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- PDB-5h9f: Crystal structure of E. coli Cascade bound to a PAM-containing ds... -

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基本情報

登録情報
データベース: PDB / ID: 5h9f
タイトルCrystal structure of E. coli Cascade bound to a PAM-containing dsDNA target at 2.45 angstrom resolution.
要素
  • (CRISPR system Cascade subunit ...) x 5
  • DNA (28-MER) Non-target
  • DNA (50-MER) Target
  • crRNA (61-MER)
キーワードImmune System/RNA / CRISPR Cascade / Immune System-RNA Complex
機能・相同性
機能・相同性情報


CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding ...CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements / RNA processing / RNA endonuclease activity / defense response to virus / nucleic acid binding / 加水分解酵素; エステル加水分解酵素 / protein-containing complex / DNA binding / RNA binding / zinc ion binding
類似検索 - 分子機能
CRISPR-associated protein Cse2 / Crispr-associated protein; domain 2 / Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 ...CRISPR-associated protein Cse2 / Crispr-associated protein; domain 2 / Alpha-Beta Plaits - #2660 / CRISPR-associated protein, CT1975 / CRISPR-associated protein Cse2 / Cse2 superfamily / CT1975-like protein / CRISPR-associated protein Cse2 (CRISPR_cse2) / CRISPR-associated protein, CasD / CRISPR-associated protein Cse1 / CRISPR-associated protein Cse1 (CRISPR_cse1) / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / CRISPR-associated protein, Cas5 / CRISPR-associated protein (Cas_Cas5) / CRISPR-associated protein Cas5, N-terminal / Peroxidase; domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR system Cascade subunit CasB / CRISPR system Cascade subunit CasE / CRISPR system Cascade subunit CasD / CRISPR system Cascade subunit CasC / CRISPR system Cascade subunit CasA
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: 2.45 Å
データ登録者Hayes, R.P. / Xiao, Y. / Ding, F. / van Erp, P.B.G. / Rajashankar, K. / Bailey, S. / Wiedenheft, B. / Ke, A.
引用ジャーナル: Nature / 年: 2016
タイトル: Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli.
著者: Hayes, R.P. / Xiao, Y. / Ding, F. / van Erp, P.B. / Rajashankar, K. / Bailey, S. / Wiedenheft, B. / Ke, A.
履歴
登録2015年12月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年2月17日Provider: repository / タイプ: Initial release
改定 1.12016年2月24日Group: Database references
改定 1.22016年3月9日Group: Database references
改定 1.32023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: CRISPR system Cascade subunit CasA
B: CRISPR system Cascade subunit CasB
C: CRISPR system Cascade subunit CasB
D: CRISPR system Cascade subunit CasC
E: CRISPR system Cascade subunit CasC
F: CRISPR system Cascade subunit CasC
G: CRISPR system Cascade subunit CasC
H: CRISPR system Cascade subunit CasC
I: CRISPR system Cascade subunit CasC
J: CRISPR system Cascade subunit CasD
L: crRNA (61-MER)
M: DNA (28-MER) Non-target
N: DNA (50-MER) Target
K: CRISPR system Cascade subunit CasE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)426,15115
ポリマ－426,08514
非ポリマー651
水18,9161050
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area64520 Å2
ΔGint-278 kcal/mol
Surface area129270 Å2
手法PISA
単位格子
Length a, b, c (Å)92.979, 150.059, 400.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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要素

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CRISPR system Cascade subunit ... , 5種, 11分子 ABCDEFGHIJK

#1: タンパク質 CRISPR system Cascade subunit CasA / CRISPR type I-E/Ecoli-associated protein CasA/Cse1 / CRISPR-associated protein CasA/Cse1


分子量: 55964.957 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: casA, cse1, ygcL, b2760, JW2730 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46901
#2: タンパク質 CRISPR system Cascade subunit CasB


分子量: 19231.049 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: casB, cse2, ygcK, b2759, JW2729 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P76632
#3: タンパク質
CRISPR system Cascade subunit CasC


