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- PDB-4v8k: 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: 4v8k
タイトルCrystal structure of the LH1-RC complex from Thermochromatium tepidum in P21 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
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 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 / Light-harvesting complex / Multiheme cytochrome c family profile. / 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.
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 / PHOSPHATE ION / Ubiquinone-8 / Reaction center protein M chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 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: 3.006 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7月9日Provider: repository / タイプ: Initial release
置き換え2014年12月10日ID: 3WMN, 3WMO
改定 1.12014年12月10日Group: Other
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
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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
AC: Photosynthetic reaction center cytochrome c subunit
AL: Photosynthetic reaction center L subunit
AM: Photosynthetic reaction center M subunit
AH: Photosynthetic reaction center H subunit
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AD: LH1 alpha polypeptide
AE: LH1 beta polypeptide
AF: LH1 alpha polypeptide
AG: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AN: LH1 beta polypeptide
AO: LH1 alpha polypeptide
AP: LH1 beta polypeptide
AQ: LH1 alpha polypeptide
AR: LH1 beta polypeptide
AS: LH1 alpha polypeptide
AT: LH1 beta polypeptide
AU: LH1 alpha polypeptide
AV: LH1 beta polypeptide
AW: LH1 alpha polypeptide
AX: LH1 beta polypeptide
AY: LH1 alpha polypeptide
AZ: LH1 beta polypeptide
A1: LH1 alpha polypeptide
A2: LH1 beta polypeptide
A3: LH1 alpha polypeptide
A4: LH1 beta polypeptide
A5: LH1 alpha polypeptide
A6: LH1 beta polypeptide
A7: LH1 alpha polypeptide
A8: LH1 beta polypeptide
A9: LH1 alpha polypeptide
A0: LH1 beta polypeptide
BC: Photosynthetic reaction center cytochrome c subunit
BL: Photosynthetic reaction center L subunit
BM: Photosynthetic reaction center M subunit
BH: Photosynthetic reaction center H subunit
BA: LH1 alpha polypeptide
BB: LH1 beta polypeptide
BD: LH1 alpha polypeptide
BE: LH1 beta polypeptide
BF: LH1 alpha polypeptide
BG: LH1 beta polypeptide
BI: LH1 alpha polypeptide
BJ: LH1 beta polypeptide
BK: LH1 alpha polypeptide
BN: LH1 beta polypeptide
BO: LH1 alpha polypeptide
BP: LH1 beta polypeptide
BQ: LH1 alpha polypeptide
BR: LH1 beta polypeptide
BS: LH1 alpha polypeptide
BT: LH1 beta polypeptide
BU: LH1 alpha polypeptide
BV: LH1 beta polypeptide
BW: LH1 alpha polypeptide
BX: LH1 beta polypeptide
BY: LH1 alpha polypeptide
BZ: LH1 beta polypeptide
B1: LH1 alpha polypeptide
B2: LH1 beta polypeptide
B3: LH1 alpha polypeptide
B4: LH1 beta polypeptide
B5: LH1 alpha polypeptide
B6: LH1 beta polypeptide
B7: LH1 alpha polypeptide
B8: LH1 beta polypeptide
B9: LH1 alpha polypeptide
B0: LH1 beta polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)785,238241
ポリマ－681,23972
非ポリマー103,999169
水37821
1
AC: Photosynthetic reaction center cytochrome c subunit
AL: Photosynthetic reaction center L subunit
AM: Photosynthetic reaction center M subunit
AH: Photosynthetic reaction center H subunit
AA: LH1 alpha polypeptide
AB: LH1 beta polypeptide
AD: LH1 alpha polypeptide
AE: LH1 beta polypeptide
AF: LH1 alpha polypeptide
