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- PDB-4m11: Crystal Structure of Murine Cyclooxygenase-2 Complex with Meloxicam -

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基本情報

登録情報
データベース: PDB / ID: 4m11
タイトルCrystal Structure of Murine Cyclooxygenase-2 Complex with Meloxicam
要素Prostaglandin G/H synthase 2
キーワードOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NSAID / COX / dioxygenase / peroxidase / glycosylation / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
機能・相同性
機能・相同性情報


Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / : / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of fever generation / response to selenium ion / prostaglandin secretion / cellular response to fluid shear stress / response to nematode / nuclear inner membrane / prostaglandin biosynthetic process / dioxygenase activity / bone mineralization / nuclear outer membrane / decidualization / brown fat cell differentiation / keratinocyte differentiation / positive regulation of brown fat cell differentiation / embryo implantation / peroxidase activity / regulation of blood pressure / regulation of cell population proliferation / response to oxidative stress / cellular response to hypoxia / neuron projection / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain ...: / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Laminin / Laminin / EGF-like domain / Haem peroxidase superfamily / EGF-like domain profile. / EGF-like domain / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
PROTOPORPHYRIN IX CONTAINING FE / Chem-MXM / Prostaglandin G/H synthase 2
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.45 Å
データ登録者Xu, S. / Banerjee, S. / Hermanson, D.J. / Marnett, L.J.
引用ジャーナル: J.Biol.Chem. / 年: 2014
タイトル: Oxicams Bind in a Novel Mode to the Cyclooxygenase Active Site via a Two-water-mediated H-bonding Network.
著者: Xu, S. / Hermanson, D.J. / Banerjee, S. / Ghebreselasie, K. / Clayton, G.M. / Garavito, R.M. / Marnett, L.J.
履歴
登録2013年8月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年1月22日Provider: repository / タイプ: Initial release
改定 1.12014年2月12日Group: Database references
改定 1.22014年5月14日Group: Database references
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_label_asym_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.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年9月20日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)261,91326
ポリマ－253,9904
非ポリマー7,92422
水18,0871004
1
A: Prostaglandin G/H synthase 2
B: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,95713
ポリマ－126,9952
非ポリマー3,96211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-25 kcal/mol
Surface area41780 Å2
手法PISA
2
C: Prostaglandin G/H synthase 2
D: Prostaglandin G/H synthase 2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,95713
ポリマ－126,9952
非ポリマー3,96211
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-22 kcal/mol
Surface area42080 Å2
手法PISA
単位格子
Length a, b, c (Å)121.627, 133.538, 180.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDモデル要素
11B-846-

HOH

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要素

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タンパク質 , 1種, 4分子 ABCD

#1: タンパク質
Prostaglandin G/H synthase 2 / Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / ...Cyclooxygenase-2 / COX-2 / Glucocorticoid-regulated inflammatory cyclooxygenase / Gripghs / Macrophage activation-associated marker protein P71/73 / PES-2 / PHS II / Prostaglandin H2 synthase 2 / PGH synthase 2 / PGHS-2 / Prostaglandin-endoperoxide synthase 2 / TIS10 protein


分子量: 63497.422 Da / 分子数: 4 / 断片: UNP residues 18-569 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Ptgs2, Cox-2, Cox2, Pghs-b, Tis10 / プラスミド: pvL1393
発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ)
株 (発現宿主): Sf21
参照: UniProt: Q05769, prostaglandin-endoperoxide synthase

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糖 , 3種, 14分子

#2: 多糖
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 糖
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 8 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: 糖 ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / オクチルβ-D-グルコピラノシド


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 2 / 由来タイプ: 組換発現 / 式: C14H28O6 / コメント: 可溶化剤*YM
識別子タイププログラム
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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非ポリマー , 3種, 1012分子

#4: 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
#5: 化合物
ChemComp-MXM / 4-hydroxy-2-methyl-N-(5-methyl-1,3-thiazol-2-yl)-2H-1,2-benzothiazine-3-carboxamide 1,1-dioxide / Meloxicam / メロキシカム