分子量: 40071.402 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: casC, cas4, cse4, ygcJ, b2758, JW2728 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46899
#4: タンパク質 CRISPR system Cascade subunit CasD


分子量: 25239.803 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: casD, cas5, ygcI, b2757, JW5844 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q46898
#8: タンパク質 CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease


分子量: 22324.002 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: casE, cas6e, ygcH, b2756, JW2726 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q46897, 加水分解酵素; エステル加水分解酵素

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RNA鎖 , 1種, 1分子 L

#5: RNA鎖 crRNA (61-MER)


分子量: 19677.646 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 発現宿主: Escherichia coli (大腸菌)

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DNA鎖 , 2種, 2分子 MN

#6: DNA鎖 DNA (28-MER) Non-target


分子量: 8598.531 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)
#7: DNA鎖 DNA (50-MER) Target


分子量: 15389.893 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Escherichia coli (大腸菌)

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非ポリマー , 2種, 1051分子

#9: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Zn
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1050 / 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

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試料調製

結晶マシュー密度: 3.29 Å3/Da / 溶媒含有率: 62.58 %
結晶化温度: 291.95 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2 / 詳細: 1.6 M Na/K Phosphate

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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: 0.979 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2015年8月25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: 0.979 Å / 相対比: 1
反射解像度: 2.45→50 Å / Num. obs: 205485 / % possible obs: 99.7 % / 冗長度: 12.1 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 12.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.4_1496精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4QYZ

