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- PDB-5v6d: Crystal structure of nucleoside diphosphate kinase from Neisseria... -

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基本情報

登録情報
データベース: PDB / ID: 5v6d
タイトルCrystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate
要素Nucleoside diphosphate kinase
キーワードTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / nucleoside diphosphate kinase
機能・相同性
機能・相同性情報


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
CITRIC ACID / Nucleoside diphosphate kinase
類似検索 - 構成要素
生物種Neisseria gonorrhoeae NCCP11945 (淋菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.85 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
引用ジャーナル: To be Published
タイトル: Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate
著者: Abendroth, J. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
履歴
登録2017年3月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年4月19日Provider: repository / タイプ: Initial release
改定 1.12023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)268,26154
ポリマ-263,82216
非ポリマー4,43938
39,9752219
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,5487
ポリマ-32,9782
非ポリマー5705
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-1 kcal/mol
Surface area12380 Å2
手法PISA
2
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,5487
ポリマ-32,9782
非ポリマー5705
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-0 kcal/mol
Surface area12270 Å2
手法PISA
3
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,4866
ポリマ-32,9782
非ポリマー5084
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-2 kcal/mol
Surface area12390 Å2
手法PISA
4
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,6108
ポリマ-32,9782
非ポリマー6336
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-5 kcal/mol
Surface area12590 Å2
手法PISA
5
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,4866
ポリマ-32,9782
非ポリマー5084
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-2 kcal/mol
Surface area12630 Å2
手法PISA
6
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,5487
ポリマ-32,9782
非ポリマー5705
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-0 kcal/mol
Surface area12410 Å2
手法PISA
7
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,5487
ポリマ-32,9782
非ポリマー5705
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint1 kcal/mol
Surface area12470 Å2
手法PISA
8
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,4866
ポリマ-32,9782
非ポリマー5084
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-4 kcal/mol
Surface area12210 Å2
手法PISA
単位格子
Length a, b, c (Å)57.240, 112.350, 112.870
Angle α, β, γ (deg.)104.310, 98.500, 105.390
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Nucleoside diphosphate kinase / NDP kinase / Nucleoside-2-P kinase


分子量: 16488.852 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Neisseria gonorrhoeae NCCP11945 (淋菌)
遺伝子: ndk, NGK_1320 / プラスミド: NegoA.00438.a.B1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: B4RMG0, nucleoside-diphosphate kinase
#2: 化合物
ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 16 / 由来タイプ: 合成 / : C6H8O7
#3: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 22 / 由来タイプ: 合成 / : C2H6O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2219 / 由来タイプ: 天然 / : H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.51 Å3/Da / 溶媒含有率: 51 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5
詳細: 17.1 mg/mL NegoA.00438.a.B1.PW37901 + JCSG+ screen B9: 20% PEG6000, 100 mM sodium citrate tribasic, pH 5.0, cryoprotectant: 20% ethylene glycol in two steps, tray 2273617b9, puck mrl5-6

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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: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2016年10月26日