AG: LH1 beta polypeptide
AI: LH1 alpha polypeptide
AJ: LH1 beta polypeptide
AK: LH1 alpha polypeptide
AN: LH1 beta polypeptide
AO: LH1 alpha polypeptide
AP: LH1 beta polypeptide
AQ: LH1 alpha polypeptide
AR: LH1 beta polypeptide
AS: LH1 alpha polypeptide
AT: LH1 beta polypeptide
AU: LH1 alpha polypeptide
AV: LH1 beta polypeptide
AW: LH1 alpha polypeptide
AX: LH1 beta polypeptide
AY: LH1 alpha polypeptide
AZ: LH1 beta polypeptide
A1: LH1 alpha polypeptide
A2: LH1 beta polypeptide
A3: LH1 alpha polypeptide
A4: LH1 beta polypeptide
A5: LH1 alpha polypeptide
A6: LH1 beta polypeptide
A7: LH1 alpha polypeptide
A8: LH1 beta polypeptide
A9: LH1 alpha polypeptide
A0: LH1 beta polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)393,752123
ポリマ－340,62036
非ポリマー53,13287
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area209450 Å2
ΔGint-1823 kcal/mol
Surface area96530 Å2
手法PISA
2
BC: Photosynthetic reaction center cytochrome c subunit
BL: Photosynthetic reaction center L subunit
BM: Photosynthetic reaction center M subunit
BH: Photosynthetic reaction center H subunit
BA: LH1 alpha polypeptide
BB: LH1 beta polypeptide
BD: LH1 alpha polypeptide
BE: LH1 beta polypeptide
BF: LH1 alpha polypeptide
BG: LH1 beta polypeptide
BI: LH1 alpha polypeptide
BJ: LH1 beta polypeptide
BK: LH1 alpha polypeptide
BN: LH1 beta polypeptide
BO: LH1 alpha polypeptide
BP: LH1 beta polypeptide
BQ: LH1 alpha polypeptide
BR: LH1 beta polypeptide
BS: LH1 alpha polypeptide
BT: LH1 beta polypeptide
BU: LH1 alpha polypeptide
BV: LH1 beta polypeptide
BW: LH1 alpha polypeptide
BX: LH1 beta polypeptide
BY: LH1 alpha polypeptide
BZ: LH1 beta polypeptide
B1: LH1 alpha polypeptide
B2: LH1 beta polypeptide
B3: LH1 alpha polypeptide
B4: LH1 beta polypeptide
B5: LH1 alpha polypeptide
B6: LH1 beta polypeptide
B7: LH1 alpha polypeptide
B8: LH1 beta polypeptide
B9: LH1 alpha polypeptide
B0: LH1 beta polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)391,486118
ポリマ－340,62036
非ポリマー50,86782
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area203930 Å2
ΔGint-1751 kcal/mol
Surface area96550 Å2
手法PISA
単位格子
Length a, b, c (Å)167.159, 145.429, 210.528
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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Photosynthetic reaction center ... , 4種, 8分子 ACBCALBLAMBMAHBH

#1: タンパク質 Photosynthetic reaction center cytochrome c subunit


分子量: 43177.531 Da / 分子数: 2 / 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: 2 / 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: 2 / 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: 2 / 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, 64分子 AAADAFAIAKAOAQASAUAWAYA1A3A5A7A9BABDBFBIBKBOBQBSBUBWBYB1B3B5...

#5: タンパク質 ...
LH1 alpha polypeptide


分子量: 7034.442 Da / 分子数: 32 / 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: 32 / 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 , 11種, 190分子

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


分子量: 616.487 Da / 分子数: 8 / 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: 34 / 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: 72 / 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: 4 / 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: 2 / 由来タイプ: 合成 / 式: C49H74O4
#12: 化合物 ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe
#13: 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: 2 / 由来タイプ: 合成 / 式: C51H72O2
#14: 化合物...