4qyz


解像度: 2.45→49.87 Å / SU ML: 0.3 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.67 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.233 2000 0.97 %
Rwork0.206 --
obs0.206 205248 99.6 %
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
精密化ステップサイクル: LAST / 解像度: 2.45→49.87 Å
タンパク質核酸リガンド溶媒全体
原子数24982 2897 1 1050 28930
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00528672
X-RAY DIFFRACTIONf_angle_d0.78439437
X-RAY DIFFRACTIONf_dihedral_angle_d17.34810725
X-RAY DIFFRACTIONf_chiral_restr0.0344511
X-RAY DIFFRACTIONf_plane_restr0.0034635
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4506-2.51190.31921380.295613991X-RAY DIFFRACTION97
2.5119-2.57980.32721420.285814358X-RAY DIFFRACTION100
2.5798-2.65570.31321410.269314421X-RAY DIFFRACTION100
2.6557-2.74140.30271420.257214396X-RAY DIFFRACTION100
2.7414-2.83940.30371420.255514399X-RAY DIFFRACTION100
2.8394-2.95310.29761420.251914463X-RAY DIFFRACTION100
2.9531-3.08750.28311430.245414484X-RAY DIFFRACTION100
3.0875-3.25020.30431420.232114436X-RAY DIFFRACTION100
3.2502-3.45380.28761420.221814557X-RAY DIFFRACTION100
3.4538-3.72040.23421430.200714552X-RAY DIFFRACTION100
3.7204-4.09460.19881440.17814563X-RAY DIFFRACTION100
4.0946-4.68670.16781440.158114666X-RAY DIFFRACTION100
4.6867-5.90330.17441460.171714763X-RAY DIFFRACTION100
5.9033-49.88420.20331490.190215199X-RAY DIFFRACTION100
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12470.2092-0.08960.2148-0.04770.09880.04290.10440.2069-0.3784-0.10610.05930.01660.0628-00.35910.1630.10910.50970.03860.11679.4866-1.7199-131.7905
20.2912-0.09530.04030.2190.09860.01170.07550.0202-0.1006-0.0654-0.0435-0.03070.029-0.0014-00.26660.0721-0.01020.33590.00570.22151.0177-4.5634-123.9969
30.1390.0976-0.16080.22470.03770.20390.01930.02830.043-0.0201-0.0209-0.003-0.01340.003700.13370.0113-0.02070.24980.01430.2198-5.0320.4795-95.1885
40.0103-0.0005-0.00720.01470.00040.00510.06930.09310.0315-0.054-0.0069-0.0276-0.01960.0274-00.9351-0.36930.20320.6473-0.10110.5295-3.729946.4801-48.262
50.00130.0019-0.00260.00220.00170.0028-0.0327-0.0081-0.0076-0.0036-0.0625-0.0244-0.03060.037-01.0139-0.23630.15540.4139-0.11450.5394-8.827851.5238-35.0785
60.0061-0.0048-0.0060.00520.00160.00440.0111-0.00790.0186-0.01140.02340.09170.0029-0.014300.94290.14080.13520.655-0.08910.4678-20.706848.4791-39.4514
70.0008-0.0007-0.00440.0097-0.00380.00060.03330.02410.0528-0.00950.04090.023-0.01590.0056-01.1092-0.04890.26790.35390.01090.7937-12.820454.2564-47.9786
8-0.0086-0.00270.00160.00570.00330.0020.0160.0714-0.05370.0075-0.0451-0.02290.0065-0.077100.7621-0.0860.07130.377-0.03340.3876-15.130244.6934-47.669
90.00390.00310.00330.00390.00090.00170.00320.0226-0.011-0.0255-0.0196-0.00060.02070.018700.8888-0.2626-0.04240.8294-0.02120.6862-2.004438.3464-39.7199
100.04220.0022-0.01170.06040.00040.04020.01630.0478-0.12880.06590.05670.0561-0.07250.053100.4214-0.09960.04890.4189-0.07730.3589-13.206529.4286-41.8704
110.04050.0255-0.02290.02280.00640.00490.09820.0852-0.1785-0.08120.1763-0.0174-0.12560.030200.3989-0.09670.01730.4331-0.09270.3335-10.115129.1546-49.3829
120.0074-0.01360.00730.01950.00710.01380.01190.0254-0.0423-0.04680.0646-0.03140.00520.139200.27570.0646-0.020.3649-0.01070.3087-9.12991.6583-57.7877
