFRACTION43(CHAIN P AND (RESID 7:46 OR RESID 101:101))P101
56X-RAY DIFFRACTION44(CHAIN Q AND (RESID 2:61 OR RESID 102:102))Q2 - 61
57X-RAY DIFFRACTION44(CHAIN Q AND (RESID 2:61 OR RESID 102:102))Q102
58X-RAY DIFFRACTION45(CHAIN R AND (RESID 7:46 OR RESID 101:101))R7 - 46
59X-RAY DIFFRACTION45(CHAIN R AND (RESID 7:46 OR RESID 101:101))R101
60X-RAY DIFFRACTION46(CHAIN S AND (RESID 2:61 OR RESID 102:102))S2 - 61
61X-RAY DIFFRACTION46(CHAIN S AND (RESID 2:61 OR RESID 102:102))S102
62X-RAY DIFFRACTION47(CHAIN T AND (RESID 7:46 OR RESID 101:101))T7 - 46
63X-RAY DIFFRACTION47(CHAIN T AND (RESID 7:46 OR RESID 101:101))T101
64X-RAY DIFFRACTION48(CHAIN U AND (RESID 2:61 OR RESID 102:102))U2 - 61
65X-RAY DIFFRACTION48(CHAIN U AND (RESID 2:61 OR RESID 102:102))U102
66X-RAY DIFFRACTION49(CHAIN V AND (RESID 7:46 OR RESID 101:101))V7 - 46
67X-RAY DIFFRACTION49(CHAIN V AND (RESID 7:46 OR RESID 101:101))V101
68X-RAY DIFFRACTION50(CHAIN W AND (RESID 2:61 OR RESID 102:102))W2 - 61
69X-RAY DIFFRACTION50(CHAIN W AND (RESID 2:61 OR RESID 102:102))W102
70X-RAY DIFFRACTION51(CHAIN X AND (RESID 7:46 OR RESID 101:101))X7 - 46
71X-RAY DIFFRACTION51(CHAIN X AND (RESID 7:46 OR RESID 101:101))X101
72X-RAY DIFFRACTION52(CHAIN Y AND (RESID 2:61 OR RESID 102:102))Y2 - 61
73X-RAY DIFFRACTION52(CHAIN Y AND (RESID 2:61 OR RESID 102:102))Y102
74X-RAY DIFFRACTION53(CHAIN Z AND (RESID 7:46 OR RESID 101:101))Z7 - 46
75X-RAY DIFFRACTION53(CHAIN Z AND (RESID 7:46 OR RESID 101:101))Z101
76X-RAY DIFFRACTION54(CHAIN 1 AND (RESID 2:61 OR RESID 102:102))12 - 61
77X-RAY DIFFRACTION54(CHAIN 1 AND (RESID 2:61 OR RESID 102:102))1102
78X-RAY DIFFRACTION55(CHAIN 2 AND (RESID 7:46 OR RESID 101:101))27 - 46
79X-RAY DIFFRACTION55(CHAIN 2 AND (RESID 7:46 OR RESID 101:101))2101
80X-RAY DIFFRACTION56(CHAIN 3 AND (RESID 2:61 OR RESID 102:102))32 - 61
81X-RAY DIFFRACTION56(CHAIN 3 AND (RESID 2:61 OR RESID 102:102))3102
82X-RAY DIFFRACTION57(CHAIN 4 AND (RESID 7:46 OR RESID 101:101))47 - 46
83X-RAY DIFFRACTION57(CHAIN 4 AND (RESID 7:46 OR RESID 101:101))4101
84X-RAY DIFFRACTION58(CHAIN 5 AND (RESID 2:61 OR RESID 102:102))52 - 61
85X-RAY DIFFRACTION58(CHAIN 5 AND (RESID 2:61 OR RESID 102:102))5102
86X-RAY DIFFRACTION59(CHAIN 6 AND (RESID 7:46 OR RESID 101:101))67 - 46
87X-RAY DIFFRACTION59(CHAIN 6 AND (RESID 7:46 OR RESID 101:101))6101
88X-RAY DIFFRACTION60(CHAIN 7 AND (RESID 2:61 OR RESID 102:102))72 - 61
89X-RAY DIFFRACTION60(CHAIN 7 AND (RESID 2:61 OR RESID 102:102))7102
90X-RAY DIFFRACTION61(CHAIN 8 AND RESID 7:46) OR (CHAIN 7 AND RESID 103:103)87 - 46
91X-RAY DIFFRACTION61(CHAIN 8 AND RESID 7:46) OR (CHAIN 7 AND RESID 103:103)7103
92X-RAY DIFFRACTION62(CHAIN 9 AND (RESID 2:61 OR RESID 102:102))92 - 61
93X-RAY DIFFRACTION62(CHAIN 9 AND (RESID 2:61 OR RESID 102:102))9102
94X-RAY DIFFRACTION63(CHAIN 0 AND (RESID 7:46 OR RESID 101:101))07 - 46
95X-RAY DIFFRACTION63(CHAIN 0 AND (RESID 7:46 OR RESID 101:101))0101
96X-RAY DIFFRACTION64(CHAIN C AND RESID 501:504)C501 - 504
97X-RAY DIFFRACTION65(CHAIN M AND (RESID 401:401 OR RESID 402:402)) OR (CHAIN L AND (RESID 301:301 OR RESID 303:303))M401
98X-RAY DIFFRACTION65(CHAIN M AND (RESID 401:401 OR RESID 402:402)) OR (CHAIN L AND (RESID 301:301 OR RESID 303:303))M402
99X-RAY DIFFRACTION66(CHAIN M AND RESID 403:403) OR (CHAIN L AND RESID 302:302)M403
100X-RAY DIFFRACTION66(CHAIN M AND RESID 403:403) OR (CHAIN L AND RESID 302:302)L302
101X-RAY DIFFRACTION67(CHAIN M AND RESID 406:406)M406
102X-RAY DIFFRACTION68(CHAIN M AND RESID 405:405)M405
103X-RAY DIFFRACTION69(CHAIN L AND RESID 304:304)L304
104X-RAY DIFFRACTION70(CHAIN A AND RESID 101:101)A101
105X-RAY DIFFRACTION71(CHAIN B AND RESID 102:102)B102
106X-RAY DIFFRACTION72(CHAIN A AND RESID 103:103)A103
107X-RAY DIFFRACTION73(CHAIN G AND RESID 102:102)G102
108X-RAY DIFFRACTION74(CHAIN J AND RESID 101:101)J101
109X-RAY DIFFRACTION75(CHAIN N AND RESID 102:102)N102
110X-RAY DIFFRACTION76(CHAIN P AND RESID 102:102)P102
111X-RAY DIFFRACTION77(CHAIN R AND RESID 102:102)R102
112X-RAY DIFFRACTION78(CHAIN T AND RESID 102:102)T102
113X-RAY DIFFRACTION79(CHAIN V AND RESID 102:102)V102
114X-RAY DIFFRACTION80(CHAIN X AND RESID 102:102)X102
115X-RAY DIFFRACTION81(CHAIN W AND RESID 103:103)W103
116X-RAY DIFFRACTION82(CHAIN 2 AND RESID 102:102)2102
117X-RAY DIFFRACTION83(CHAIN 4 AND RESID 102:102)4102
118X-RAY DIFFRACTION84(CHAIN 3 AND RESID 103:103)3103
119X-RAY DIFFRACTION85(CHAIN 8 AND RESID 101:101)8101

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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