放射モノクロメーター: diamond(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97872 Å / 相対比: 1
反射解像度: 1.85→50 Å / Num. obs: 212120 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / 冗長度: 2.972 % / Biso Wilson estimate: 23.07 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.074 / Χ2: 0.992 / Net I/σ(I): 11.92
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.92.9850.5172.6155070.8910.6396.2
1.9-1.952.9810.3943.26151880.9260.48296.4
1.95-2.012.9850.3164.04148170.9460.38696.4
2.01-2.072.9830.2325.24143290.9690.28496.6
2.07-2.142.9890.1946.1139450.9780.23796.8
2.14-2.212.9830.1617.06135530.9820.19896.7
2.21-2.292.980.1228.65130710.9890.14997
2.29-2.392.9780.1059.87125900.990.12997.1
2.39-2.492.980.09310.88120830.9910.11497.3
2.49-2.622.9730.08212.03115990.9920.10197.5
2.62-2.762.9710.06814.2109680.9940.08397.6
2.76-2.932.9680.05716.43104160.9950.0797.6
2.93-3.132.9650.0518.898550.9950.06197.7
3.13-3.382.9670.04421.1991390.9960.05497.9
3.38-3.72.9540.03823.7383750.9960.04797.9
3.7-4.142.9550.03625.4976360.9960.04597.9
4.14-4.782.9530.03526.9367290.9960.04397.9
4.78-5.852.9390.03626.6956450.9960.04497.9
5.85-8.272.9320.03527.2543790.9960.04397.6
8.27-502.8320.03428.2822960.9960.04394.2

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
XSCALEデータスケーリング
PDB_EXTRACT3.22データ抽出
XDSデータ削減
MOLREP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 3VGS
解像度: 1.85→44.089 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 22.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.1884 1974 0.93 %
Rwork0.15 210063 -
obs0.1504 212037 97.12 %
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: 112.95 Å2 / Biso mean: 33.5398 Å2 / Biso min: 11.02 Å2
精密化ステップサイクル: final / 解像度: 1.85→44.089 Å
タンパク質核酸リガンド溶媒全体
原子数17051 0 296 2244 19591
Biso mean--37.96 39.73 -
残基数----2245
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00618124
X-RAY DIFFRACTIONf_angle_d0.75524620
X-RAY DIFFRACTIONf_chiral_restr0.0532822
X-RAY DIFFRACTIONf_plane_restr0.0053241
X-RAY DIFFRACTIONf_dihedral_angle_d15.68111147
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.32261280.247148051493396
1.8963-1.94750.29661360.2197148671500396
1.9475-2.00480.25491640.2039149341509896
2.0048-2.06960.2591140.1798148921500697
2.0696-2.14350.20381460.1686149811512797
2.1435-2.22930.19881440.1556149671511197
2.2293-2.33080.19541320.1481150151514797
2.3308-2.45370.20661330.1503150001513397
2.4537-2.60740.20411610.1599150921525398
2.6074-2.80870.20381540.1543150631521798
2.8087-3.09130.1791370.1546150731521098
3.0913-3.53840.19721540.1461151681532298
3.5384-4.45730.14451380.1231151611529998
4.4573-44.10140.14371330.1276150451517897
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.4402-1.49040.16073.65422.36882.02950.09170.0239-0.57210.38330.3954-0.91330.2480.3483-0.30120.29660.0232-0.06970.2546-0.09630.5831-5.0666106.304571.9026
23.42081.33422.21762.3473-2.0166.07270.1749-0.44350.0566-0.0586-0.1029-0.90640.34471.0959-0.11270.33740.0078-0.12220.6451-0.17460.70863.1515120.865383.5542
32.79660.05070.29741.6618-0.03242.916-0.0807-0.0115-0.0506-0.00650.4141-0.89-0.00090.4718-0.27450.24390.0047-0.03620.3178-0.12380.6051-1.2496114.455476.3588
43.9724-1.9564-0.37071.8917-0.40152.7349-0.1734-0.5521-0.18620.50350.7807-0.55430.05880.23210.20060.4010.3059-0.36130.5061-0.04371.17220.896100.168478.8396
55.0338-0.4068-0.74860.98380.65350.48710.009-0.03370.4079-0.02670.1491-0.82590.00660.3933-0.48110.55780.1803-0.17210.533-0.39051.714311.9122102.738972.1303
63.4682-0.2724-0.86511.77471.68741.64140.0903-0.1457-0.6380.39090.3355-1.37470.45610.5355-0.22960.39530.0599-0.19310.4556-0.12260.94741.4446109.702178.8324