130.03840.00280.00740.0260.0380.04610.1087-0.0390.01690.13630.09260.0716-0.00470.1518-00.2732-0.02290.00240.3604-0.02730.3098-16.242511.9059-53.2409
140.0527-0.0189-0.00640.02590.02310.07970.02560.0098-0.06510.13290.06370.02240.07570.1808-00.20170.033-0.03950.2554-0.01590.2695-16.92380.7539-65.3829
15-0.00190.0107-0.01410.0138-0.00330.0087-0.08380.16480.1144-0.1487-0.01120.0996-0.1545-0.0341-00.17010.0056-0.03380.2159-0.00980.2093-25.85637.0721-72.0756
160.0148-0.02420.02540.01680.03490.0073-0.04520.03170.1445-0.10790.0372-0.108-0.00590.295900.21480.041-0.00560.2690.00320.2571-15.78181.2206-73.5023
17-0.032-0.11090.00980.09340.13210.0528-0.1661-0.3013-0.70530.2944-0.6558-1.0019-0.73150.7721-01.0325-0.5203-0.1937-0.3431-0.9694-0.4156-8.205654.2102-11.1111
18-0.184-0.37650.2467-0.22310.258-0.1346-0.1179-0.4887-0.82950.3296-1.0435-1.3732-0.68041.061200.9541-0.21-0.15830.2329-0.3917-0.0932-9.104945.114-5.025
19-0.1199-0.1010.0184-0.10540.1772-0.040.15580.0283-0.23750.24440.27010.337-0.2968-0.2933-00.66690.35410.6168-2.5856-3.8158-4.71-32.197353.2929-0.0962
200.00660.0004-0.00260.0006-0.00150.00770.0005-0.0468-0.10160.03970.00920.0386-0.0395-0.0226-01.1009-0.05230.14210.8033-0.16870.4999-34.360756.744910.9042
210.001-0.00280.00170.00330.00460.00760.0306-0.0490.00790.02230.0349-0.02060.01690.069401.2956-0.1043-0.04540.4562-0.02210.3777-23.74754.127411.8923
220.0479-0.0980.0310.0510.04470.04350.0013-0.321-0.45570.0084-0.2842-0.3862-0.16740.255600.7074-0.05640.08460.2786-0.1610.177-31.514234.4806-17.962
230.0552-0.0121-0.05590.0496-0.070.1063-0.0080.01260.00430.1876-0.04150.03730.04770.0591-00.5871-0.0291-0.00210.3422-0.0380.2696-17.42697.3644-11.6732
24-0.0242-0.06230.0324-0.01960.06560.0244-0.4117-0.09740.11350.2206-0.5309-0.5847-0.50330.6832-00.53870.0970.0766-1.186-1.5072-1.3296-23.278743.6959-20.9993
250.07270.1274-0.11080.02260.03330.20630.0142-0.0594-0.14370.45870.06530.2863-0.3375-0.1474-00.75250.03530.16340.3829-0.10150.2853-42.17332.7348-13.0825
26-0.0754-0.0674-0.00310.14590.05570.19650.0612-0.09-0.0130.1974-0.05010.0215-0.0244-0.067300.2773-0.02650.03640.2525-0.02050.2482-42.12435.8089-36.3996
270.01080.0118-0.00130.00580.00660.00840.1325-0.0857-0.06570.01060.11170.0477-0.01790.015100.5513-0.1116-0.00810.37450.00320.4272-52.3389-17.4462-42.4024
280.2347-0.27360.0518-0.0019-0.15870.494-0.0017-0.06-0.01880.1071-0.00220.086-0.1336-0.1449-00.25780.02730.10020.2763-0.07660.2334-50.882821.1144-37.9643
290.0838-0.02830.01270.0088-0.02840.1603-0.0069-0.0354-0.00130.14250.04970.0425-0.0194-0.0059-00.12210.0130.01570.20630.00570.2392-51.240311.5221-66.5798
300.0128-0.00990.0080.00030.01310.02390.0518-0.0775-0.20720.12280.1282-0.0142-0.04120.095200.1827-0.0272-0.0590.2440.01230.3775-54.0726-9.2794-77.6861
310.08690.12090.01430.1482-0.28280.1272-0.0140.01340.04920.09320.06650.10220.00270.0137-00.09030.03480.01660.2067-0.02160.2707-53.889110.5602-72.2676
320.19690.0494-0.00560.08380.28360.15970.2775-0.26060.11150.4074-0.26540.1829-0.42060.3209-0-0.02820.28890.0517-0.0198-0.09510.3775-53.677933.1783-66.5167
330.1270.0107-0.01240.02380.03410.0481-0.18910.0272-0.05360.17320.12670.16750.38430.10390-0.2676-0.0192-0.13170.13680.01490.2322-36.233626.1296-87.9287