分子量: 351.401 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C14H13N3O4S2 / コメント: 抗炎症剤*YM
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1004 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 2.88 Å3/Da / 溶媒含有率: 57.31 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM ...詳細: mCOX-2 protein reconstituted with a 2-fold molar excess of heme in phosphtate buffer, pH 6.7, 100 mM NaCl, 1.2% (w/v) -OG, and 0.1% NaN3, and 10-fold molar excess of inhibitors from 25 mM DMSO stocks were added to protein samples. Mixing 3 uL of the protein-inhibitor complex with 3 uL crystallization solution containing 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550 against reservoir solutions comprised of 50 mM EPPS, pH 8.0, 120 mM MgCl2, 22-26% PEG MME-550, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2012年11月19日
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: 0.9792 Å / 相対比: 1
反射解像度: 2.45→49.954 Å / Num. all: 106951 / Num. obs: 106951 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.1 % / Biso Wilson estimate: 34.48 Å2 / Rsym value: 0.133 / Net I/σ(I): 9.2
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.45-2.585.70.6541.187103154070.65498.4
2.58-2.746.40.4951.593657146840.49599.4
2.74-2.936.30.3582.187936138900.35899.6
2.93-3.166.20.2512.979737129340.25199.4
3.16-3.465.90.1614.568752117480.16198.3
3.46-3.876.30.1086.468535108070.10899.3
3.87-4.476.10.0867.65829495660.08699.1
4.47-5.485.90.0748.14703579440.07497.2
5.48-7.746.50.0748.64149864120.07499.7
7.74-49.95460.044112138435590.04496.4

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解析

ソフトウェア
名称バージョン分類NB
SCALA3.3.20データスケーリング
PHENIX1.8.2_1309精密化
PDB_EXTRACT3.11データ抽出
HKL-2000データ収集
XSCALEデータスケーリング
PHASES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 3NT1, chain A