75.0551-2.6728-2.43396.58182.81966.38420.1792-0.1605-0.28840.5833-0.22870.11320.5311-0.0871-0.0240.4409-0.0371-0.11540.20720.05060.2773-17.2113108.492580.0833
82.63130.5330.76312.69220.13191.0515-0.03020.2648-0.0388-0.72350.2891-0.5585-0.3050.2912-0.20730.3887-0.05040.10820.2076-0.04680.2757-13.2004109.690761.7254
92.43720.86392.7846.5179-3.69086.7320.1145-0.13490.36850.2211-0.360.7152-0.5761-0.3270.12340.3140.0438-0.0380.273-0.10860.378-30.3305111.990769.6163
105.53031.61592.55113.89090.55855.6961-0.16560.1585-0.0487-0.6152-0.11240.5087-0.4501-0.59820.16740.32220.058-0.08220.2404-0.06290.2732-33.0806106.395562.6751
111.5819-0.5641-2.05340.24770.92433.49340.19210.09850.0539-0.66620.1323-0.5714-0.55560.4177-0.33330.4469-0.08050.07970.2149-0.02820.3221-13.8341114.915861.2091
121.3882-0.36520.09754.9587-1.99650.8130.00650.4333-0.0445-0.99920.1204-0.0393-0.65720.3519-0.1040.8627-0.11090.12310.3637-0.03550.2483-15.8972112.099750.622
134.3744-0.4241-2.60999.84143.07684.77370.01710.3825-0.3272-1.36550.15290.2020.3148-0.099-0.26090.84440.01580.01290.35970.01510.3239-19.749399.586349.3364
141.32650.6110.02361.5265-0.44740.62010.02750.14050.0108-1.0915-0.06280.0521-0.4226-0.01190.03770.5260.0308-0.04760.201-0.01630.225-22.5859110.241357.905
155.2419-4.03-2.86577.64734.39636.7417-0.003-0.31270.1666-1.06760.1626-1.086-0.49880.4543-0.19880.4641-0.04190.07890.2254-0.01850.3571-12.5496123.223467.252
167.26840.3144-0.53973.33830.68257.1607-0.09640.29260.6755-0.00070.2155-0.2147-0.4650.1529-0.10230.21160.0247-0.05870.1675-0.00490.2134-4.190280.76564.3149
174.0255-3.3628-1.20523.46270.43422.5612-0.2-0.5121-0.00880.75660.1588-0.08680.24660.04370.01160.45370.0822-0.04060.26260.0380.1643-11.189671.29478.3768
186.56082.35331.46065.3641-4.9487.2715-0.2322-0.23390.36430.51940.19190.0116-0.43190.06610.05850.37040.1157-0.06980.2356-0.03480.2129-10.315984.134675.0721
193.85871.1546-0.21838.8312-2.10283.9605-0.1184-0.07910.12670.18450.2259-0.0964-0.11950.0012-0.11480.17780.0328-0.02420.15240.01440.124-12.073579.042165.0929
207.19311.9106-2.24683.6839-0.41973.2588-0.03780.0631-0.189-0.00540.1751-0.11920.52510.2082-0.13330.33340.0759-0.06120.2398-0.00470.1818-5.342462.156964.1118
215.2224-1.29733.08995.3438-3.55485.438-0.0328-0.0159-0.15920.4358-0.1041-1.01540.33871.37830.10880.33690.1575-0.11570.4866-0.02080.40976.864962.958268.5866
228.9505-2.06230.37972.499-0.88032.8548-0.1778-0.2819-0.32620.54610.1821-0.11230.54010.343-0.03710.40820.1034-0.07930.26810.01770.191-3.933461.988972.4249
235.04835.27-1.56188.3881-2.2663.4414-0.1799-0.00090.33-0.08530.2720.2432-0.10940.0242-0.03890.24850.0362-0.07170.20480.00540.1791-7.184980.812165.8193
245.3115-1.7528-1.19055.1637-3.40733.4756-0.0192-0.00450.35940.21150.2121-0.35950.05890.4481-0.23110.2947-0.0048-0.15990.2832-0.05630.31710.950983.119871.2537
253.84561.54172.27332.2638-1.40744.6181-0.4064-0.71320.52250.87840.1505-0.6254-0.11790.64360.27680.45370.1261-0.1790.4631-0.04190.30893.317778.513282.5773
260.639-0.29380.33510.6872-0.31831.7621-0.0731-0.12590.02070.34220.1213-0.1997-0.01880.2055-0.00890.28410.0556-0.09090.24530.00380.1982-1.111274.290870.2398
272.572-3.04790.09967.76493.5693.8954-0.02-0.00160.0911-0.51450.01010.251-1.1146-0.22770.0110.34750.0226-0.03820.20530.02750.1826-12.296680.611956.4778
282.94770.25730.17573.19790.27982.0823-0.1597-0.32150.01970.4308-0.03680.16940.067-0.13740.1850.2710.05250.01880.18830.00610.153-22.49280.100872.4548
294.2464-0.6551-0.01983.5852-1.93244.12820.12140.34660.1041-0.5506-0.29110.62120.0855-0.17950.22050.27110.0747-0.10380.2267-0.05940.2914-29.355982.165354.5693
