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- PDB-3kgd: Crystal structure of E. coli RNA 3' cyclase -

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基本情報

登録情報
データベース: PDB / ID: 3kgd
タイトルCrystal structure of E. coli RNA 3' cyclase
要素RNA 3'-terminal phosphate cyclase
キーワードLIGASE / Cyclase / RNA processing / 3' modifying enzymes / adenylate / phosphoramidate
機能・相同性
機能・相同性情報


RNA 3'-terminal-phosphate cyclase (ATP) / RNA-3'-phosphate cyclase activity / RNA processing / ATP binding / cytoplasm
類似検索 - 分子機能
RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily ...RNA 3'-terminal phosphate cyclase type 1 / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase-like, conserved site / RNA 3'-terminal phosphate cyclase signature. / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase, insert domain / RNA 3'-terminal phosphate cyclase domain / RNA 3'-terminal phosphate cyclase, insert domain superfamily / RNA 3'-terminal phosphate cyclase domain superfamily / RNA 3'-terminal phosphate cyclase / RNA 3'-terminal phosphate cyclase (RTC), insert domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE MONOPHOSPHATE / RNA 3'-terminal phosphate cyclase
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.68 Å
データ登録者Shuman, S. / Tanaka, N. / Smith, P.
引用ジャーナル: Structure / 年: 2010
タイトル: Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer.
著者: Tanaka, N. / Smith, P. / Shuman, S.
履歴
登録2009年10月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年4月21日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Source and taxonomy / Version format compliance
改定 1.22012年3月21日Group: Database references
改定 1.32017年11月1日Group: Refinement description / カテゴリ: software
改定 1.42023年9月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_alt_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: RNA 3'-terminal phosphate cyclase
B: RNA 3'-terminal phosphate cyclase
C: RNA 3'-terminal phosphate cyclase
D: RNA 3'-terminal phosphate cyclase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)156,57231
ポリマ－153,3794
非ポリマー3,19327
水27,1671508
1
A: RNA 3'-terminal phosphate cyclase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,1878
ポリマ－38,3451
非ポリマー8437
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: RNA 3'-terminal phosphate cyclase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,0917
ポリマ－38,3451
非ポリマー7476
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: RNA 3'-terminal phosphate cyclase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,2069
ポリマ－38,3451
非ポリマー8628
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: RNA 3'-terminal phosphate cyclase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,0877
ポリマ－38,3451
非ポリマー7436
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)83.728, 81.932, 105.176
Angle α, β, γ (deg.)90.000, 103.440, 90.000
Int Tables number4
Space group name H-MP1211

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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
RNA 3'-terminal phosphate cyclase / RNA-3'-phosphate cyclase / RNA cyclase


分子量: 38344.633 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: Encodes an N-terminal decahistidine tag / 由来: (組換発現) Escherichia coli (大腸菌) / 株: K-12 substr. MG1655 / 遺伝子: b4475, JW5688, rtcA, yhgJ, yhgK, YP_026219 / プラスミド: pET16b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)-CodonPlus