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


分子量: 596.925 Da / 分子数: 34 / 由来タイプ: 合成 / 式: C42H60O2
#15: 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: 7 / 由来タイプ: 合成 / 式: C37H74NO8P / コメント: リン脂質*YM
#16: 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
#17: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 21 / 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: 3.56 Å3/Da / 溶媒含有率: 65.47 %
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: 2011年1月30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: 167629 / Num. obs: 167629 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 5.4 % / Biso Wilson estimate: 55.76 Å2 / Rsym value: 0.087 / Net I/σ(I): 9.14
反射 シェル解像度: 3→3.11 Å / 冗長度: 2.1 % / Mean I/σ(I) obs: 1.73 / Rsym value: 0.377 / % possible all: 71.8

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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: 3.006→43.794 Å / FOM work R set: 0.5941 / SU ML: 0.8 / σ(F): 3 / 位相誤差: 45.07 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射Selection details
Rfree0.3564 8410 5.02 %RANDOM
Rwork0.3354 159128 --
obs0.3364 167538 --
all-167629 --
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: 134.85 Å2
精密化ステップサイクル: LAST / 解像度: 3.006→43.794 Å
タンパク質核酸リガンド溶媒全体
原子数21858 0 3711 12 25581
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.02953035
X-RAY DIFFRACTIONf_angle_d2.31273591
X-RAY DIFFRACTIONf_chiral_restr0.1087492
X-RAY DIFFRACTIONf_plane_restr0.0148518
X-RAY DIFFRACTIONf_dihedral_angle_d19.85719393
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0059-3.11340.41686480.411126721332070
3.1134-3.2380.41837650.4105144951526081
3.238-3.38530.41458390.407157091654888
3.3853-3.56370.41368040.3984161471695190
3.5637-3.78680.38628760.3766161311700790
3.7868-4.0790.37198640.3496159991686389
4.079-4.48920.36428470.3242161591700690
4.4892-5.13790.30969050.2888166191752492
5.1379-6.46980.33869320.3006172971822996
6.4698-43.79810.31529300.29179001883097
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)
10.3665-0.5120.18040.6553-0.19340.8011-0.14910.28040.14710.26670.30510.0175-0.5248-0.00070.10060.4778-0.14890.06740.78710.08070.308-10.0337-6.2513127.718
20.204-0.0562-0.01590.01770.0183-0.0046-0.199-0.1665-0.35930.17720.2786-0.2646-0.4279-0.03710.2540.9715-0.16640.23590.64180.19140.5499-20.15466.5184134.7996
30.58730.1572-0.10110.655-0.12710.04680.07160.55750.02380.4747-0.06180.20440.1451-0.3915-0.04060.373-0.02950.09730.4903-0.1280.3319-20.05642.0871116.4823
40.0682-0.01550.04870.11690.06260.1050.12690.0269-0.06230.2154-0.169-0.01260.3098-0.1717-0.13510.4798-0.4886-0.03790.745-0.49610.6226-6.1327-11.213769.2509
50.7632-0.1848-0.17650.424-0.12510.28720.1947-0.017-0.1247-0.41340.0943-0.1111-0.09490.56760.62090.0917-0.254-0.00031.08280.05690.595929.57090.018466.398
60.47750.12680.17820.07030.14070.3319-0.0623-0.1486-0.46120.18820.18130.00830.14740.0660.20840.58940.42880.24260.6094-0.01390.58621.8909-20.305269.4041
70.5606-0.20260.18010.63930.84321.498-0.17550.33280.11170.62080.0316-0.02450.80070.5103-0.62270.2736-0.06890.062-0.0829-0.09040.4745.1182-7.35790.2978