3nt1


解像度: 2.45→49.954 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 27.54 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2306 5330 5 %RANDOM
Rwork0.2018 ---
obs0.2032 106689 98.4 %-
all-106951 --
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 max: 102.93 Å2 / Biso mean: 34.2024 Å2 / Biso min: 9.62 Å2
精密化ステップサイクル: LAST / 解像度: 2.45→49.954 Å
タンパク質核酸リガンド溶媒全体
原子数17896 0 528 1004 19428
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00919104
X-RAY DIFFRACTIONf_angle_d1.16625942
X-RAY DIFFRACTIONf_chiral_restr0.0842734
X-RAY DIFFRACTIONf_plane_restr0.0053308
X-RAY DIFFRACTIONf_dihedral_angle_d14.9087010
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.47670.31331760.27443389356598
2.4767-2.50580.35611740.27573326350099
2.5058-2.53640.31021770.25823310348798
2.5364-2.56850.32111650.26443232339795
2.5685-2.60230.30331790.25913362354199
2.6023-2.63790.27441770.25193341351899
2.6379-2.67560.32231770.25083392356999
2.6756-2.71550.30351770.23693346352399
2.7155-2.7580.29491730.23353393356699
2.758-2.80320.26031790.23383383356299
2.8032-2.85150.2851780.24173370354899
2.8515-2.90340.26981800.24083393357399
2.9034-2.95920.28371740.24253346352099
2.9592-3.01960.29311790.23743392357199
3.0196-3.08530.26321730.24563368354199
3.0853-3.1570.28971810.23023408358999
3.157-3.23590.2411750.22093359353499
3.2359-3.32340.25141740.22153269344396
3.3234-3.42120.23991790.21583343352298
3.4212-3.53160.24041760.1953395357199
3.5316-3.65780.21661790.19233401358099
3.6578-3.80420.22751810.18213435361699
3.8042-3.97720.18111780.17083356353499
3.9772-4.18680.18071820.16423450363299
4.1868-4.4490.17171780.1583370354899
4.449-4.79230.16771810.15783418359998
4.7923-5.2740.17311770.15013266344394
5.274-6.03610.19791850.18423496368199
6.0361-7.60050.18141830.18233505368899
7.6005-49.96420.21681830.193545372896
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)
15.93170.24990.14732.7641-1.63574.12320.3497-0.26160.5350.30430.36640.5501-0.3126-0.4201-0.50320.79020.17230.09350.33190.0660.335-6.394361.294536.5819
26.69552.6199-3.66693.0338-0.00683.02870.27770.68140.84630.5680.08440.2291-0.5711-0.6064-0.16730.62110.22970.0710.42750.05040.3962-12.48664.843442.3365
30.84280.2868-1.15292.2123-1.71832.82060.25050.26790.6995-0.561-0.1269-0.3862-0.42410.2925-0.09940.7036-0.07570.19550.2650.05610.44652.990569.108941.0052
40.2105-1.0137-0.84364.64163.92283.31680.83260.01830.7509-0.43690.049-0.7026-0.7537-0.4504-0.98210.6164-0.03440.32140.3552-0.01050.747316.471864.374332.5606
53.4894-2.50242.77261.9003-1.32875.7760.61430.45170.29930.1661-0.4749-0.1101-0.57081.3092-0.01980.3786-0.18810.15320.33990.01640.489930.703649.279731.5745
62.5989-1.19820.95751.17750.66112.6491-0.3387-0.29431.3025-0.05220.2970.0916-0.33260.51040.08770.4653-0.06670.0640.3617-0.00680.438317.147452.914939.4178
70.9603-0.2182-0.92741.05560.6322.60790.15440.00050.0677-0.0842-0.137-0.1401-0.4103-0.2911-0.01110.31670.065-0.01710.20630.00950.2281-4.06547.128845.0372
81.1526-0.8725-1.23313.39561.98072.4022-0.03330.4078-0.0031-0.2555-0.33150.6092-0.4116-0.20660.31870.50130.2617-0.07570.6508-0.00990.3346-10.857447.98422.0486