参照: UniProt: P46849, RNA 3'-terminal-phosphate cyclase (ATP)

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非ポリマー , 5種, 1535分子

#2: 化合物
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / AMP


分子量: 347.221 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H14N5O7P / コメント: AMP*YM
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 10 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Na
#5: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1508 / 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: 2.29 Å3/Da / 溶媒含有率: 46.23 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 100 mM Na MES pH 6.5, 200 mM Ammonium sulfate, 20% w/v PEG 5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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データ収集

回折平均測定温度: 130 K
放射光源由来: シンクロトロン / サイト: NSLS / ビームライン: X29A / 波長: 1.1 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2009年7月11日
詳細: See Beamline Documentation http://www.px.nsls.bnl.gov/x29/x29_info.html
放射モノクロメーター: 3 sweeps with various exposure times and oscillation angles
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.1 Å / 相対比: 1
Reflection冗長度: 3.2 % / Av σ(I) over netI: 17.15 / 数: 1062888 / Rmerge(I) obs: 0.074 / Χ2: 1.13 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 336366 / % possible obs: 93.9
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.975098.810.0481.3213.7
3.954.9799.510.0551.4644
3.453.9599.310.0661.6094.5
3.133.4598.610.0751.6534
2.913.1398.510.0791.6333.7
2.742.9197.810.0661.7093.3
2.62.7497.510.0731.693.4
2.492.697.110.0831.6693.4
2.392.4996.810.0871.5373.4
2.312.3996.410.0871.3843.4
2.242.3195.910.0931.2333.5
2.172.2495.510.0971.1663.4
2.112.1795.510.111.0663.5
2.062.119510.1210.9793.5
2.022.069510.1420.9133.5
1.972.0295.110.1570.8633.5
1.931.9794.810.1890.7933.5
1.91.939410.2190.7413.4
1.861.99310.2520.6983.1
1.831.8692.210.2940.6393
1.81.8391.610.3210.6332.9
1.771.890.810.3750.5962.8
1.751.7790.610.410.5692.7
1.721.7589.910.4750.5462.6
1.71.7289.510.5250.5482.5
1.681.789.410.6020.542.4
1.661.6888.810.6930.5492.3
1.641.6687.210.620.5891.8
1.621.6486.610.720.5831.8
1.61.6286.110.8050.5731.8
反射解像度: 1.68→40 Å / Num. obs: 155565 / % possible obs: 93.9 % / 冗長度: 6.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.13 / Net I/σ(I): 10.5
反射 シェル解像度: 1.68→1.7 Å / 冗長度: 4.1 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.13 / Num. unique all: 5035 / Χ2: 0.573 / % possible all: 96.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER位相決定
PHENIX1.4_125精密化
PDB_EXTRACT3.005データ抽出
HKL-2000データ収集
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 1QMH

1qmh


解像度: 1.68→35.137 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.22 / Isotropic thermal model: Isotropic with Anisotropic TLS / 交差検証法: THROUGHOUT / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.207 7847 5.04 %Random
Rwork0.168 ---
obs0.17 155565 98.87 %-
溶媒の処理減衰半径: 0.8 Å / VDWプローブ半径: 1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 55.963 Å2 / ksol: 0.338 e/Å3
原子変位パラメータBiso max: 147.78 Å2 / Biso mean: 32.107 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.114 Å2-0 Å20.559 Å2
2---4.18 Å2-0 Å2
3---4.066 Å2
精密化ステップサイクル: LAST / 解像度: 1.68→35.137 Å
タンパク質核酸リガンド溶媒全体
原子数10103 0 193 1508 11804
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01210918
X-RAY DIFFRACTIONf_angle_d1.46114939