302.2075-2.00831.56963.5167-2.79972.2291-0.0543-0.30740.55730.0851-0.2061.4454-0.4977-0.9183-0.16430.35410.1814-0.13140.5009-0.17730.8052-40.774787.414759.3322
312.7386-0.2926-0.00133.6396-0.56963.2953-0.0860.08420.1121-0.0969-0.25190.3267-0.1093-0.20450.25920.18140.054-0.02880.1775-0.04780.1974-27.200183.448363.3067
325.88734.07121.4233.33-0.00122.9598-0.1065-0.8323-0.30050.4291-0.18080.8389-0.3436-0.89880.29510.35410.05730.14670.3767-0.01210.3348-32.523279.192877.7576
333.1981-1.54240.52998.10941.90963.2646-0.4917-0.55910.85740.76640.16830.5305-1.3389-0.01790.28780.66980.10860.06180.4166-0.07670.4183-32.290792.65378.5464
341.53510.06820.52384.43962.00512.3237-0.0426-0.10880.00990.2345-0.26980.618-0.0904-0.28530.29030.19090.04440.02940.2133-0.03120.2838-31.241782.787368.4629
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1206.9143-1.0841-3.97754.69762.74277.57760.1925-0.4663-0.23830.592-0.0705-0.44380.55450.3205-0.03930.2521-0.0103-0.07890.18610.0540.170212.8084-36.287910.2456
1212.72883.15133.53315.01822.42896.64090.02710.1628-0.2533-0.09610.0436-0.07880.5714-0.1144-0.12190.37150.0142-0.03340.19970.00210.19955.7779-42.16140.3377
1227.17131.7471.41195.7306-2.09153.3791-0.2015-0.08880.0078-0.36280.0860.18120.2009-0.15660.10130.16390.00830.03470.18650.02270.0952.8641-32.0969-0.8372
1236.29971.935-3.35263.7837-2.97345.81650.18390.15630.15950.4243-0.13580.0564-0.6719-0.3188-0.03070.2825-0.0148-0.03190.22920.00620.12862.731-22.455315.3503
1240.33880.2031.0994.0951-3.47887.96910.0114-1.4159-0.7260.95940.01070.561.2319-0.24470.00420.5524-0.09510.080.5830.10620.2779-3.5332-30.282223.5211
1253.44120.2661.60422.65420.75294.2370.0853-0.1503-0.16140.32560.0403-0.0050.17320.0101-0.09430.2379-0.03690.0050.1380.05330.12773.7003-31.083511.0488
1268.6122-3.56541.22775.3678-3.93463.20240.0954-0.1076-0.67190.37280.1930.73550.9575-0.7008-0.29710.4319-0.1620.00680.26560.04390.2482-5.0806-42.66995.8053
1276.4584-0.4664-0.88222.96810.00952.80790.2556-1.073-0.9560.7281-0.3707-0.17510.74440.44260.13440.9502-0.1541-0.13190.35770.12760.35062.5996-48.796215.2163
1280.9897-0.83440.81442.7284-0.52342.10930.1347-0.2067-0.16290.4452-0.08570.19840.4433-0.226-0.07470.3207-0.10110.02210.23130.0330.1712-0.7153-35.599311.344
1294.3661-3.7502-2.34233.28922.40523.71890.35970.4109-0.1762-0.8085-0.56340.52590.1145-0.21080.28770.27910.0116-0.05310.2701-0.00410.2001-2.5417-26.0748-4.8507
1301.5662-1.2724-1.35613.1721-0.16931.93380.1683-0.47980.2514-0.1255-0.0272-1.03910.16850.63870.02710.20590.03140.00050.3354-0.03860.415622.3208-28.0903-3.9786
1313.82271.21731.73242.81421.39325.63890.1067-0.0439-0.2304-0.0930.0474-0.39050.54060.1216-0.22260.30260.05210.00640.1557-0.00840.195312.293-38.6093-6.7078
1329.1634-0.72762.51733.13871.274.770.0649-0.1429-0.0729-0.04310.1272-0.39390.22470.336-0.10940.1161-0.00410.00120.1678-0.00690.170713.7365-29.141-1.1116
1333.9383-0.5589-0.11710.11920.09985.5497-0.05840.8349-0.1752-0.9513-0.0074-0.5855-0.28470.339-0.02310.5605-0.02260.20720.3351-0.01820.299312.9617-21.6105-20.7436
1342.76470.30650.51612.63080.35774.00670.06460.1192-0.103-0.58290.0518-0.37510.0082-0.012-0.05450.27950.02320.07090.1502-0.0190.177312.2655-28.0837-12.8918
1356.94713.09242.5563.7715-0.52422.09960.3626-0.0634-0.2903-0.77150.0084-1.0457-0.01510.9546-0.13550.29620.08040.15630.4642-0.10330.547325.5521-34.1555-8.464
1364.1805-0.75761.74219.3473-0.76231.83170.39661.1336-0.9566-2.0253-0.1874-0.2340.79580.687-0.08940.66550.19210.12520.5484-0.06510.550221.3937-42.4376-18.433