99.62042.59911.8152.95351.30593.0630.56971.44260.4535-0.3884-0.4946-0.00610.1856-0.14180.01250.40410.17090.10530.52470.04430.274911.070935.92413.9372
101.9912-0.89220.37171.08820.43991.0664-0.09640.1542-0.2299-0.1194-0.0610.1901-0.0012-0.33070.12960.25190.00250.02390.2053-0.0320.23525.246730.430338.6902
112.24920.30060.15682.09220.39342.72490.0458-0.1016-0.610.0026-0.18160.14140.34940.05950.09070.2452-0.00350.02570.0977-0.02520.331712.060712.77344.6407
123.90523.04641.68893.5402-0.17696.22240.2259-0.0201-0.7587-0.3063-0.12990.54690.8311-0.4659-0.1320.2774-0.0483-0.03230.2447-0.13680.4823-0.53813.257437.7421
133.72671.28781.89291.6743.08475.95410.2010.2122-0.8139-0.0914-0.59070.75480.4844-0.60420.46790.3647-0.0398-0.0630.2812-0.05750.44723.463215.131735.5278
141.1101-0.1242-0.461.22070.18272.7926-0.0132-0.0454-0.01220.062-0.0193-0.00030.190.41360.01350.16650.01340.01770.2229-0.01320.201919.34324.531543.5478
151.50440.0245-1.35031.70570.33928.72510.04770.08290.4689-0.2496-0.1193-0.2924-0.41081.9377-0.03230.30820.01340.08850.49680.05080.365125.366544.030637.8067
161.9785-0.6334-1.32780.64220.73663.13560.04510.23510.2075-0.1475-0.1547-0.0996-0.08570.08410.07430.25960.05540.05680.1860.03070.22999.042542.251738.4343
173.72460.40871.7313.9748-0.63611.90090.16580.7227-0.4022-0.5334-0.116-0.00970.0058-0.1911-0.05590.27350.0555-0.01240.4106-0.11240.274112.241318.228121.2919
181.1883-0.3285-0.05941.57970.31431.09080.19520.38950.1687-0.4139-0.0999-0.037-0.4252-0.3178-0.08880.44260.16970.04210.38760.0870.24220.159147.429121.4863
191.3065-0.3941-0.14670.14580.1032.15180.0885-0.01990.1534-0.0069-0.0611-0.2027-0.16280.175-0.01460.1957-0.03810.0190.2052-0.02990.252120.577535.358139.132
203.4238-0.1365-2.7224.48140.28532.18160.29980.3255-0.1386-0.657-0.1772-0.51050.10451.5139-0.10130.36420.0940.00150.5295-0.01350.309923.478231.117123.1212
211.14850.4522-0.67962.50741.07392.57690.1146-0.08260.10410.2492-0.0035-0.14430.4288-0.153-0.10160.35950.1509-0.06460.7520.02230.343727.005428.485167.8615
221.3892-0.32021.08681.6752-0.63572.538-0.0075-0.1517-0.03030.07680.2441-0.38490.32991.0708-0.12550.26390.0933-0.10010.8453-0.12180.42432.574634.5865.3129
232.05520.7190.10366.758-0.33132.28780.0919-0.94052.18350.4006-0.1119-0.7798-0.70020.89440.07040.4989-0.29770.02340.9983-0.24680.901635.60249.808668.3972
243.07650.3610.144.0457-0.45581.99870.0331-1.0533-0.1573-0.31070.2866-1.0325-0.23940.3097-0.17230.392-0.0156-0.08050.741-0.24390.782321.678256.715179.2626
254.6605-1.45683.42943.11060.49456.3504-0.7279-0.5580.8027-0.06560.0706-0.0458-0.95750.33270.58250.4696-0.13540.05140.484-0.2020.709912.470169.274174.9888
261.78743.2224-1.00326.1324-0.7693.7888-0.0107-0.0694-0.51140.2368-0.3102-1.89190.38260.52790.4180.2572-0.27220.06740.7973-0.19020.656716.082957.56866.6881
273.0018-0.05890.34472.41720.31063.4313-0.1032-0.60320.0677-0.09330.0594-0.02810.22820.53490.00980.27110.0873-0.00890.2792-0.01710.221912.814731.299463.5644
283.0888-1.3714-1.3293.21381.25710.7362-0.2238-0.2391-0.20650.88430.0619-0.06120.43180.50380.15180.4990.19030.01450.67650.0520.215610.640229.241488.9799
290.7467-0.7133-0.1661.24850.07751.06340.047-0.4122-0.04370.23880.019-0.05950.0048-0.0357-0.09590.2845-0.00210.01280.4453-0.02750.2904-3.04647.719879.1048