X-RAY DIFFRACTIONf_chiral_restr0.0981760
X-RAY DIFFRACTIONf_plane_restr0.0071951
X-RAY DIFFRACTIONf_dihedral_angle_d16.2373990
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 (%)
1.68-1.740.2597700.216144371520797
1.74-1.810.2477690.2144661523597
1.81-1.8920.2497730.193146091538298
1.892-1.9920.237540.182147091546399
1.992-2.1170.2297900.176147731556399
2.117-2.280.2037950.162148321562799
2.28-2.5090.2177940.1661482715621100
2.509-2.8720.2248460.1711487415720100
2.872-3.6180.1947390.1621504815787100
3.618-35.1370.1798170.1521514315960100
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)
19.1947-4.66342.93222.3939-1.37471.4568-0.11250.56490.0402-0.2810.3430.4507-0.2353-0.1601-0.05121.1750.114-0.29080.6093-0.17970.4866-37.90711.6071-29.8155
21.00390.0133-0.01621.94880.66511.17120.03430.08640.1336-0.25210.01120.0117-0.0578-0.1172-0.03420.1302-0.00090.00590.15260.00370.1717-34.837211.8182-13.2342
32.2661-1.9347-2.39692.72832.40643.09290.1809-1.43370.24330.47530.6823-0.84650.08980.7023-0.76950.19150.0075-0.0770.2973-0.05630.3838-25.060316.3088-4.8436
40.34950.12120.05222.7046-0.01240.61840.0117-0.07460.17980.22790.181-1.00380.0070.0746-0.15750.2272-0.01160.06760.1735-0.00740.2779-21.14098.3807-18.0094
51.37950.8333-0.50312.20730.91641.4521-0.0028-0.1360.3072-0.42270.0832-0.533-0.72990.4493-0.12630.2102-0.04420.02750.1757-0.01260.3045-27.193919.7208-14.724
62.4768-0.9368-1.51661.82441.31391.64580.31580.8524-0.0845-0.9705-0.375-0.2159-0.3533-0.04280.04630.2499-0.01550.10160.2985-0.0130.199-24.32457.5214-25.0073
70.42420.52730.82012.6475-0.53434.4278-0.07670.3194-0.1737-0.2256-0.0417-0.8678-0.17811.4286-0.06140.15070.02370.09020.301-0.02390.3435-14.22280.8945-14.3059
81.2575-0.15460.13360.1155-0.33851.0724-0.51750.31850.9237-0.89580.1147-0.05380.08570.29880.37230.4023-0.0444-0.22880.1308-0.04560.7373-18.13697.8707-1.0239
91.0303-0.9131-0.4791.1945-0.09251.44040.02440.05030.0122-0.1379-0.1367-0.19780.21380.29770.07650.16250.020.04160.20940.00720.2246-22.6998-2.1002-13.9553
101.48121.2261-0.07891.3583-0.65690.81090.1352-0.47780.01270.1741-0.293-0.2460.1120.07430.17770.1665-0.0008-0.010.25880.01420.2622-25.7037-6.7773-2.2503
111.90151.04670.87651.09120.60351.88920.22280.0877-0.19950.1210.005-0.28660.28780.3137-0.18340.16460.02040.03050.1677-0.01580.277-21.4313-7.1988-7.5891
120.4349-0.634-0.15430.89190.03821.00730.0760.0161-0.2523-0.22960.09310.12480.2234-0.1653-0.08290.2123-0.02-0.00970.1546-0.01660.22-40.5054-17.6132-9.0653
131.3046-1.0667-0.0370.8236-0.00630.6801-0.19010.2657-0.0857-0.12810.1984-0.2991-0.29740.16560.04550.216-0.0268-0.06820.17790.01250.2872-24.8627-14.09679.3694
143.74131.94371.97473.15570.52431.01130.3339-0.4313-0.31030.8393-0.2139-0.21440.0083-0.0059-0.08720.3373-0.03360.01650.2122-0.00180.1387-25.6524-15.227915.6037
156.68870.3249-0.45485.72571.84574.24040.2932-0.00160.16391.4844-0.4269-2.9393-0.10711.07460.45640.4266-0.1643-0.25820.22040.0130.7141-12.4314-5.320611.4838
161.0163-1.05340.08381.60420.09121.15810.0430.09270.07750.12480.1486-0.04690.0350.2045-0.11450.1547-0.0070.02060.14580.00180.2151-32.1343-12.92994.2506
172.79012.73661.2615.54661.90081.37450.7373-1.36450.90840.6139-1.0440.1097-1.76080.46050.39170.7538-0.2740.0050.4944-0.21470.4665-25.49051.392217.3643
182.0362.48221.08633.16160.82242.9453-0.1366-0.18171.0447-0.0311-0.11930.8121-0.5431-0.11830.45510.15420.01490.11770.1907-0.1180.2917-36.1289-8.139113.0141