1370.52860.04120.36653.21790.50831.31010.02040.2481-0.1579-0.42720.2105-0.58920.08780.2941-0.19330.28050.0110.14080.2859-0.04710.283818.1987-29.7146-13.3107
1383.06270.6474-1.30592.06591.09424.03960.1192-0.2305-0.24170.44260.2335-0.47720.18430.1528-0.19630.2123-0.024-0.02780.26930.01520.297615.4002-21.52783.502
1396.4623-1.86231.51854.4688-0.43135.3682-0.0633-0.86990.33990.8012-0.1581-0.36880.17390.38820.09860.4933-0.0942-0.05790.40830.03040.2633-1.2954-60.2205-11.0175
1405.0175-2.03731.81026.8443-0.46833.6990.1212-0.46840.21430.742-0.31680.9770.2531-0.60860.23150.3641-0.12180.10430.4034-0.10910.3755-17.7647-57.6587-17.489
1412.1294-0.21052.72690.41230.57165.31830.1731-0.54730.47640.6599-0.59920.5599-0.12240.02880.35870.5485-0.1810.12560.3659-0.12460.2807-8.546-50.1121-11.201
1422.9879-1.7821-0.35481.9957-1.21142.26420.2092-0.66440.24180.2734-0.1945-0.08730.2170.08060.03420.3314-0.09590.01110.3451-0.05630.175-2.3432-55.9599-17.3701
1433.2680.22820.04274.8851-0.66434.7416-0.1123-0.0327-0.52130.8227-0.34240.09510.4976-0.10870.30640.5013-0.16170.0440.29420.00720.3014-9.4383-72.7995-20.7252
1444.88410.9872-0.18022.5341-2.31322.22750.0454-1.233-0.91110.98650.00960.90940.4689-0.33250.05090.9941-0.24650.17640.62650.12950.5387-12.8082-77.719-9.2633
1452.0766-0.3179-0.97754.2151-2.47432.10960.1281-0.4022-0.34990.4683-0.20260.73950.9159-0.3923-0.11010.5464-0.25230.0660.4003-0.01510.4302-16.8102-70.8567-17.6094
1464.331-1.45681.95632.0070.55684.24250.1621-0.72950.18610.7034-0.1416-0.1337-0.0083-0.06730.12020.4479-0.169-0.01260.367-0.00960.1731-1.741-57.4814-12.0517
1475.2842-3.62732.84622.7555-0.67597.4676-0.0905-1.1159-0.23321.20370.07270.4030.3890.15690.06240.7625-0.22950.08560.66590.00760.2703-5.9877-58.4342-3.4218
1480.0140.13990.0061.27070.08540.00650.2344-0.07950.02860.7084-0.06960.52970.0269-1.19790.51791.1274-0.31360.51431.0451-0.36060.4307-18.0319-58.8222-1.0486
1493.1418-0.7299-1.30983.29130.83823.09460.2786-0.7591-0.21550.874-0.29890.52610.2633-0.2680.03310.6101-0.23270.07960.47410.01620.3062-9.26-64.3327-9.7876
1504.57-4.7771-4.0238.93262.41934.3190.12-0.22390.15590.33430.0875-0.8713-0.01270.0589-0.16770.3619-0.0496-0.10650.3562-0.00930.30036.0038-58.5498-19.6596
1516.61530.27251.88018.6952.22056.55930.52650.3192-0.4091-0.5545-0.2490.9207-0.0099-0.4442-0.31850.39210.0306-0.06820.2959-0.04330.3079-12.665-47.6681-33.2277
1520.65130.6825-0.41233.55021.08562.3530.151-0.06230.17250.2223-0.3510.5346-0.0801-0.26230.20660.3841-0.00670.01760.289-0.08230.2912-7.2171-44.1909-19.5352
1532.66460.1340.85575.7441.09332.66010.3292-0.1364-0.117-0.1024-0.32030.3802-0.0217-0.21430.01410.3001-0.0127-0.00950.2571-0.07130.1978-8.4544-52.8946-26.2384
1544.79481.8266-0.11194.3635-2.42683.3322-0.06480.51230.2307-0.92080.1363-0.418-0.81480.1478-0.01250.6527-0.06270.1910.3142-0.04550.32987.5097-43.1668-35.9837
1556.5281.04390.78955.23521.00743.53860.19210.05180.0583-0.3603-0.0781-0.1818-0.3242-0.0054-0.13080.29790.00940.03220.1422-0.03460.14080.5178-45.5473-28.849
1566.19674.49812.3613.58991.40181.7116-0.4452-0.32370.8183-1.04610.04830.565-1.1528-0.5290.22740.48660.1148-0.13230.2937-0.08740.4612-13.4102-40.077-31.4098
1571.3102-1.4384-0.88074.30914.00164.0098-0.4595-0.80110.98690.02450.01370.1844-1.5327-0.06230.42860.63870.063-0.12040.4356-0.09890.5517-7.5675-30.1938-25.0272
1581.40290.29390.55434.97152.44992.8723-0.03780.0040.1487-0.3493-0.19120.3001-0.4352-0.10890.24920.41480.0167-0.02040.2217-0.02970.2114-3.7877-41.7693-31.1545
1594.7698-1.7718-1.12037.11865.01543.54730.0512-0.609-0.07460.1593-0.65150.7124-0.1549-0.96030.59080.3831-0.019-0.0240.3782-0.08370.2881-9.8602-59.746-31.896