303.1024-4.0362-0.1185.3863-0.66845.2029-0.20650.352-0.87910.1898-0.01241.43970.36690.00350.24660.35460.03340.08250.39430.0060.3164-1.625328.822667.2072
313.0138-0.4197-0.68180.46640.29042.80650.0434-0.0763-0.1561-0.0001-0.01850.16710.0636-0.3292-0.01150.18380.00040.00910.16910.0040.2394-17.664345.277862.701
322.71390.64920.44455.2906-2.83583.03360.1557-0.5683-0.5342-0.1730.53930.7691-0.139-0.7739-0.66490.23270.0109-0.07140.38330.03920.5595-21.173834.862870.4986
331.96270.17530.28710.52560.2871.30360.0294-0.25560.16120.03570.0065-0.0253-0.2608-0.0856-0.020.30010.0360.02480.2247-0.03180.2559-10.048553.458866.0589
340.4562-0.6625-0.48510.97470.63681.9294-0.0294-0.40140.07620.1509-0.0316-0.1618-0.07650.3220.07870.1921-0.0413-0.00010.4136-0.06430.26355.709946.113370.0832
356.55171.1961-0.46217.4087-0.67736.2111-0.0959-0.81940.3090.93470.46580.71620.8762-0.4302-0.31250.57250.09980.0570.64270.0080.2918-16.56545.783890.2209
365.4009-1.28062.22131.2215-1.09572.5822-0.2709-1.0492-0.0860.29730.33380.072-0.0132-0.631-0.05120.37460.0420.09170.5904-0.0680.341-17.41750.452883.7138
370.8368-0.4513-0.91420.53720.40780.9233-0.0894-0.46-0.01840.30870.1979-0.07310.02280.395-0.10090.35370.1124-0.06340.6635-0.03970.280111.60337.219583.1746
383.4571-2.44471.81343.4688-2.333.3505-0.3582-0.33630.05290.5169-0.3323-0.089-0.27990.21580.33420.5910.2741-0.13291.2841-0.09030.41215.827337.017196.5325
391.1193-0.5316-0.43421.06970.12341.1706-0.0696-0.3490.24610.09820.1286-0.1864-0.14730.2008-0.02830.2809-0.03430.0150.3195-0.10460.25143.000851.911571.9989
403.02522.4637-0.8022.0642-1.46072.0004-0.3715-0.96791.28740.30340.14090.1165-1.0016-0.1524-0.12270.36930.26280.03550.8517-0.18180.28-4.529359.60484.265
414.6586-0.40053.77941.5666-1.67574.24590.6214-0.9314-0.6097-0.2508-0.0244-0.1586-0.4775-0.406-0.20530.5489-0.0761-0.05410.0966-0.04770.243955.09914.993458.9094
426.5534-3.69964.72875.2156-0.18955.4196-0.163-0.2331-1.0288-0.02640.3239-0.13560.7945-0.9769-0.0660.459-0.0666-0.0010.33840.05780.301648.97941.42653.1275
430.7199-0.49980.68682.1817-0.74242.490.0678-0.1983-0.23920.8445-0.121-0.16610.4499-0.294-0.0570.65330.0107-0.0357-0.0580.0540.3263.7078-2.048854.0888
446.7293-1.55360.39811.57890.85317.2342-0.51310.18350.28920.69740.1954-1.53720.10540.57080.31540.27450.2199-0.12480.3011-0.01580.81877.0906-2.795758.5081
454.1191-1.5534-0.61650.7289-0.25083.6696-0.26460.2087-1.71170.46320.0238-0.56530.2576-0.27790.18590.24740.0437-0.08570.44480.03010.707179.51529.41568.4486
462.58860.8286-1.60262.3847-2.4576.26490.2822-0.167-0.19750.0551-0.4992-0.2532-0.13321.35690.23520.26980.0749-0.02190.43910.0220.377291.984817.535363.7471
473.17093.125-0.42893.0846-0.46530.4396-0.2222-0.1429-0.9491-1.0604-0.2242-0.17870.7841-0.22170.37910.81070.16690.03050.43040.02050.420979.287814.075855.9234
480.7243-0.0849-0.35490.5454-0.11042.5463-0.0311-0.013-0.08660.1034-0.09270.04460.1059-0.1640.0920.2088-0.050.00110.14520.00610.222457.388419.263450.9724
491.75312.35611.68285.61724.994.66110.0526-0.44960.09050.7391-0.87720.65510.6985-1.0160.69160.3454-0.11010.04990.4077-0.02180.351447.498713.698869.6842