191.52540.28870.24211.5491-0.71560.28750.0637-0.268-0.0130.1311-0.07930.14530.012-0.00720.00250.1330.00340.01180.14920.00790.214-40.9635-7.6106-7.7361
200.9594-0.3485-0.24221.4159-0.98310.5297-0.0094-0.06720.0998-0.02890.06650.36730.0652-0.0844-0.06320.1753-0.0142-0.02690.192-0.00120.2319-42.66091.9233-13.9624
210.37210.3052-0.43112.3025-1.31093.49710.03140.1646-0.0164-0.08180.55051.06720.7446-1.2536-0.70030.1597-0.02060.00330.30350.13240.4019-51.3323-7.5582-9.094
223.4562-0.6604-0.57774.02550.06250.0905-0.0070.68450.0249-1.4602-0.0224-0.53220.8451.1243-0.05080.350.09610.09130.378-0.05120.2649-0.6648-51.6905-20.9208
23-0.24390.2802-0.29311.5566-0.4771-0.05530.01820.0812-0.1127-0.17930.0259-0.1495-0.06890.092-0.0480.2118-0.0018-0.01540.1820.00210.1582-6.2216-48.8789-14.2902
243.2489-2.7536-0.87624.6714-0.91731.7445-0.1481-1.093-0.20221.13820.50831.04190.0957-0.1773-0.2950.2105-0.00820.04060.21590.03330.2848-15.4564-54.7121-6.1574
250.5702-0.94490.34532.10130.49992.1586-0.00540.1304-0.211-0.3690.05180.67420.4101-0.5902-0.01080.2458-0.04-0.04930.1729-0.02070.1964-17.6613-46.9339-19.0779
260.65160.14430.67811.8418-1.31722.26550.12630.1642-0.148-0.6034-0.09360.20040.8461-0.2609-0.13580.29550.0085-0.08930.2246-0.0180.2137-12.8756-57.7373-16.0263
271.6387-0.60630.28173.71970.68750.1880.28840.0967-0.0021-0.8914-0.17860.150.0538-0.1231-0.10730.31360.0201-0.08880.22360.00110.1132-17.5667-42.5367-24.0552
282.16580.14080.2832.73721.58721.0431-0.13370.1136-0.1037-0.0445-0.1150.1821-0.1424-0.23940.20220.1829-0.0059-0.04180.2258-0.03540.147-18.7701-36.8243-13.2347
292.1422-0.01290.8220.59150.97331.9771-0.0111-0.28520.082-0.0752-0.06610.2332-0.153-0.29180.12040.23860.0069-0.03850.2228-0.02560.1669-12.0145-28.0319-7.5094
304.5971.835-3.00432.8991-1.89485.79680.6112-0.21341.13340.0185-0.17070.8275-0.9817-0.2858-0.00090.19090.0333-0.00360.2826-0.08760.2432-24.0632-29.8683-5.9613
312.59080.54291.24472.08931.43561.31550.0501-0.0875-0.1717-0.1128-0.13220.02770.5951-0.05920.04660.15150.0115-0.01150.1823-0.05060.1497-21.0704-34.6122-6.9317
320.81230.38960.33111.6637-0.22070.1212-0.00390.11710.1911-0.50440.10390.0235-0.23110.1304-0.04520.2458-0.0086-0.01740.19020.00090.1867-1.4421-19.7724-7.9726
334.79393.2647-0.79944.1958-0.12340.9392-0.3237-0.14990.5797-0.3070.40160.58720.0498-0.1021-0.02690.21990.01750.03180.19740.00760.1994-18.8937-27.19389.5605
344.24191.04580.83881.0255-0.41470.59120.3429-1.57630.14050.9741-0.20920.1207-0.5988-0.2477-0.09560.38530.01180.0620.4896-0.01960.136-15.7756-26.621318.0799
352.1428-1.471-0.26992.6496-0.43540.8072-0.0387-0.18510.31660.17710.21730.2955-0.1896-0.1725-0.16290.21660.01180.0170.2361-0.00530.1787-20.985-23.16059.8455
361.3331-1.34330.02811.23390.09811.3069-0.0691-0.068-0.29550.06020.03590.10230.0178-0.06180.01130.1548-0.01020.00560.2006-0.01760.1404-13.9297-27.66854.4645
373.60551.881-2.09772.5337-3.11383.84670.1513-0.9961-2.7138-0.0546-0.0246-0.22910.9481-0.8657-0.7040.3105-0.12410.02810.37090.22220.5964-15.6413-39.381111.3927
384.56992.3094-1.50451.8651-1.63582.3771-0.1373-0.8152-1.06480.1272-0.3255-0.43990.58710.11930.28030.32-0.04830.01850.35590.10210.3097-8.2995-33.921214.2952
390.1120.11690.22961.04781.56291.24790.067-0.0584-0.08250.0017-0.018-0.16310.0490.1236-0.02720.2029-0.0128-0.00950.1977-0.0110.15410.2987-29.6708-6.2465