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 40 )A2 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 59 )A41 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 80 )A60 - 80
4X-RAY DIFFRACTION4chain 'A' and (resid 81 through 90 )A81 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 102 )A91 - 102
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 132 )A103 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 141 )A133 - 141
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 40 )B2 - 40
9X-RAY DIFFRACTION9chain 'B' and (resid 41 through 50 )B41 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 71 )B51 - 71
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 80 )B72 - 80
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 90 )B81 - 90
13X-RAY DIFFRACTION13chain 'B' and (resid 91 through 102 )B91 - 102
14X-RAY DIFFRACTION14chain 'B' and (resid 103 through 132 )B103 - 132
15X-RAY DIFFRACTION15chain 'B' and (resid 133 through 141 )B133 - 141
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 10 )C3 - 10
17X-RAY DIFFRACTION17chain 'C' and (resid 11 through 19 )C11 - 19
18X-RAY DIFFRACTION18chain 'C' and (resid 20 through 30 )C20 - 30
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 40 )C31 - 40
20X-RAY DIFFRACTION20chain 'C' and (resid 41 through 50 )C41 - 50
21X-RAY DIFFRACTION21chain 'C' and (resid 51 through 59 )C51 - 59
22X-RAY DIFFRACTION22chain 'C' and (resid 60 through 71 )C60 - 71
23X-RAY DIFFRACTION23chain 'C' and (resid 72 through 81 )C72 - 81
24X-RAY DIFFRACTION24chain 'C' and (resid 82 through 90 )C82 - 90
25X-RAY DIFFRACTION25chain 'C' and (resid 91 through 102 )C91 - 102
26X-RAY DIFFRACTION26chain 'C' and (resid 103 through 132 )C103 - 132
27X-RAY DIFFRACTION27chain 'C' and (resid 133 through 141 )C133 - 141
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 40 )D2 - 40
29X-RAY DIFFRACTION29chain 'D' and (resid 41 through 50 )D41 - 50
30X-RAY DIFFRACTION30chain 'D' and (resid 51 through 59 )D51 - 59
31X-RAY DIFFRACTION31chain 'D' and (resid 60 through 80 )D60 - 80
32X-RAY DIFFRACTION32chain 'D' and (resid 81 through 90 )D81 - 90
33X-RAY DIFFRACTION33chain 'D' and (resid 91 through 102 )D91 - 102
34X-RAY DIFFRACTION34chain 'D' and (resid 103 through 132 )D103 - 132
35X-RAY DIFFRACTION35chain 'D' and (resid 133 through 141 )D133 - 141
36X-RAY DIFFRACTION36chain 'E' and (resid 3 through 30 )E3 - 30
37X-RAY DIFFRACTION37chain 'E' and (resid 31 through 40 )E31 - 40
38X-RAY DIFFRACTION38chain 'E' and (resid 41 through 50 )E41 - 50
39X-RAY DIFFRACTION39chain 'E' and (resid 51 through 59 )E51 - 59
40X-RAY DIFFRACTION40chain 'E' and (resid 60 through 81 )E60 - 81
41X-RAY DIFFRACTION41chain 'E' and (resid 82 through 90 )E82 - 90
42X-RAY DIFFRACTION42chain 'E' and (resid 91 through 102 )E91 - 102
43X-RAY DIFFRACTION43chain 'E' and (resid 103 through 132 )E103 - 132
44X-RAY DIFFRACTION44chain 'E' and (resid 133 through 141 )E133 - 141
45X-RAY DIFFRACTION45chain 'F' and (resid 1 through 10 )F1 - 10
46X-RAY DIFFRACTION46chain 'F' and (resid 11 through 19 )F11 - 19
47X-RAY DIFFRACTION47chain 'F' and (resid 20 through 30 )F20 - 30
48X-RAY DIFFRACTION48chain 'F' and (resid 31 through 40 )F31 - 40
49X-RAY DIFFRACTION49chain 'F' and (resid 41 through 50 )F41 - 50
50X-RAY DIFFRACTION50chain 'F' and (resid 51 through 59 )F51 - 59
51X-RAY DIFFRACTION51chain 'F' and (resid 60 through 68 )F60 - 68
52X-RAY DIFFRACTION52chain 'F' and (resid 69 through 80 )F69 - 80
53X-RAY DIFFRACTION53chain 'F' and (resid 81 through 90 )F81 - 90
54X-RAY DIFFRACTION54chain 'F' and (resid 91 through 102 )F91 - 102
55X-RAY DIFFRACTION55chain 'F' and (resid 103 through 132 )F103 - 132