80.61360.5013-0.09630.27880.07890.55040.19780.3219-0.2292-0.12820.32550.2579-0.57620.01981.6310.224-0.36070.0373-0.11460.3250.52535.246222.409886.0415
90.77980.2766-0.32070.227-0.09720.7782-0.06010.6020.45550.00810.15980.035-0.0932-0.25930.52870.16190.0005-0.0826-0.089-0.18940.4181-6.02993.54981.9791
100.1329-0.164-0.01550.20890.02610.0132-0.0422-0.02670.019-0.0101-0.0808-0.0267-0.0684-0.0318-0.03371.441-0.01030.56221.42010.05110.574-23.93315.1155148.2662
110.07050.00840.06170.01690.00940.0536-0.07110.02740.0649-0.013-0.03550.0142-0.1803-0.0412-0.02691.04690.03120.02740.9539-0.08010.2195-19.98087.8588134.9268
120.00350.0016-0.0035-0.0014-0.00180.0026-0.06170.00310.031-0.0004-0.04190.0270.01390.0705-0.1021.2917-0.0131-0.15561.2543-0.31360.3307-18.9242-2.8536108.5375
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980.017-0.02670.01890.05490.01870.1042-0.13940.20.03050.05910.0878-0.346-0.21890.2822-02.8484-0.82510.54431.5542-0.23711.856554.634939.115817.9783
990.07270.02030.06150.04380.03110.0453-0.12020.10430.1663-0.1127-0.093-0.2066-0.06790.0111-02.2091-0.46480.55951.3756-0.37421.78252.214848.425220.7239
1000.0064-0.00230.0078-0.0139-0.00680.04110.01710.1319-0.12350.3422-0.0180.0198-0.08740.108501.6593-0.14750.33930.8508-0.15810.952543.530240.93247.4375
1010.2284-0.14320.15660.1075-0.12060.1604-0.1518-0.26540.18930.27110.16590.0882-0.066-0.06840.02132.5455-0.3220.36970.9104-0.31171.792638.34649.79097.4197
1020.1248-0.09020.01820.13430.14780.3411-0.0420.07050.06960.1799-0.0853-0.1039-0.46450.21030.04472.06650.4206-0.1091.03210.29651.260332.624936.2043-2.6398
1030.4065-0.19380.1910.2516-0.02550.3201-0.4309-0.17450.4080.245-0.0122-0.2605-0.2506-0.1729-0.6481.2620.78810.04221.00410.48120.764624.792342.2686-5.1302
1040.093-0.00060.01460.0855-0.01420.0941-0.14290.03020.20060.0059-0.0741-0.0043-0.1861-0.0088-0.44780.68830.5681-0.06950.55920.52710.38824.237325.7089-10.4746
1050.1950.0436-0.04150.32810.21910.2075-0.32970.19180.43780.0364-0.51540.0537-0.4480.1602-0.09760.99890.37920.03071.89290.29910.978814.933827.8476-14.09
1060.05150.07230.01410.13180.0426-0.00060.10520.152-0.1790.29180.0225-0.06690.01040.00510.00110.47950.2756-0.16330.49890.34580.499419.850611.0783-14.3834
1070.034-0.00330.00090.07110.08430.0622-0.02450.49830.7594-0.2543-0.31940.4832-0.15460.2274-01.30250.4360.21622.38690.17681.322910.83599.5024-18.2598
1080.22-0.11310.04320.1121-0.07190.06110.3173-0.10950.0710.11630.1727-0.18370.075-0.01760.01081.48010.1019-0.37991.0509-0.10160.952219.7965-4.5995-14.3133
1090.01470.01890.0269-0.01330.00460.03090.30510.31580.3949-0.2559-0.15840.57590.057-0.14840.0031.4978-0.61140.2362.08410.05021.01911.4092-9.0544-17.6247
1100.1816-0.06440.0330.4988-0.48210.46450.502-0.0245-0.3666-0.34030.4533-0.218700.1890.36971.3962-0.56740.03931.3439-0.45961.379923.0865-20.139-10.7293
1110.2001-0.15280.12110.33620.02680.1280.1382-0.2457-0.08460.1311-0.2220.5560.2244-0.17650.13231.7872-0.827-0.0892.1609-0.83511.8215.7635-26.6018-12.8913
1120.1572-0.04950.1250.1459-0.02640.1234-0.0250.2298-0.47410.4527-0.13920.25830.27830.08260.00772.5255-0.2798-0.21771.2821-0.42931.506429.433-32.8362-3.6908