400.83130.48960.38422.23391.210.57080.043-0.0235-0.3186-0.07140.149-0.417-0.03070.1457-0.13140.1512-0.00870.00910.1995-0.01930.23733.9043-38.4743-12.9641
410.9183-0.07120.17541.90281.16162.8591-0.040.16980.0373-0.12340.3478-0.8438-0.83950.8928-0.38630.1953-0.03680.04040.27-0.05120.257810.0616-28.9414-7.8347
421.9426-0.6731-0.97381.93550.33360.5544-0.0858-0.4551-0.00750.21640.0904-0.19290.29150.593-0.08570.2737-0.0019-0.0090.24420.05070.2036-31.2334-25.9571-34.6773
430.1138-0.6445-0.41491.5724-0.571.1711-0.084-0.07120.01360.22280.05440.12450.02250.31150.0420.21780.03340.00370.20680.02070.1621-36.8016-28.5587-36.1204
442.02754.04831.46743.9641-0.77122.5709-0.28381.5853-0.1445-1.04120.8090.6189-0.1671-0.6036-0.32710.22610.02980.01490.23850.02110.2713-44.8341-21.425-45.5762
450.07640.2097-0.31371.29840.4321.0867-0.2039-0.11830.0060.2043-0.04780.78770.3386-0.52170.26920.25440.05420.07120.2147-0.02230.3078-47.4865-30.0817-33.5203
460.6615-0.60240.1861.3814-1.61753.6782-0.0276-0.00290.05060.40810.05370.5201-0.8862-0.438-0.03090.33740.05780.0330.20850.0090.2422-43.1926-19.3801-34.9581
471.26941.2260.21441.39860.04710.0350.0071-0.62810.0471.0124-0.32580.0185-0.23840.35350.04360.42160.07060.11450.27690.01710.1724-41.857-29.3666-26.1748
480.09210.23890.14290.81770.13792.7421-0.3404-0.2992-0.01550.2310.21380.8328-0.2763-1.21370.14140.21210.05410.17770.35220.00050.5716-54.0687-38.7098-31.8706
492.4593-0.9615-0.0312.58621.42681.63-0.09430.1126-0.2907-0.0274-0.05230.7506-0.0715-0.26660.13560.14610.00370.05670.17690.01630.3261-45.8027-42.9587-41.1621
502.7513-0.79760.76581.53631.4460.9058-0.01660.2003-0.3734-0.0448-0.34120.70.10290.03130.23110.16290.01910.01510.2054-0.02640.5223-48.1398-46.9936-43.6902
511.0752-0.6831-0.78331.20560.03211.95080.364-0.0492-0.260.0249-0.16730.2688-0.23460.2634-0.26670.21280.04150.00770.20250.00110.6224-52.3095-42.6475-42.4884
521.283-0.28691.01311.0617-0.69291.28830.0029-0.1522-0.37320.27910.2790.16330.10840.1419-0.04080.19960.0210.04170.15740.07770.1893-31.6676-55.8938-39.9453
531.6204-1.0240.48882.6354-0.77280.3444-0.4275-0.63280.16420.11720.80330.5516-0.0622-0.2531-0.2370.2116-0.0073-0.11040.25430.05910.4651-47.3785-52.3677-59.2867
543.7807-0.2972.47472.7788-1.44632.3547-0.04691.697-0.3788-0.87680.41571.01950.45770.3506-0.21640.2986-0.0838-0.14690.49380.18490.4064-45.8475-51.2598-68.5535
551.86160.78420.86881.03011.45682.2064-0.21250.36660.8186-0.0055-0.03150.2527-0.0445-0.210.23710.18390.0014-0.0590.21580.02970.4949-53.1172-49.1588-59.8927
561.69151.3514-0.17640.9773-0.00810.99130.05280.09320.1477-0.0538-0.01120.31380.0638-0.1112-0.00220.16390.0357-0.01250.1908-0.0050.2775-38.2846-52.6418-53.8913
573.1291.9351-0.92952.2666-2.17422.68791.6171-0.14930.63550.5349-0.31650.3888-1.3484-0.54-0.70220.57060.2319-0.07220.50930.56691.0648-47.7253-35.1826-67.2258
581.32261.372-0.39411.95150.39581.8281-0.44270.96950.732-0.14840.51840.3869-0.3470.2773-0.0840.2071-0.1023-0.05390.33770.19860.3629-35.63-46.3756-63.2952
591.6242-0.631-0.3911.86160.59940.14590.05750.0554-0.084-0.0771-0.0140.1336-0.20260.0253-0.04540.16460.01770.01770.1708-0.00140.1273-29.4199-46.8416-43.639
601.0656-1.172-0.92291.09850.8730.5571-0.0635-0.15990.1046-0.01390.0633-0.1172-0.20490.16720.04680.21850.0218-0.00790.22050.01570.1732-28.3764-36.0243-39.1018