56X-RAY DIFFRACTION56chain 'F' and (resid 133 through 141 )F133 - 141
57X-RAY DIFFRACTION57chain 'G' and (resid 1 through 19 )G1 - 19
58X-RAY DIFFRACTION58chain 'G' and (resid 20 through 30 )G20 - 30
59X-RAY DIFFRACTION59chain 'G' and (resid 31 through 40 )G31 - 40
60X-RAY DIFFRACTION60chain 'G' and (resid 41 through 50 )G41 - 50
61X-RAY DIFFRACTION61chain 'G' and (resid 51 through 59 )G51 - 59
62X-RAY DIFFRACTION62chain 'G' and (resid 60 through 71 )G60 - 71
63X-RAY DIFFRACTION63chain 'G' and (resid 72 through 80 )G72 - 80
64X-RAY DIFFRACTION64chain 'G' and (resid 81 through 90 )G81 - 90
65X-RAY DIFFRACTION65chain 'G' and (resid 91 through 102 )G91 - 102
66X-RAY DIFFRACTION66chain 'G' and (resid 103 through 115 )G103 - 115
67X-RAY DIFFRACTION67chain 'G' and (resid 116 through 132 )G116 - 132
68X-RAY DIFFRACTION68chain 'G' and (resid 133 through 141 )G133 - 141
69X-RAY DIFFRACTION69chain 'H' and (resid 1 through 10 )H1 - 10
70X-RAY DIFFRACTION70chain 'H' and (resid 11 through 30 )H11 - 30
71X-RAY DIFFRACTION71chain 'H' and (resid 31 through 40 )H31 - 40
72X-RAY DIFFRACTION72chain 'H' and (resid 41 through 59 )H41 - 59
73X-RAY DIFFRACTION73chain 'H' and (resid 60 through 80 )H60 - 80
74X-RAY DIFFRACTION74chain 'H' and (resid 81 through 90 )H81 - 90
75X-RAY DIFFRACTION75chain 'H' and (resid 91 through 102 )H91 - 102
76X-RAY DIFFRACTION76chain 'H' and (resid 103 through 132 )H103 - 132
77X-RAY DIFFRACTION77chain 'H' and (resid 133 through 141 )H133 - 141
78X-RAY DIFFRACTION78chain 'I' and (resid 2 through 19 )I2 - 19
79X-RAY DIFFRACTION79chain 'I' and (resid 20 through 30 )I20 - 30
80X-RAY DIFFRACTION80chain 'I' and (resid 31 through 40 )I31 - 40
81X-RAY DIFFRACTION81chain 'I' and (resid 41 through 50 )I41 - 50
82X-RAY DIFFRACTION82chain 'I' and (resid 51 through 59 )I51 - 59
83X-RAY DIFFRACTION83chain 'I' and (resid 60 through 68 )I60 - 68
84X-RAY DIFFRACTION84chain 'I' and (resid 69 through 80 )I69 - 80
85X-RAY DIFFRACTION85chain 'I' and (resid 81 through 90 )I81 - 90
86X-RAY DIFFRACTION86chain 'I' and (resid 91 through 132 )I91 - 132
87X-RAY DIFFRACTION87chain 'I' and (resid 133 through 141 )I133 - 141
88X-RAY DIFFRACTION88chain 'J' and (resid 1 through 10 )J1 - 10
89X-RAY DIFFRACTION89chain 'J' and (resid 11 through 30 )J11 - 30
90X-RAY DIFFRACTION90chain 'J' and (resid 31 through 40 )J31 - 40
91X-RAY DIFFRACTION91chain 'J' and (resid 41 through 50 )J41 - 50
92X-RAY DIFFRACTION92chain 'J' and (resid 51 through 59 )J51 - 59
93X-RAY DIFFRACTION93chain 'J' and (resid 60 through 71 )J60 - 71
94X-RAY DIFFRACTION94chain 'J' and (resid 72 through 80 )J72 - 80
95X-RAY DIFFRACTION95chain 'J' and (resid 81 through 90 )J81 - 90
96X-RAY DIFFRACTION96chain 'J' and (resid 91 through 102 )J91 - 102
97X-RAY DIFFRACTION97chain 'J' and (resid 103 through 132 )J103 - 132
98X-RAY DIFFRACTION98chain 'J' and (resid 133 through 141 )J133 - 141
99X-RAY DIFFRACTION99chain 'K' and (resid 2 through 10 )K2 - 10
100X-RAY DIFFRACTION100chain 'K' and (resid 11 through 19 )K11 - 19
101X-RAY DIFFRACTION101chain 'K' and (resid 20 through 30 )K20 - 30
102X-RAY DIFFRACTION102chain 'K' and (resid 31 through 40 )K31 - 40
103X-RAY DIFFRACTION103chain 'K' and (resid 41 through 50 )K41 - 50
104X-RAY DIFFRACTION104chain 'K' and (resid 51 through 59 )K51 - 59
105X-RAY DIFFRACTION105chain 'K' and (resid 60 through 78 )K60 - 78
106X-RAY DIFFRACTION106chain 'K' and (resid 79 through 90 )K79 - 90
107X-RAY DIFFRACTION107chain 'K' and (resid 91 through 102 )K91 - 102
108X-RAY DIFFRACTION108chain 'K' and (resid 103 through 115 )K103 - 115
109X-RAY DIFFRACTION109chain 'K' and (resid 116 through 132 )K116 - 132