34-0.0071-0.0151-0.011-0.01130.01760.00840.3582-0.0090.3797-0.17970.39180.3711-0.0205-0.19450-1.1046-0.5977-1.5280.1878-0.4056-0.7171-49.29511.5625-111.9604
350.0257-0.00660.0095-0.02610.00430.0044-0.044-0.12860.1751-0.33270.20480.3590.10350.0342-0-0.89420.1406-1.35520.28480.3321-0.6795-44.217121.8427-119.0422
360.0549-0.0080.00480.04730.0053-0.00530.03720.0187-0.0045-0.00120.04030.02350.1535-0.033200.12970.0181-0.05780.18810.00550.1733-31.325727.8432-90.8327
370.0139-0.00590.03240.0054-0.00890.0161-0.0433-0.02830.06480.04550.0459-0.03670.0367-0.038500.15580.0097-0.00090.18080.00270.2501-40.71517.689-68.4856
380.0330.0536-0.03390.0629-0.0426-0.01260.0864-0.06950.22350.2856-0.05420.3036-0.0539-0.0853-0-0.03230.0971-0.12230.13650.08430.3178-41.116334.3083-93.5665
390.02690.01670.01970.0018-0.01810.005-0.05110.0890.2543-0.0339-0.0531-0.0063-0.00790.0167-00.2139-0.054-0.04530.21280.03370.2836-26.01138.0439-83.4271
40-0.00860.0199-0.0171-0.00910.004-0.0023-0.1443-0.13680.22590.1919-0.0346-0.0023-0.1078-0.0443-00.22380.0119-0.06250.2134-0.03050.334-26.466744.9865-83.9556
410.0349-0.0078-0.02410.00960.01280.0096-0.0245-0.13540.10910.0468-0.05120.0623-0.1763-0.103-00.27330.0522-0.02240.26740.04670.4476-41.076147.6594-90.7623
420.0444-0.0674-0.03590.0293-0.03190.02720.05970.05330.07680.0574-0.00630.02850.09920.0044-00.1051-0.0078-0.02010.18170.0140.2611-12.110928.4424-98.0823
430.02930.0097-0.00580.02660.02240.0049-0.06890.05680.14280.21040.02220.0310.06570.1034-00.0888-0.01440.00030.1750.03510.2014-11.523727.8881-101.125
44-0.0012-0.0011-0.00510.003-0.0049-0.0001-0.1223-0.240.2165-0.1525-0.2180.1435-0.0673-0.1436-00.2240.1405-0.05750.17620.3740.3314-14.320746.3718-119.72
450.00420.0005-0.0040.01190.0020.0162-0.0187-0.01430.0341-0.0239-0.0662-0.0262-0.0242-0.017700.8293-0.04670.0560.76490.3050.63750.56544.1367-139.0768
460.08610.02230.0020.03390.05840.0034-0.054-0.49590.77770.0718-0.45410.19050.1713-0.25200.00930.3394-0.3017-0.65291.1631-0.6849-7.053634.7459-126.0731
470.1727-0.2281-0.10710.1621-0.04160.02940.17390.03910.2269-0.035-0.0932-0.0532-0.0856-0.09380-0.1525-0.1123-0.07360.11380.04020.3242-13.204333.8575-96.905
480.0394-0.0080.01450.0255-0.00220.0184-0.0666-0.18560.2610.0053-0.044-0.1354-0.2241-0.017500.344-0.02620.00750.33130.07810.5504-5.045349.4616-92.9599
490.00380.00040.00640.0102-0.00160.0069-0.0571-0.0046-0.0099-0.0345-0.0799-0.0864-0.02760.0139-0-0.1487-0.1454-0.02160.27330.08280.530821.391129.3372-101.3675
500.0028-0.00120.0002-0.0003-0.0009-0.0002-0.00660.01060.0185-0.0187-0.0528-0.03490.0086-0.00500.1270.0119-0.00960.25640.0440.27961.253324.4229-100.4024
510.00120.0010.00010.00150.00510.0033-0.0559-0.04380.00470.0237-0.039-0.02520.01540.012800.20340.0286-0.00320.28940.03490.2224.558516.4527-110.9784
520.0049-0.0045-0.0111-0.00660.00320.01390.02910.07920.1519-0.0449-0.08-0.0810.0574-0.0500.189-0.0133-0.01770.31180.03670.28136.871221.276-110.5792
530.00370.00070.0014-0.0016-0.0003-0.00080.02440.05110.0196-0.0716-0.05920.0723-0.02050.0121-00.4066-0.05630.05990.46160.15270.49339.036334.6842-120.4711
540.00270.0020.0020.0004-0.00080.001-0.03810.0779-0.0209-0.0544-0.0642-0.00360.0165-0.022500.28690.05050.27130.46550.20730.54117.964129.6347-120.5813