611.8776-0.48291.65481.8784-0.71211.4241-0.0297-0.1789-0.09050.22820.2833-0.3844-0.0614-0.2055-0.13580.17690.0241-0.00750.198-0.01330.1533-20.5547-45.314-39.1515
620.1489-0.0501-0.02022.04421.86532.1156-0.5460.904-0.50640.409-0.7002-0.53281.62590.09470.66621.14340.15270.0420.32070.19790.68910.8567-46.7565-81.2276
630.82190.16080.17881.7459-1.50241.61620.0112-0.0117-0.231-0.1274-0.0326-0.092-0.03080.18070.0220.17260.0103-0.02620.1788-0.00520.19175.2646-48.8647-64.4447
641.5822-0.41120.88891.7933-1.06211.2953-0.0252-0.5199-0.35970.47480.47950.8579-0.5517-0.4453-0.28820.23280.02190.02740.22880.04060.2999-5.0357-51.0214-57.9432
651.63940.26611.12631.1132-0.13241.01120.1230.0177-0.4283-0.38910.05490.40950.2557-0.1554-0.1430.2779-0.0139-0.09330.1893-0.02210.2322-5.1598-49.3666-70.5367
660.37031.1437-1.11814.1836-1.3295.68890.0416-0.15310.09530.1525-0.05971.1950.3864-1.13260.23660.2088-0.0075-0.09040.2412-0.05450.3168-14.2683-39.317-63.4283
671.7221-0.49020.37392.42721.06971.1252-0.1122-0.10240.02850.0265-0.07450.2599-0.0219-0.18670.17160.2004-0.0036-0.03960.2024-0.03610.2019-5.0671-32.622-59.8942
682.00910.5699-0.65781.03090.20720.85910.13420.37870.6141-0.05590.02250.4588-0.2569-0.3421-0.01090.2953-0.01550.00340.1971-0.01780.2487-6.0602-26.0554-62.113
691.3476-0.2308-0.18171.1612-0.19850.88650.2529-0.0042-0.0239-0.0038-0.27360.1721-0.26530.2952-0.02020.1937-0.0355-0.03170.1716-0.02710.2102-10.2684-33.0335-57.4972
700.4007-0.1784-0.20821.33621.37431.1685-0.0459-0.01720.2044-0.3090.15880.0066-0.54260.1099-0.01790.2423-0.0385-0.02070.13770.00550.238311.2371-19.0108-60.4332
716.14223.6484-3.55427.3618-1.51523.5436-0.0365-0.23171.27380.57810.3591.75340.45120.0757-0.20190.2075-0.01010.10130.1179-0.00580.3192-4.6546-22.5265-42.7096
720.34120.1418-0.37322.0373-1.63672.212-0.1130.0746-0.61230.2208-1.27861.42251.4197-0.32030.75521.23870.05220.21470.54060.01040.4382-12.089-27.505-32.3003
732.0714-1.62942.76097.1680.28520.8448-0.6363-2.7217-0.85892.1430.79051.1109-0.1291-0.29140.49570.57780.1409-0.17490.3935-0.3534-0.36190.9388-20.928-34.766
744.3822.8033-3.00643.9425-1.73282.8119-0.76690.56470.3369-0.37140.87580.29110.3525-0.5411-0.0250.2461-0.0391-0.00480.2605-0.02790.2577-7.9587-19.7671-41.6253
750.96330.1166-0.88240.90611.1192.4609-0.733-0.1629-1.1583-0.1268-1.65070.61020.9017-1.04551.76290.6076-0.27180.0040.3098-0.32931.9486-18.0345-32.7867-42.9917
762.3132-1.9995-0.61172.45340.62021.5959-0.20260.1691-0.00730.29140.180.1646-0.034-0.21830.05660.1857-0.0176-0.01970.1658-0.02470.16152.4854-23.3732-47.8872
771.02571.6545-1.01087.16710.09131.6822-0.4657-1.6493-0.54332.56090.9393-0.7225-0.7080.3025-0.01640.20150.10490.4690.46380.75561.2186-4.0365-38.5679-34.9986
783.64190.7891-0.49723.2871-2.18893.2896-0.3489-0.7727-0.98380.6404-0.0423-0.70350.2943-0.0719-0.04010.389-0.0007-0.10380.31240.08110.25276.596-28.8383-39.1076
790.539-0.10150.0471.64371.78011.21690.0321-0.07880.05940.04920.0937-0.22810.03160.0224-0.1170.2096-0.0302-0.03330.1788-0.01780.206411.3761-28.7674-59.1992
801.55450.0513-0.12943.37610.54610.7282-0.02650.1362-0.1882-0.03990.1991-0.49250.07920.1386-0.15410.17920.01090.00180.2057-0.01450.213513.4669-38.9302-64.2677
810.29660.33750.85572.65413.15357.26720.19780.5026-0.1599-0.12481.1054-1.3365-0.34162.5014-1.25960.1757-0.0452-0.00450.4639-0.19730.473221.9251-29.4254-60.4465