1130.07280.05070.05220.0391-0.00580.1047-0.1215-0.0290.1292-0.1536-0.06960.3929-0.02790.0171-0.01151.9109-0.55180.35650.9995-0.37771.533124.1616-41.692-3.8813
1140.0745-0.06590.08910.0535-0.07390.1040.1006-0.005-0.14210.0867-0.14610.13910.23560.14030.03852.57540.07170.20450.78920.41241.347339.3978-41.55115.4315
1150.0645-0.00620.04250.0102-0.03160.47750.11690.0234-0.0673-0.2121-0.07770.10820.2194-0.12210.0092.3578-0.0420.79640.7058-0.00741.386137.1239-51.16148.1117
1160.133-0.0840.00590.3241-0.06010.0930.23450.1565-0.1114-0.3438-0.1618-0.2010.26040.08830.25372.29330.498-0.08850.69870.41880.936351.1974-42.809615.3073
1170.1157-0.03250.0860.1273-0.04450.06570.1249-0.09890.04160.3846-0.33430.14520.1816-0.073603.25730.9762-0.09242.6954-0.13582.040251.8963-51.350820.5383
1180.71380.2848-0.4970.1065-0.19170.3284-0.5416-0.2309-0.79930.2204-0.29820.10720.42290.1619-0.03383.25210.2138-0.49072.8710.05291.912574.4857-22.116652.2642
1190.09090.107-0.00550.10240.01240.03440.1352-0.1070.3126-0.03880.3128-0.0053-0.1420.161902.7777-0.0631-0.75132.4796-0.90943.70745.948249.231729.0323
1200.0379-0.02590.00810.0144-0.0024-0.00310.22670.1629-0.3477-0.10360.13560.16120.0603-0.089901.37260.94580.12212.3588-0.00782.57136.200133.7031-8.6428
1210.0067-0.0374-0.02210.09670.08930.0588-0.1942-0.1156-0.0569-0.1134-0.1075-0.04390.09880.0217-02.6830.18680.47722.4795-0.14012.278329.2725-49.379112.2829
1220.00750.04360.02840.02350.06150.0057-0.32910.1267-0.0414-0.0011-0.2715-0.04330.2507-0.0984-02.26770.45420.50963.12350.14322.778184.3066-29.94299.7277
123-0.0014-0.03820.02540.009-0.0190.01210.241-0.393-1.02910.1317-0.1512-0.46920.23550.2226-0.00024.0313-0.5647-0.41553.7727-0.88722.839288.004423.514311.0763
1240.0565-0.00280.10940.0916-0.11350.2568-0.09690.0078-0.57390.176-0.18950.0369-0.22610.1652-0.08942.65290.58140.54332.5192-0.91251.908846.481431.5174-25.4345
125-0.001-0.0056-0.00130.0029-0.0085-0.0033-0.2950.0540.45460.0317-0.17070.0890.20.0107-02.71640.15610.51142.93450.17993.092141.0772-17.6124-30.5433
1260.3649-0.1396-0.27470.53990.2340.61290.0917-0.0836-0.6436-0.33550.27390.3116-0.0605-0.58710.21981.4093-0.70630.03631.26160.34411.152742.5768-0.988717.2006
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN AC AND RESID 17:84)
2X-RAY DIFFRACTION2(CHAIN AC AND RESID 85:183)
3X-RAY DIFFRACTION3(CHAIN AC AND RESID 184:333)
4X-RAY DIFFRACTION4(CHAIN AH AND RESID 2:45)
5X-RAY DIFFRACTION5(CHAIN AH AND RESID 46:259)
6X-RAY DIFFRACTION6(CHAIN AL AND RESID 2:30)
7X-RAY DIFFRACTION7(CHAIN AL AND RESID 31:281)
8X-RAY DIFFRACTION8(CHAIN AM AND RESID 2:102)
9X-RAY DIFFRACTION9(CHAIN AM AND RESID 103:320)
10X-RAY DIFFRACTION10(CHAIN AC AND RESID 501:501)
11X-RAY DIFFRACTION11(CHAIN AC AND RESID 502:502)
12X-RAY DIFFRACTION12(CHAIN AC AND RESID 503:503)
13X-RAY DIFFRACTION13(CHAIN AC AND RESID 504:504)
14X-RAY DIFFRACTION14(CHAIN AM AND RESID 401:401)
15X-RAY DIFFRACTION15(CHAIN AL AND RESID 301:301)
16X-RAY DIFFRACTION16(CHAIN AM AND RESID 402:402)
17X-RAY DIFFRACTION17(CHAIN AL AND RESID 303:303)
18X-RAY DIFFRACTION18(CHAIN AM AND RESID 403:403)
19X-RAY DIFFRACTION19(CHAIN AL AND RESID 302:302)