55-0.0084-0.0067-0.0217-0.0171-0.0025-0.007-0.06670.08370.1236-0.1357-0.0699-0.14270.02560.073200.212-0.0265-0.0120.41120.01340.365314.099422.1853-97.7634
560.006-0.00040.00270.0034-0.00190.0065-0.0071-0.01240.0221-0.00760.02680.02910.0325-0.018600.13930.0215-0.08410.2778-0.06140.2155.316618.4429-85.2557
57-0.0055-0.00020.0094-0.0036-0.0044-0.00540.0211-0.0189-0.05490.0795-0.0516-0.08210.0347-0.069800.14410.0116-0.03950.23910.05180.267-10.115518.9495-106.6425
580.0034-0.00390.00670.02210.0040.0063-0.09590.0483-0.10320.0303-0.15410.11440.0709-0.027900.51280.113-0.16890.32870.06580.2374-13.814223.6408-126.3703
590.02330.00240.0208-0.01640.0075-0.0230.1452-0.04370.0205-0.1604-0.1607-0.0408-0.0162-0.030300.18010.03630.02690.2390.07610.25638.862723.6714-107.8346
600.0031-0.005-0.0130.01010.00840.00460.00610.0880.06490.0008-0.1244-0.0687-0.0774-0.0521-00.216-0.0420.03870.26620.06430.563114.488739.2219-108.6153
610.00980.005-0.01190.0194-0.01890.00910.05550.02340.0997-0.1048-0.1211-0.1567-0.1167-0.0775-00.1624-0.033-0.01680.25830.05770.39229.106831.5495-102.1535
620.00340.00620.00420.0014-0.00040.0025-0.00250.00650.04050.0159-0.0263-0.00340.04540.040600.163-0.0767-0.07290.50010.07350.472526.844823.7064-97.0562
630.0110.0029-0.00010.01060.00060.00290.06690.01920.13890.0834-0.0274-0.0537-0.06360.059300.2061-0.00120.00470.37490.0540.36720.627719.7982-98.6415
640.0050.0005-0.00270.00240.00070.00380.0186-0.02920.0001-0.00330.1239-0.08170.04750.0326-00.2310.02580.02320.31270.05010.365422.38599.9566-104.7459
650.00180.0025-0.00140.0044-0.0014-0.00310.05320.0010.05150.0472-0.0053-0.0835-0.04780.0527-00.25510.05460.05170.43540.09130.34111.025919.8994-121.137
660.00630.00390.00070.01280.00530.00360.01410.0946-0.02370.1197-0.0916-0.1239-0.0069-0.0485-00.21660.0151-0.00370.37490.03110.344617.40314.2138-108.901
670.00990.04190.01130.00210.02710.02160.03780.06770.047-0.0611-0.0692-0.12690.0335-0.0273-00.15660.01370.00150.28350.10210.2702-6.47825.4453-112.9165
68-0.01090.0322-0.0021-0.0279-0.021-0.0034-0.01570.03010.1029-0.01720.01680.0177-0.0545-0.0791-00.1302-0.0236-0.05620.1734-0.00120.1854-34.473817.8407-98.576
69-0.23770.07670.23930.08450.0212-0.0630.12330.0183-0.03440.08810.03970.0186-0.2024-0.2421-00.2834-0.04650.02040.2351-0.06710.1903-34.374316.1908-45.0574
70-0.01250.00150.00620.00260.00940.0208-0.0157-0.3405-0.11420.02490.051-0.031-0.00720.056601.169-0.51240.0295-0.4318-0.737-0.02-12.662556.0565-17.7592
710.0051-0.00170.00020.0040.00360.0047-0.0186-0.0146-0.03750.0247-0.01560.02710.0180.016201.3972-0.2890.13910.5222-0.13271.457-7.880873.3812-23.5765
72-0.0050.00740.00380.0118-0.00130.0296-0.0138-0.0501-0.0568-0.00820.1186-0.0761-0.1084-0.071-02.1514-0.25620.53170.8018-0.12050.9387-11.417893.1067-34.7325
730.0031-0.00090.00130.0030.00650.00320.0581-0.05540.1123-0.03360.0257-0.22180.03450.027101.6647-0.1650.24720.6248-0.10610.7686-14.46393.6297-29.5232
740.0007-0.04380.0797-0.01390.0159-0.00910.04760.247-0.05190.090.00520.14340.3017-0.130600.3690.2133-0.04350.7640.01890.4873-27.8222.2429-143.1736
750.03250.022-0.02150.06970.02340.0033-0.06660.3485-0.0742-0.03570.01650.10390.02370.0547-00.8879-0.01880.04080.60320.01080.5011-14.4015-9.2728-101.3265