501.5837-0.1362-0.37240.3961-0.37040.9065-0.0055-0.16750.15260.0421-0.0184-0.12310.0397-0.1086-0.00590.251-0.03370.00180.1867-0.060.189867.375432.233371.8341
517.16853.9033-0.03143.5596-2.42545.1979-0.14380.12931.17240.18070.38870.0964-0.7435-0.31690.06360.1006-0.0733-0.07120.1039-0.04010.14358.393632.214153.3388
521.7409-0.69590.32511.7447-0.19222.3828-0.02740.01770.31160.0189-0.13370.2529-0.27840.00070.13550.1723-0.03050.00790.1210.01470.27170.342451.158351.3229
530.2818-0.0754-0.70333.76521.07027.04310.1718-0.00990.248-0.1599-0.44690.3635-1.3055-0.25220.24020.29920.0110.0230.1848-0.02950.379761.965752.689861.8869
540.16480.01280.27831.1485-0.60312.11450.02740.059-0.0438-0.0124-0.025-0.123-0.11770.2570.00850.1444-0.0383-0.00010.1951-0.01180.217979.812440.841853.9412
551.32790.1603-0.1571.44411.23451.4391-0.0129-0.1570.02450.1384-0.04480.07160.05730.15590.03460.2592-0.0269-0.02510.15110.09340.172273.063331.372963.4546
560.3869-0.1137-0.65123.279-1.13121.58580.3198-0.1711-0.02170.3431-0.36650.1677-0.1930.07960.1920.3781-0.0745-0.05710.2764-0.05120.303475.47648.567672.1548
571.76510.5970.32731.06270.14571.7910.0891-0.1285-0.0676-0.0329-0.0793-0.06260.2784-0.03120.0060.2574-0.03120.02320.20090.00390.144861.712519.752371.8087
583.2109-1.00630.51510.671-0.53635.8275-0.0264-0.5695-0.3540.3861-0.04660.2770.0934-0.7310.0660.4267-0.0637-0.01150.31180.0640.210859.056115.449879.1282
590.35150.01380.00060.3782-0.0260.79650.0309-0.0153-0.03450.10190.0852-0.11320.1530.2017-0.11920.19410.0006-0.01090.20180.00510.258680.461930.418357.9395
604.54292.2291-4.03933.6404-4.2335.5943-0.2925-0.2917-0.2527-0.4755-0.0086-0.68641.27191.35740.24590.35260.0456-0.00620.389-0.03980.257884.736436.15872.1975
610.8705-1.09730.43744.62591.48611.48680.27290.05930.0173-0.6769-0.4172-0.1187-0.67140.44040.1410.4075-0.10870.09130.51590.01850.234887.58639.031828.0144
624.2346-1.48540.1612.7298-0.04773.97540.14370.2284-0.3223-0.15680.0015-0.29960.19950.8822-0.15840.20990.02460.03790.4567-0.02220.31594.452127.627429.284
631.76670.2155-0.77893.3532-1.02712.4887-0.07890.2613-0.2918-0.16730.4856-0.4780.05870.4937-0.2940.25430.07370.05060.3651-0.11920.550280.48187.407415.2882
644.1297-0.602-1.44193.8767-0.15094.0927-0.0836-0.3051-0.27240.23130.0724-0.19071.06170.46910.08290.35540.05310.03080.3555-0.09340.37573.0022-1.90525.2725
654.2983.680.80563.9792-0.88143.14020.57220.0352-0.4495-0.2566-0.0593-0.81520.23330.6942-0.31980.38070.1413-0.04990.4672-0.07920.520977.916712.613328.372
661.2036-0.5265-0.21760.3792-0.23322.9699-0.03040.1303-0.0160.0072-0.0051-0.1136-0.28580.30420.03210.2259-0.0674-0.03650.2255-0.01550.195673.936536.457931.1599
674.89680.59441.22872.21790.34652.27160.05340.1840.0952-0.0389-0.19-0.2158-0.25790.05110.17760.2954-0.0682-0.03250.29350.0920.183669.642537.72495.5878
681.49810.6380.34031.75070.07280.86-0.17780.055-0.0145-0.16120.04370.2055-0.18930.05670.04740.1627-0.00220.00160.1632-0.01340.137957.637619.569516.7106
692.88061.4162-0.80112.3936-1.56193.67090.30520.56030.1745-0.4072-0.36050.5592-0.0161-0.0748-0.02870.2629-0.0076-0.06250.2070.00320.264559.315534.30530.4409
703.6709-0.1290.45010.27980.30373.2613-0.13280.05080.1976-0.13370.02990.0748-0.2219-0.36410.13410.19830.01320.0130.1624-0.00790.271141.581620.494133.4582