20X-RAY DIFFRACTION20(CHAIN AM AND RESID 406:406)
21X-RAY DIFFRACTION21(CHAIN AM AND RESID 405:405)
22X-RAY DIFFRACTION22(CHAIN AL AND RESID 304:304)
23X-RAY DIFFRACTION23(CHAIN AA AND (RESID 103:103 OR RESID 8:52 OR RESID 101:101))
24X-RAY DIFFRACTION24(CHAIN AB AND (RESID 7:46 OR RESID 101:101))
25X-RAY DIFFRACTION25(CHAIN AD AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
26X-RAY DIFFRACTION26(CHAIN AE AND (RESID 7:46 OR RESID 101:101))
27X-RAY DIFFRACTION27(CHAIN AF AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
28X-RAY DIFFRACTION28(CHAIN AG AND (RESID 7:46 OR RESID 101:101))
29X-RAY DIFFRACTION29(CHAIN AI AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
30X-RAY DIFFRACTION30(CHAIN AJ AND (RESID 7:46 OR RESID 101:101))
31X-RAY DIFFRACTION31(CHAIN AK AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
32X-RAY DIFFRACTION32(CHAIN AN AND (RESID 7:46 OR RESID 101:101))
33X-RAY DIFFRACTION33(CHAIN AO AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
34X-RAY DIFFRACTION34(CHAIN AP AND (RESID 7:46 OR RESID 101:101))
35X-RAY DIFFRACTION35(CHAIN AQ AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
36X-RAY DIFFRACTION36(CHAIN AR AND (RESID 7:46 OR RESID 101:101))
37X-RAY DIFFRACTION37(CHAIN AS AND (RESID 8:52 OR RESID 103:103 OR RESID 102:102))
38X-RAY DIFFRACTION38(CHAIN AT AND (RESID 7:46 OR RESID 101:101))
39X-RAY DIFFRACTION39(CHAIN AU AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
40X-RAY DIFFRACTION40(CHAIN AV AND (RESID 7:46 OR RESID 102:102))
41X-RAY DIFFRACTION41(CHAIN AW AND (RESID 8:52 OR RESID 101:101)) OR (CHAIN AV AND RESID 101:101)
42X-RAY DIFFRACTION42(CHAIN AX AND (RESID 7:46 OR RESID 101:101))
43X-RAY DIFFRACTION43(CHAIN AY AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
44X-RAY DIFFRACTION44(CHAIN AZ AND (RESID 7:46 OR RESID 101:101))
45X-RAY DIFFRACTION45(CHAIN A1 AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
46X-RAY DIFFRACTION46(CHAIN A2 AND (RESID 7:46 OR RESID 101:101))
47X-RAY DIFFRACTION47(CHAIN A3 AND (RESID 102:102 OR RESID 8:52 OR RESID 103:103))
48X-RAY DIFFRACTION48(CHAIN A3 AND RESID 104:104) OR (CHAIN A4 AND RESID 7:46)
49X-RAY DIFFRACTION49(CHAIN A5 AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
50X-RAY DIFFRACTION50(CHAIN A6 AND (RESID 7:46 OR RESID 101:101))
51X-RAY DIFFRACTION51(CHAIN A7 AND (RESID 8:52 OR RESID 103:103 OR RESID 101:101))
52X-RAY DIFFRACTION52(CHAIN A8 AND (RESID 7:46 OR RESID 101:101))
53X-RAY DIFFRACTION53(CHAIN A9 AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
54X-RAY DIFFRACTION54(CHAIN A0 AND (RESID 7:46 OR RESID 102:102))
55X-RAY DIFFRACTION55(CHAIN AI AND RESID 3:7) OR (CHAIN AD AND RESID 5:7) OR (CHAIN AF AND RESID 3:7)
56X-RAY DIFFRACTION56(CHAIN AQ AND RESID 5:7) OR (CHAIN AK AND RESID 4:7) OR (CHAIN AS AND RESID 3:7) OR (CHAIN AO AND RESID 3:7)
57X-RAY DIFFRACTION57(CHAIN AY AND RESID 2:7) OR (CHAIN A1 AND RESID 4:7) OR (CHAIN AU AND RESID 2:7) OR (CHAIN AW AND RESID 2:7)
58X-RAY DIFFRACTION58(CHAIN A9 AND RESID 2:7) OR (CHAIN A3 AND RESID 5:7) OR (CHAIN A5 AND RESID 4:7) OR (CHAIN A7 AND RESID 2:7)