823.8275-1.1622-0.5195.28583.85633.102-0.2193-1.4532-0.31790.0146-0.03510.56450.1827-0.0858-0.02580.2781-0.0097-0.02640.32170.00540.1911-7.9324-37.8491-2.0964
832.70311.37340.23220.97040.50640.5921-0.0234-0.34890.0547-0.47650.2688-0.22150.07150.026-0.33140.1709-0.00070.01660.2831-0.05160.2486-33.0423-0.2959-1.3804
844.8837-0.4534-0.33220.962-0.10461.4334-0.03250.9334-0.25670.2176-0.04750.8693-0.25130.1142-0.00030.25190.0063-0.03390.2570.00170.2692-37.8125-39.348-49.0217
853.2156-1.339-0.17132.34751.74061.58140.0544-1.06480.0877-0.0586-0.15940.57810.19540.1457-0.0120.3084-0.01870.05520.2818-0.00790.23933.4925-36.2141-52.7801
860.2021-0.00280.06970.0651-0.02260.2241-0.8825-0.10171.5681.58970.3871.9809-0.1664-0.37230.47450.73660.138-0.18350.50910.22720.7439-6.0557-50.9178-3.3283
870.0036-0.0019-00.0010.0003-0.0003-0.7377-4.7727-2.5517-3.7784-1.1270.9201-2.5998-0.00562.00070.86620.05490.72150.6018-0.15450.9286-34.742513.3406-1.8219
880.001-0.0007-0.0010-0.00070.00080.01070.125-1.9829-0.54460.08210.9049-1.6356-1.68060.08040.7469-0.044-0.1170.38040.05980.4435-35.7417-26.209-48.2766
890.0009-0.00040.00030.0001-0.00010-0.2712-5.96471.4163-1.7473-0.2279-1.76070.85971.38520.54860.83140.044-0.40970.66550.07060.56825.0011-49.8268-52.5555
903.2269-0.57551.21440.3546-0.27194.2503-1.2981-0.46121.234-0.1410.1873-0.81970.18641.38090.80840.3271-0.14910.03120.70870.01720.9177-10.6641-1.7688-21.88
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid -2:4)B-2 - 4
2X-RAY DIFFRACTION2(chain B and resid 5:44)B5 - 44
3X-RAY DIFFRACTION3(chain B and resid 45:53)B45 - 53
4X-RAY DIFFRACTION4(chain B and resid 54:66)B54 - 66
5X-RAY DIFFRACTION5(chain B and resid 67:78)B67 - 78
6X-RAY DIFFRACTION6(chain B and resid 79:86)B79 - 86
7X-RAY DIFFRACTION7(chain B and resid 87:92)B87 - 92
8X-RAY DIFFRACTION8(chain B and resid 93:96)B93 - 96
9X-RAY DIFFRACTION9(chain B and resid 97:121)B97 - 121
10X-RAY DIFFRACTION10(chain B and resid 122:142)B122 - 142
11X-RAY DIFFRACTION11(chain B and resid 143:176)B143 - 176
12X-RAY DIFFRACTION12(chain B and resid 177:190)B177 - 190
13X-RAY DIFFRACTION13(chain B and resid 191:200)B191 - 200
14X-RAY DIFFRACTION14(chain B and resid 201:225)B201 - 225
15X-RAY DIFFRACTION15(chain B and resid 226:234)B226 - 234
16X-RAY DIFFRACTION16(chain B and resid 235:253)B235 - 253
17X-RAY DIFFRACTION17(chain B and resid 254:258)B254 - 258
18X-RAY DIFFRACTION18(chain B and resid 259:275)B259 - 275
19X-RAY DIFFRACTION19(chain B and resid 276:305)B276 - 305
20X-RAY DIFFRACTION20(chain B and resid 306:326)B306 - 326
21X-RAY DIFFRACTION21(chain B and resid 327:339)B327 - 339
22X-RAY DIFFRACTION22(chain A and resid 1:9)A1 - 9
23X-RAY DIFFRACTION23(chain A and resid 10:44)A10 - 44
24X-RAY DIFFRACTION24(chain A and resid 45:51)A45 - 51
25X-RAY DIFFRACTION25(chain A and resid 52:67)A52 - 67
26X-RAY DIFFRACTION26(chain A and resid 68:77)A68 - 77
27X-RAY DIFFRACTION27(chain A and resid 78:90)A78 - 90
28X-RAY DIFFRACTION28(chain A and resid 91:126)A91 - 126
29X-RAY DIFFRACTION29(chain A and resid 127:151)A127 - 151
30X-RAY DIFFRACTION30(chain A and resid 152:157)A152 - 157
31X-RAY DIFFRACTION31(chain A and resid 158:175)A158 - 175
32X-RAY DIFFRACTION32(chain A and resid 176:191)A176 - 191
33X-RAY DIFFRACTION33(chain A and resid 192:201)A192 - 201
34X-RAY DIFFRACTION34(chain A and resid 202:218)A202 - 218