76-0.1792-0.0035-0.09290.1696-0.02580.03790.1290.10020.02540.09160.0270.00640.1210.129200.1768-0.02880.03690.2807-0.05980.2188-23.699415.5755-61.7754
770.0042-0.0114-0.0051-0.00580.00260.0065-0.03850.0653-0.011-0.0717-0.08330.02150.02330.0467-00.65470.575-0.34190.80350.27710.1262-23.545910.568-139.4585
780.0076-0.0046-0.0024-0.0036-0.0036-0.00080.0041-0.0559-0.06590.0359-0.0202-0.0380.01570.0124-02.43730.1056-0.01142.53570.47252.2835-29.69733.9567-150.5386
790.0011-0.00160.01180.0073-0.00060.0274-0.08820.07610.0146-0.02170.1020.1268-0.0393-0.098-01.7899-0.00470.05140.7213-0.07290.4965-31.838377.4739-44.1724
800.0049-0.00230.00260.0394-0.01850.0049-0.10170.04110.19410.07110.03030.0016-0.0358-0.0343-01.18740.1219-0.19850.74960.02320.4935-42.05781.1778-38.1983
81-0.01120.0096-0.0359-0.0320.0514-0.0364-0.07830.0887-0.1286-0.1375-0.3067-0.5384-0.0028-0.038401.3016-0.18080.1556-1.8626-1.8188-1.5404-21.376580.994-24.7917
820.0116-0.02470.01670.0509-0.00670.0379-0.1848-0.3782-0.19810.00680.13770.058-0.0402-0.0611-02.00870.01980.0330.0887-0.6518-0.5096-28.802380.5877-27.2864
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 212 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 213 THROUGH 375 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 376 THROUGH 495 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 3 THROUGH 16 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 17 THROUGH 26 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 27 THROUGH 37 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 38 THROUGH 51 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 52 THROUGH 67 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 68 THROUGH 75 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 76 THROUGH 124 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 125 THROUGH 159 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 3 THROUGH 15 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 16 THROUGH 51 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 52 THROUGH 98 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 99 THROUGH 124 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 125 THROUGH 156 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 2 THROUGH 115 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 116 THROUGH 243 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 244 THROUGH 334 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 335 THROUGH 349 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 350 THROUGH 361 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 2 THROUGH 57 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 58 THROUGH 175 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 176 THROUGH 212 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 213 THROUGH 361 )
26X-RAY DIFFRACTION26CHAIN 'F' AND (RESID 2 THROUGH 115 )
27X-RAY DIFFRACTION27CHAIN 'F' AND (RESID 116 THROUGH 145 )
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESID 146 THROUGH 362 )
29X-RAY DIFFRACTION29CHAIN 'G' AND (RESID 2 THROUGH 84 )
30X-RAY DIFFRACTION30CHAIN 'G' AND (RESID 85 THROUGH 115 )
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESID 116 THROUGH 260 )