59X-RAY DIFFRACTION59(CHAIN AA AND RESID 53:55) OR (CHAIN AI AND RESID 53:61) OR (CHAIN AD AND RESID 53:61) OR (CHAIN AF AND RESID 53:61)
60X-RAY DIFFRACTION60(CHAIN AQ AND RESID 53:61) OR (CHAIN AK AND RESID 53:61) OR (CHAIN AS AND RESID 53:61) OR (CHAIN AO AND RESID 53:61)
61X-RAY DIFFRACTION61(CHAIN AY AND RESID 53:61) OR (CHAIN A1 AND RESID 53:61) OR (CHAIN AU AND RESID 53:61) OR (CHAIN AW AND RESID 53:61)
62X-RAY DIFFRACTION62(CHAIN A9 AND RESID 53:61) OR (CHAIN A3 AND RESID 53:61) OR (CHAIN A5 AND RESID 53:59)
63X-RAY DIFFRACTION63(CHAIN AA AND RESID 102:102) OR (CHAIN AB AND RESID 102:102) OR (CHAIN A7 AND RESID 102:102) OR (CHAIN AG AND RESID 102:102) OR (CHAIN AP AND RESID 102:102) OR (CHAIN AJ AND RESID 102:102) OR (CHAIN AN AND RESID 102:102) OR (CHAIN A1 AND RESID 103:103) OR (CHAIN A0 AND RESID 101:101) OR (CHAIN AS AND RESID 104:104) OR (CHAIN AR AND RESID 102:102) OR (CHAIN A5 AND RESID 103:103) OR (CHAIN AT AND RESID 102:102) OR (CHAIN AW AND RESID 102:102) OR (CHAIN AX AND RESID 102:102) OR (CHAIN A2 AND RESID 102:102)
64X-RAY DIFFRACTION64(CHAIN BC AND RESID 17:84)
65X-RAY DIFFRACTION65(CHAIN BC AND RESID 85:183)
66X-RAY DIFFRACTION66(CHAIN BC AND RESID 184:333)
67X-RAY DIFFRACTION67(CHAIN BH AND RESID 2:45)
68X-RAY DIFFRACTION68(CHAIN BH AND RESID 46:259)
69X-RAY DIFFRACTION69(CHAIN BL AND RESID 2:30)
70X-RAY DIFFRACTION70(CHAIN BL AND RESID 31:281)
71X-RAY DIFFRACTION71(CHAIN BM AND RESID 2:102)
72X-RAY DIFFRACTION72(CHAIN BM AND RESID 103:320)
73X-RAY DIFFRACTION73(CHAIN BC AND RESID 501:501)
74X-RAY DIFFRACTION74(CHAIN BC AND RESID 502:502)
75X-RAY DIFFRACTION75(CHAIN BC AND RESID 503:503)
76X-RAY DIFFRACTION76(CHAIN BC AND RESID 504:504)
77X-RAY DIFFRACTION77(CHAIN BM AND RESID 401:401)
78X-RAY DIFFRACTION78(CHAIN BL AND RESID 301:301)
79X-RAY DIFFRACTION79(CHAIN BM AND RESID 402:402)
80X-RAY DIFFRACTION80(CHAIN BL AND RESID 303:303)
81X-RAY DIFFRACTION81(CHAIN BM AND RESID 403:403)
82X-RAY DIFFRACTION82(CHAIN BL AND RESID 302:302)
83X-RAY DIFFRACTION83(CHAIN BM AND RESID 406:406)
84X-RAY DIFFRACTION84(CHAIN BM AND RESID 405:405)
85X-RAY DIFFRACTION85(CHAIN BL AND RESID 304:304)
86X-RAY DIFFRACTION86(CHAIN BA AND (RESID 103:103 OR RESID 8:52 OR RESID 101:101))
87X-RAY DIFFRACTION87(CHAIN BB AND (RESID 7:46 OR RESID 101:101))
88X-RAY DIFFRACTION88(CHAIN BD AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
89X-RAY DIFFRACTION89(CHAIN BE AND (RESID 7:46 OR RESID 101:101))
90X-RAY DIFFRACTION90(CHAIN BF AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
91X-RAY DIFFRACTION91(CHAIN BG AND (RESID 7:46 OR RESID 101:101))
92X-RAY DIFFRACTION92(CHAIN BI AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
93X-RAY DIFFRACTION93(CHAIN BJ AND (RESID 7:46 OR RESID 101:101))
94X-RAY DIFFRACTION94(CHAIN BK AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
95X-RAY DIFFRACTION95(CHAIN BN AND (RESID 7:46 OR RESID 101:101))
96X-RAY DIFFRACTION96(CHAIN BO AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
97X-RAY DIFFRACTION97(CHAIN BP AND (RESID 7:46 OR RESID 101:101))
98X-RAY DIFFRACTION98(CHAIN BQ AND (RESID 8:52 OR RESID 103:103 OR RESID 102:102))