35X-RAY DIFFRACTION35(chain A and resid 219:228)A219 - 228
36X-RAY DIFFRACTION36(chain A and resid 229:251)A229 - 251
37X-RAY DIFFRACTION37(chain A and resid 252:256)A252 - 256
38X-RAY DIFFRACTION38(chain A and resid 257:273)A257 - 273
39X-RAY DIFFRACTION39(chain A and resid 274:305)A274 - 305
40X-RAY DIFFRACTION40(chain A and resid 306:329)A306 - 329
41X-RAY DIFFRACTION41(chain A and resid 330:339)A330 - 339
42X-RAY DIFFRACTION42(chain C and resid 1:14)C1 - 14
43X-RAY DIFFRACTION43(chain C and resid 15:44)C15 - 44
44X-RAY DIFFRACTION44(chain C and resid 45:50)C45 - 50
45X-RAY DIFFRACTION45(chain C and resid 51:66)C51 - 66
46X-RAY DIFFRACTION46(chain C and resid 67:76)C67 - 76
47X-RAY DIFFRACTION47(chain C and resid 77:84)C77 - 84
48X-RAY DIFFRACTION48(chain C and resid 85:92)C85 - 92
49X-RAY DIFFRACTION49(chain C and resid 93:145)C93 - 145
50X-RAY DIFFRACTION50(chain C and resid 146:161)C146 - 161
51X-RAY DIFFRACTION51(chain C and resid 162:173)C162 - 173
52X-RAY DIFFRACTION52(chain C and resid 174:190)C174 - 190
53X-RAY DIFFRACTION53(chain C and resid 191:201)C191 - 201
54X-RAY DIFFRACTION54(chain C and resid 202:218)C202 - 218
55X-RAY DIFFRACTION55(chain C and resid 219:236)C219 - 236
56X-RAY DIFFRACTION56(chain C and resid 237:253)C237 - 253
57X-RAY DIFFRACTION57(chain C and resid 254:258)C254 - 258
58X-RAY DIFFRACTION58(chain C and resid 259:275)C259 - 275
59X-RAY DIFFRACTION59(chain C and resid 276:305)C276 - 305
60X-RAY DIFFRACTION60(chain C and resid 306:321)C306 - 321
61X-RAY DIFFRACTION61(chain C and resid 322:339)C322 - 339
62X-RAY DIFFRACTION62(chain D and resid 0:4)D0 - 4
63X-RAY DIFFRACTION63(chain D and resid 5:44)D5 - 44
64X-RAY DIFFRACTION64(chain D and resid 45:57)D45 - 57
65X-RAY DIFFRACTION65(chain D and resid 58:86)D58 - 86
66X-RAY DIFFRACTION66(chain D and resid 87:94)D87 - 94
67X-RAY DIFFRACTION67(chain D and resid 95:145)D95 - 145
68X-RAY DIFFRACTION68(chain D and resid 146:157)D146 - 157
69X-RAY DIFFRACTION69(chain D and resid 158:176)D158 - 176
70X-RAY DIFFRACTION70(chain D and resid 177:190)D177 - 190
71X-RAY DIFFRACTION71(chain D and resid 191:200)D191 - 200
72X-RAY DIFFRACTION72(chain D and resid 201:205)D201 - 205
73X-RAY DIFFRACTION73(chain D and resid 206:219)D206 - 219
74X-RAY DIFFRACTION74(chain D and resid 220:227)D220 - 227
75X-RAY DIFFRACTION75(chain D and resid 228:233)D228 - 233
76X-RAY DIFFRACTION76(chain D and resid 234:252)D234 - 252
77X-RAY DIFFRACTION77(chain D and resid 253:259)D253 - 259
78X-RAY DIFFRACTION78(chain D and resid 260:274)D260 - 274
79X-RAY DIFFRACTION79(chain D and resid 275:304)D275 - 304
80X-RAY DIFFRACTION80(chain D and resid 305:326)D305 - 326
81X-RAY DIFFRACTION81(chain D and resid 327:339)D327 - 339
82X-RAY DIFFRACTION82(chain A and resid 501)A501
83X-RAY DIFFRACTION83(chain B and resid 501)B501
84X-RAY DIFFRACTION84(chain C and resid 501)C501
85X-RAY DIFFRACTION85(chain D and resid 501)D501
86X-RAY DIFFRACTION86(chain S and resid 1)A1 - 343
87X-RAY DIFFRACTION87(chain S and resid 2)B2 - 343
88X-RAY DIFFRACTION88(chain S and resid 3)C3 - 345
89X-RAY DIFFRACTION89(chain S and resid 4)D4 - 344
90X-RAY DIFFRACTION90(chain E and resid 1:999)E1 - 999

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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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