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESID 261 THROUGH 362 )
33X-RAY DIFFRACTION33CHAIN 'H' AND (RESID 2 THROUGH 57 )
34X-RAY DIFFRACTION34CHAIN 'H' AND (RESID 58 THROUGH 115 )
35X-RAY DIFFRACTION35CHAIN 'H' AND (RESID 116 THROUGH 175 )
36X-RAY DIFFRACTION36CHAIN 'H' AND (RESID 176 THROUGH 195 )
37X-RAY DIFFRACTION37CHAIN 'H' AND (RESID 196 THROUGH 221 )
38X-RAY DIFFRACTION38CHAIN 'H' AND (RESID 222 THROUGH 284 )
39X-RAY DIFFRACTION39CHAIN 'H' AND (RESID 285 THROUGH 304 )
40X-RAY DIFFRACTION40CHAIN 'H' AND (RESID 305 THROUGH 323 )
41X-RAY DIFFRACTION41CHAIN 'H' AND (RESID 324 THROUGH 361 )
42X-RAY DIFFRACTION42CHAIN 'I' AND (RESID 2 THROUGH 31 )
43X-RAY DIFFRACTION43CHAIN 'I' AND (RESID 32 THROUGH 49 )
44X-RAY DIFFRACTION44CHAIN 'I' AND (RESID 50 THROUGH 71 )
45X-RAY DIFFRACTION45CHAIN 'I' AND (RESID 72 THROUGH 97 )
46X-RAY DIFFRACTION46CHAIN 'I' AND (RESID 107 THROUGH 195 )
47X-RAY DIFFRACTION47CHAIN 'I' AND (RESID 196 THROUGH 319 )
48X-RAY DIFFRACTION48CHAIN 'I' AND (RESID 320 THROUGH 361 )
49X-RAY DIFFRACTION49CHAIN 'J' AND (RESID 1 THROUGH 10 )
50X-RAY DIFFRACTION50CHAIN 'J' AND (RESID 11 THROUGH 15 )
51X-RAY DIFFRACTION51CHAIN 'J' AND (RESID 16 THROUGH 20 )
52X-RAY DIFFRACTION52CHAIN 'J' AND (RESID 21 THROUGH 43 )
53X-RAY DIFFRACTION53CHAIN 'J' AND (RESID 44 THROUGH 50 )
54X-RAY DIFFRACTION54CHAIN 'J' AND (RESID 51 THROUGH 60 )
55X-RAY DIFFRACTION55CHAIN 'J' AND (RESID 61 THROUGH 72 )
56X-RAY DIFFRACTION56CHAIN 'J' AND (RESID 73 THROUGH 79 )
57X-RAY DIFFRACTION57CHAIN 'J' AND (RESID 80 THROUGH 89 )
58X-RAY DIFFRACTION58CHAIN 'J' AND (RESID 90 THROUGH 102 )
59X-RAY DIFFRACTION59CHAIN 'J' AND (RESID 103 THROUGH 129 )
60X-RAY DIFFRACTION60CHAIN 'J' AND (RESID 130 THROUGH 143 )
61X-RAY DIFFRACTION61CHAIN 'J' AND (RESID 144 THROUGH 163 )
62X-RAY DIFFRACTION62CHAIN 'J' AND (RESID 164 THROUGH 173 )
63X-RAY DIFFRACTION63CHAIN 'J' AND (RESID 174 THROUGH 187 )
64X-RAY DIFFRACTION64CHAIN 'J' AND (RESID 188 THROUGH 196 )
65X-RAY DIFFRACTION65CHAIN 'J' AND (RESID 197 THROUGH 206 )
66X-RAY DIFFRACTION66CHAIN 'J' AND (RESID 207 THROUGH 219 )
67X-RAY DIFFRACTION67CHAIN 'L' AND (RESID 1 THROUGH 10 )
68X-RAY DIFFRACTION68CHAIN 'L' AND (RESID 11 THROUGH 15 )
69X-RAY DIFFRACTION69CHAIN 'L' AND (RESID 16 THROUGH 35 )
70X-RAY DIFFRACTION70CHAIN 'L' AND (RESID 36 THROUGH 40 )
71X-RAY DIFFRACTION71CHAIN 'L' AND (RESID 41 THROUGH 43 )
72X-RAY DIFFRACTION72CHAIN 'L' AND (RESID 44 THROUGH 53 )
73X-RAY DIFFRACTION73CHAIN 'L' AND (RESID 54 THROUGH 60 )
74X-RAY DIFFRACTION74CHAIN 'M' AND (RESID 1 THROUGH 18 )
75X-RAY DIFFRACTION75CHAIN 'M' AND (RESID 19 THROUGH 28 )
76X-RAY DIFFRACTION76CHAIN 'N' AND (RESID 1 THROUGH 34 )
77X-RAY DIFFRACTION77CHAIN 'N' AND (RESID 35 THROUGH 40 )
78X-RAY DIFFRACTION78CHAIN 'N' AND (RESID 41 THROUGH 50 )
79X-RAY DIFFRACTION79CHAIN 'K' AND (RESID 1 THROUGH 56 )
80X-RAY DIFFRACTION80CHAIN 'K' AND (RESID 57 THROUGH 82 )
81X-RAY DIFFRACTION81CHAIN 'K' AND (RESID 83 THROUGH 130 )
82X-RAY DIFFRACTION82CHAIN 'K' AND (RESID 131 THROUGH 199 )

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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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