99X-RAY DIFFRACTION99(CHAIN BQ AND RESID 104:104) OR (CHAIN BR AND RESID 7:46)
100X-RAY DIFFRACTION100(CHAIN BS AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
101X-RAY DIFFRACTION101(CHAIN BT AND (RESID 7:46 OR RESID 101:101))
102X-RAY DIFFRACTION102(CHAIN BU AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
103X-RAY DIFFRACTION103(CHAIN BV AND (RESID 7:46 OR RESID 101:101))
104X-RAY DIFFRACTION104(CHAIN BW AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
105X-RAY DIFFRACTION105(CHAIN BX AND (RESID 7:46 OR RESID 101:101))
106X-RAY DIFFRACTION106(CHAIN BY AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
107X-RAY DIFFRACTION107(CHAIN BZ AND (RESID 7:46 OR RESID 101:101))
108X-RAY DIFFRACTION108(CHAIN B1 AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
109X-RAY DIFFRACTION109(CHAIN B2 AND (RESID 7:46 OR RESID 101:101))
110X-RAY DIFFRACTION110(CHAIN B3 AND (RESID 101:101 OR RESID 8:52 OR RESID 102:102))
111X-RAY DIFFRACTION111(CHAIN B4 AND (RESID 7:46 OR RESID 101:101))
112X-RAY DIFFRACTION112(CHAIN B5 AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
113X-RAY DIFFRACTION113(CHAIN B6 AND (RESID 7:46 OR RESID 101:101))
114X-RAY DIFFRACTION114(CHAIN B7 AND (RESID 8:52 OR RESID 103:103 OR RESID 101:101))
115X-RAY DIFFRACTION115(CHAIN B8 AND (RESID 7:46 OR RESID 101:101))
116X-RAY DIFFRACTION116(CHAIN B9 AND (RESID 8:52 OR RESID 102:102 OR RESID 101:101))
117X-RAY DIFFRACTION117(CHAIN B0 AND (RESID 7:46 OR RESID 102:102))
118X-RAY DIFFRACTION118(CHAIN BA AND RESID 2:7) OR (CHAIN BI AND RESID 7:7) OR (CHAIN BF AND RESID 4:7)
119X-RAY DIFFRACTION119(CHAIN BQ AND RESID 2:7) OR (CHAIN BK AND RESID 2:7) OR (CHAIN BS AND RESID 3:7) OR (CHAIN BO AND RESID 3:7)
120X-RAY DIFFRACTION120(CHAIN BU AND RESID 2:7) OR (CHAIN BW AND RESID 4:7)
121X-RAY DIFFRACTION121(CHAIN B9 AND RESID 2:7) OR (CHAIN B3 AND RESID 2:7) OR (CHAIN B5 AND RESID 2:7)
122X-RAY DIFFRACTION122(CHAIN BA AND RESID 53:56) OR (CHAIN BI AND RESID 53:56) OR (CHAIN BF AND RESID 53:59)
123X-RAY DIFFRACTION123(CHAIN BQ AND RESID 53:60) OR (CHAIN BK AND RESID 53:61) OR (CHAIN BS AND RESID 53:61) OR (CHAIN BO AND RESID 53:61)
124X-RAY DIFFRACTION124(CHAIN BY AND RESID 53:61) OR (CHAIN B1 AND RESID 53:61) OR (CHAIN BU AND RESID 53:59) OR (CHAIN BW AND RESID 53:61)
125X-RAY DIFFRACTION125(CHAIN B3 AND RESID 53:61) OR (CHAIN B7 AND RESID 53:61)
126X-RAY DIFFRACTION126(CHAIN BA AND RESID 102:102) OR (CHAIN BB AND RESID 102:102) OR (CHAIN B7 AND RESID 102:102) OR (CHAIN BG AND RESID 102:102) OR (CHAIN BF AND RESID 103:103) OR (CHAIN BO AND RESID 103:103) OR (CHAIN BN AND RESID 102:102) OR (CHAIN B1 AND RESID 103:103) OR (CHAIN B0 AND RESID 101:101) OR (CHAIN BS AND RESID 103:103) OR (CHAIN B2 AND RESID 102:102) OR (CHAIN BU AND RESID 103:103) OR (CHAIN BW AND RESID 103:103) OR (CHAIN BV AND RESID 102:102) OR (CHAIN B5 AND RESID 103:103) OR (CHAIN BP AND RESID 102:102)

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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。

-
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

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