712.6692-0.5605-1.76554.2855-3.28147.0333-0.1358-0.17180.52180.14660.00680.2718-0.2913-0.91140.13480.12640.0417-0.07130.2836-0.01240.351338.602831.687126.2337
723.2923-1.50344.1441.5588-2.22745.5609-0.1806-0.02140.392-0.132-0.01220.0057-0.4422-0.09960.10030.2710.01180.00060.3101-0.05740.281740.632727.871823.5898
730.6711-0.30220.02510.4970.17591.81570.01840.0372-0.1560.0247-0.00220.03980.1963-0.0770.01440.1863-0.05140.00840.1267-0.03410.199653.608210.511431.1842
741.8718-0.58211.33440.43450.28512.11220.00890.0405-0.0612-0.2302-0.03510.01450.0826-0.0687-0.00450.1963-0.03420.03060.2125-0.03230.178363.154121.900821.9676
754.551-2.1311-0.04423.0541-1.55254.10110.11150.7456-0.0493-0.5634-0.10960.2879-0.0999-0.3628-0.00580.2517-0.0422-0.02490.3258-0.03830.23142.683318.949910.4493
762.6590.2881-0.08561.5101-0.1280.6733-0.07770.30890.1496-0.0264-0.13670.2039-0.13940.00970.1690.203-0.0093-0.0170.22480.05120.166962.32630.54499.5999
770.84450.26251.42471.06881.16022.95450.31940.49960.2558-0.07790.1814-0.2927-0.32430.5249-0.39170.2184-0.03720.05590.35710.06290.17979.677628.725913.6291
782.04340.2856-2.43637.74551.11073.1707-0.0460.7482-0.078-0.1392-0.120.1178-0.103-0.39480.18890.2594-0.01310.02890.59350.04690.236675.606933.68110.0051
791.09130.8323-0.11321.1952-0.71452.5328-0.04450.2231-0.104-0.2160.0303-0.03180.00520.22780.02270.1874-0.02830.04760.27070.00170.184973.782724.884912.8013
801.91750.08281.3521.35350.79122.6879-0.03930.203-0.0342-0.0439-0.002-0.09280.23880.10940.01390.1746-0.01560.03330.12590.00330.188955.99257.347730.4365
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 33:45)A33 - 45
2X-RAY DIFFRACTION2(CHAIN A AND RESID 46:56)A46 - 56
3X-RAY DIFFRACTION3(CHAIN A AND RESID 57:74)A57 - 74
4X-RAY DIFFRACTION4(CHAIN A AND RESID 75:89)A75 - 89
5X-RAY DIFFRACTION5(CHAIN A AND RESID 90:114)A90 - 114
6X-RAY DIFFRACTION6(CHAIN A AND RESID 115:123)A115 - 123
7X-RAY DIFFRACTION7(CHAIN A AND RESID 124:156)A124 - 156
8X-RAY DIFFRACTION8(CHAIN A AND RESID 157:183)A157 - 183
9X-RAY DIFFRACTION9(CHAIN A AND RESID 184:193)A184 - 193
10X-RAY DIFFRACTION10(CHAIN A AND RESID 194:239)A194 - 239
11X-RAY DIFFRACTION11(CHAIN A AND RESID 240:266)A240 - 266
12X-RAY DIFFRACTION12(CHAIN A AND RESID 267:278)A267 - 278
13X-RAY DIFFRACTION13(CHAIN A AND RESID 279:292)A279 - 292
14X-RAY DIFFRACTION14(CHAIN A AND RESID 293:352)A293 - 352
15X-RAY DIFFRACTION15(CHAIN A AND RESID 353:366)A353 - 366
16X-RAY DIFFRACTION16(CHAIN A AND RESID 367:391)A367 - 391
17X-RAY DIFFRACTION17(CHAIN A AND RESID 392:429)A392 - 429
18X-RAY DIFFRACTION18(CHAIN A AND RESID 430:511)A430 - 511
19X-RAY DIFFRACTION19(CHAIN A AND RESID 512:578)A512 - 578
20X-RAY DIFFRACTION20(CHAIN A AND RESID 579:583)A579 - 583
21X-RAY DIFFRACTION21(CHAIN B AND RESID 33:52)B33 - 52
22X-RAY DIFFRACTION22(CHAIN B AND RESID 53:70)B53 - 70
23X-RAY DIFFRACTION23(CHAIN B AND RESID 71:81)B71 - 81
24X-RAY DIFFRACTION24(CHAIN B AND RESID 82:92)B82 - 92
25X-RAY DIFFRACTION25(CHAIN B AND RESID 93:110)B93 - 110
26X-RAY DIFFRACTION26(CHAIN B AND RESID 111:122)B111 - 122
27X-RAY DIFFRACTION27(CHAIN B AND RESID 123:160)B123 - 160