110X-RAY DIFFRACTION110chain 'K' and (resid 133 through 141 )K133 - 141
111X-RAY DIFFRACTION111chain 'L' and (resid 1 through 10 )L1 - 10
112X-RAY DIFFRACTION112chain 'L' and (resid 11 through 30 )L11 - 30
113X-RAY DIFFRACTION113chain 'L' and (resid 31 through 40 )L31 - 40
114X-RAY DIFFRACTION114chain 'L' and (resid 41 through 71 )L41 - 71
115X-RAY DIFFRACTION115chain 'L' and (resid 72 through 90 )L72 - 90
116X-RAY DIFFRACTION116chain 'L' and (resid 91 through 102 )L91 - 102
117X-RAY DIFFRACTION117chain 'L' and (resid 103 through 132 )L103 - 132
118X-RAY DIFFRACTION118chain 'L' and (resid 133 through 141 )L133 - 141
119X-RAY DIFFRACTION119chain 'M' and (resid 1 through 10 )M1 - 10
120X-RAY DIFFRACTION120chain 'M' and (resid 11 through 19 )M11 - 19
121X-RAY DIFFRACTION121chain 'M' and (resid 20 through 30 )M20 - 30
122X-RAY DIFFRACTION122chain 'M' and (resid 31 through 40 )M31 - 40
123X-RAY DIFFRACTION123chain 'M' and (resid 41 through 50 )M41 - 50
124X-RAY DIFFRACTION124chain 'M' and (resid 51 through 59 )M51 - 59
125X-RAY DIFFRACTION125chain 'M' and (resid 60 through 80 )M60 - 80
126X-RAY DIFFRACTION126chain 'M' and (resid 81 through 90 )M81 - 90
127X-RAY DIFFRACTION127chain 'M' and (resid 91 through 102 )M91 - 102
128X-RAY DIFFRACTION128chain 'M' and (resid 103 through 132 )M103 - 132
129X-RAY DIFFRACTION129chain 'M' and (resid 133 through 141 )M133 - 141
130X-RAY DIFFRACTION130chain 'N' and (resid 1 through 10 )N1 - 10
131X-RAY DIFFRACTION131chain 'N' and (resid 11 through 30 )N11 - 30
132X-RAY DIFFRACTION132chain 'N' and (resid 31 through 40 )N31 - 40
133X-RAY DIFFRACTION133chain 'N' and (resid 41 through 59 )N41 - 59
134X-RAY DIFFRACTION134chain 'N' and (resid 60 through 80 )N60 - 80
135X-RAY DIFFRACTION135chain 'N' and (resid 81 through 90 )N81 - 90
136X-RAY DIFFRACTION136chain 'N' and (resid 91 through 102 )N91 - 102
137X-RAY DIFFRACTION137chain 'N' and (resid 103 through 132 )N103 - 132
138X-RAY DIFFRACTION138chain 'N' and (resid 133 through 141 )N133 - 141
139X-RAY DIFFRACTION139chain 'O' and (resid 3 through 10 )O3 - 10
140X-RAY DIFFRACTION140chain 'O' and (resid 11 through 19 )O11 - 19
141X-RAY DIFFRACTION141chain 'O' and (resid 20 through 30 )O20 - 30
142X-RAY DIFFRACTION142chain 'O' and (resid 31 through 40 )O31 - 40
143X-RAY DIFFRACTION143chain 'O' and (resid 41 through 50 )O41 - 50
144X-RAY DIFFRACTION144chain 'O' and (resid 51 through 59 )O51 - 59
145X-RAY DIFFRACTION145chain 'O' and (resid 60 through 71 )O60 - 71
146X-RAY DIFFRACTION146chain 'O' and (resid 72 through 81 )O72 - 81
147X-RAY DIFFRACTION147chain 'O' and (resid 82 through 90 )O82 - 90
148X-RAY DIFFRACTION148chain 'O' and (resid 91 through 102 )O91 - 102
149X-RAY DIFFRACTION149chain 'O' and (resid 103 through 132 )O103 - 132
150X-RAY DIFFRACTION150chain 'O' and (resid 133 through 141 )O133 - 141
151X-RAY DIFFRACTION151chain 'P' and (resid 1 through 10 )P1 - 10
152X-RAY DIFFRACTION152chain 'P' and (resid 11 through 30 )P11 - 30
153X-RAY DIFFRACTION153chain 'P' and (resid 31 through 40 )P31 - 40
154X-RAY DIFFRACTION154chain 'P' and (resid 41 through 59 )P41 - 59
155X-RAY DIFFRACTION155chain 'P' and (resid 60 through 80 )P60 - 80
156X-RAY DIFFRACTION156chain 'P' and (resid 81 through 90 )P81 - 90
157X-RAY DIFFRACTION157chain 'P' and (resid 91 through 102 )P91 - 102
158X-RAY DIFFRACTION158chain 'P' and (resid 103 through 132 )P103 - 132
159X-RAY DIFFRACTION159chain 'P' and (resid 133 through 141 )P133 - 141

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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

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