28X-RAY DIFFRACTION28(CHAIN B AND RESID 161:186)B161 - 186
29X-RAY DIFFRACTION29(CHAIN B AND RESID 187:212)B187 - 212
30X-RAY DIFFRACTION30(CHAIN B AND RESID 213:222)B213 - 222
31X-RAY DIFFRACTION31(CHAIN B AND RESID 223:267)B223 - 267
32X-RAY DIFFRACTION32(CHAIN B AND RESID 268:278)B268 - 278
33X-RAY DIFFRACTION33(CHAIN B AND RESID 279:364)B279 - 364
34X-RAY DIFFRACTION34(CHAIN B AND RESID 365:394)B365 - 394
35X-RAY DIFFRACTION35(CHAIN B AND RESID 395:407)B395 - 407
36X-RAY DIFFRACTION36(CHAIN B AND RESID 408:430)B408 - 430
37X-RAY DIFFRACTION37(CHAIN B AND RESID 431:482)B431 - 482
38X-RAY DIFFRACTION38(CHAIN B AND RESID 483:493)B483 - 493
39X-RAY DIFFRACTION39(CHAIN B AND RESID 494:578)B494 - 578
40X-RAY DIFFRACTION40(CHAIN B AND RESID 579:583)B579 - 583
41X-RAY DIFFRACTION41(CHAIN C AND RESID 33:45)C33 - 45
42X-RAY DIFFRACTION42(CHAIN C AND RESID 46:56)C46 - 56
43X-RAY DIFFRACTION43(CHAIN C AND RESID 57:73)C57 - 73
44X-RAY DIFFRACTION44(CHAIN C AND RESID 74:83)C74 - 83
45X-RAY DIFFRACTION45(CHAIN C AND RESID 84:89)C84 - 89
46X-RAY DIFFRACTION46(CHAIN C AND RESID 90:114)C90 - 114
47X-RAY DIFFRACTION47(CHAIN C AND RESID 115:122)C115 - 122
48X-RAY DIFFRACTION48(CHAIN C AND RESID 123:156)C123 - 156
49X-RAY DIFFRACTION49(CHAIN C AND RESID 157:174)C157 - 174
50X-RAY DIFFRACTION50(CHAIN C AND RESID 175:214)C175 - 214
51X-RAY DIFFRACTION51(CHAIN C AND RESID 215:228)C215 - 228
52X-RAY DIFFRACTION52(CHAIN C AND RESID 229:271)C229 - 271
53X-RAY DIFFRACTION53(CHAIN C AND RESID 272:289)C272 - 289
54X-RAY DIFFRACTION54(CHAIN C AND RESID 290:357)C290 - 357
55X-RAY DIFFRACTION55(CHAIN C AND RESID 358:407)C358 - 407
56X-RAY DIFFRACTION56(CHAIN C AND RESID 408:430)C408 - 430
57X-RAY DIFFRACTION57(CHAIN C AND RESID 431:482)C431 - 482
58X-RAY DIFFRACTION58(CHAIN C AND RESID 483:506)C483 - 506
59X-RAY DIFFRACTION59(CHAIN C AND RESID 507:577)C507 - 577
60X-RAY DIFFRACTION60(CHAIN C AND RESID 578:583)C578 - 583
61X-RAY DIFFRACTION61(CHAIN D AND RESID 33:52)D33 - 52
62X-RAY DIFFRACTION62(CHAIN D AND RESID 53:80)D53 - 80
63X-RAY DIFFRACTION63(CHAIN D AND RESID 81:99)D81 - 99
64X-RAY DIFFRACTION64(CHAIN D AND RESID 100:114)D100 - 114
65X-RAY DIFFRACTION65(CHAIN D AND RESID 115:122)D115 - 122
66X-RAY DIFFRACTION66(CHAIN D AND RESID 123:164)D123 - 164
67X-RAY DIFFRACTION67(CHAIN D AND RESID 165:186)D165 - 186
68X-RAY DIFFRACTION68(CHAIN D AND RESID 187:212)D187 - 212
69X-RAY DIFFRACTION69(CHAIN D AND RESID 213:228)D213 - 228
70X-RAY DIFFRACTION70(CHAIN D AND RESID 229:265)D229 - 265
71X-RAY DIFFRACTION71(CHAIN D AND RESID 266:278)D266 - 278
72X-RAY DIFFRACTION72(CHAIN D AND RESID 279:293)D279 - 293
73X-RAY DIFFRACTION73(CHAIN D AND RESID 294:367)D294 - 367
74X-RAY DIFFRACTION74(CHAIN D AND RESID 368:398)D368 - 398
75X-RAY DIFFRACTION75(CHAIN D AND RESID 399:428)D399 - 428
76X-RAY DIFFRACTION76(CHAIN D AND RESID 429:457)D429 - 457
77X-RAY DIFFRACTION77(CHAIN D AND RESID 458:485)D458 - 485
78X-RAY DIFFRACTION78(CHAIN D AND RESID 486:494)D486 - 494
79X-RAY DIFFRACTION79(CHAIN D AND RESID 495:530)D495 - 530
80X-RAY DIFFRACTION80(CHAIN D AND RESID 531:583)D531 - 583

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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