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- PDB-5dcx: Structural studies of AAV2 Rep68 reveal a partially structured li... -

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基本情報

登録情報
データベース: PDB / ID: 5dcx
タイトルStructural studies of AAV2 Rep68 reveal a partially structured linker and compact domain conformation
要素Protein Rep68
キーワードDNA BINDING PROTEIN / Parvovirus / Adeno-Associated Virus / DNA replication / Small-angle X-ray scattering / Rep proteins
機能・相同性
機能・相同性情報


symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont entry into host cell via permeabilization of host membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity ...symbiont-mediated arrest of host cell cycle during G2/M transition / symbiont entry into host cell via permeabilization of host membrane / viral DNA genome replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / endonuclease activity / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / host cell nucleus / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
類似検索 - 分子機能
Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. ...Rep protein catalytic-like / Rep protein catalytic domain like / : / Parvovirus (PV) NS1 nuclease (NS1-Nuc) domain profile. / Parvovirus non-structural protein 1, helicase domain / Parvovirus non-structural protein NS1 / Replication Protein E1; Chain: A, - #20 / Replication Protein E1; Chain: A, / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
生物種Adeno-associated virus 2 (アデノ随伴ウイルス)
手法X線回折 / 分子置換 / 解像度: 2.6 Å
データ登録者Musayev, F.N. / Zarate-Perez, F.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM092854 米国
引用ジャーナル: Biochemistry / 年: 2015
タイトル: Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation.
著者: Musayev, F.N. / Zarate-Perez, F. / Bardelli, M. / Bishop, C. / Saniev, E.F. / Linden, R.M. / Henckaerts, E. / Escalante, C.R.
履歴
登録2015年8月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年9月23日Provider: repository / タイプ: Initial release
改定 1.12015年10月14日Group: Database references
改定 1.22017年9月13日Group: Author supporting evidence / Database references / Derived calculations
カテゴリ: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.32017年11月22日Group: Refinement description / カテゴリ: software
改定 1.42019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52023年9月27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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: Protein Rep68
B: Protein Rep68
C: Protein Rep68
D: Protein Rep68
E: Protein Rep68
F: Protein Rep68
G: Protein Rep68
H: Protein Rep68
I: Protein Rep68
J: Protein Rep68
K: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)287,40722
ポリマ－287,13911
非ポリマー26711
水3,117173
1
A: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
9
I: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
10
J: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
11
K: Protein Rep68
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)26,1282
ポリマ－26,1041
非ポリマー241
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)75.644, 178.706, 130.358
Angle α, β, γ (deg.)90.000, 91.660, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Protein Rep68


分子量: 26103.561 Da / 分子数: 11 / 断片: origin binding domain (UNP residues 1-224) / 変異: C151S / 由来タイプ: 組換発現
由来: (組換発現) Adeno-associated virus 2 (アデノ随伴ウイルス)
遺伝子: Rep68 / プラスミド: pET15b / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) pLysS / 参照: UniProt: P03132, DNA helicase
#2: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 11 / 由来タイプ: 合成 / 式: Mg
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 173 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.06 Å3/Da / 溶媒含有率: 59.79 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 50 mM sodium cacodylate, pH 6.0, 90 mM potassium chloride, 20 mM magnesium chloride, 14-17% isopropanol
PH範囲: 6

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データ収集

回折平均測定温度: 110 K
放射光源由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.54 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2014年11月2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: 1.54 Å / 相対比: 1
反射解像度: 2.6→29.81 Å / Num. obs: 105074 / % possible obs: 99.1 % / 冗長度: 3.82 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.94 / Net I/σ(I): 12 / Scaling rejects: 24497
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.6-2.693.890.3114.141772104370.96120998.9
2.69-2.83.870.2674.741941104700.97140499
2.8-2.933.860.2185.641911104540.96154599.1
2.93-3.083.870.1756.642264104980.95165899.3
3.08-3.283.860.1288.442680105720.93192099.6
3.28-3.533.840.09411.242580105330.93211199.7
3.53-3.883.810.07214.642950105810.95265699.8
3.88-4.443.830.05318.843234106010.91259799.8
4.44-5.593.80.0452243325105810.91316399.7
5.59-29.813.590.03825.643373103470.92623496.4

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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
d*TREKデータスケーリング
PDB_EXTRACT3.15データ抽出
d*TREKデータ削減
PHENIX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 4ZO0

4zo0


解像度: 2.6→29.814 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 23.91 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2375 5233 4.98 %
Rwork0.1905 99774 -
obs0.1928 105007 99.07 %
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: 529.84 Å2 / Biso mean: 59.2862 Å2 / Biso min: 14.7 Å2
精密化ステップサイクル: final / 解像度: 2.6→29.814 Å
タンパク質核酸リガンド溶媒全体
原子数17442 0 11 173 17626
Biso mean--84.79 46.74 -
残基数----2169
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00317956
X-RAY DIFFRACTIONf_angle_d0.78124454
X-RAY DIFFRACTIONf_chiral_restr0.0282709
X-RAY DIFFRACTIONf_plane_restr0.0043128
X-RAY DIFFRACTIONf_dihedral_angle_d14.9226551
LS精密化 シェル

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

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.62950.29211890.25353285347499
2.6295-2.66040.30141840.26013286347099
2.6604-2.69290.30661640.26513327349199
2.6929-2.72690.31611690.25973323349299
2.7269-2.76280.3061700.24163288345899
2.7628-2.80060.30611590.23953362352199
2.8006-2.84060.27361780.23443276345499
2.8406-2.8830.29211590.22753346350599
2.883-2.9280.30571820.22873312349499
2.928-2.97590.26151870.2333323351099
2.9759-3.02720.2941620.24443394355699
3.0272-3.08220.27211780.24123252343099
3.0822-3.14140.30641770.239633533530100
3.1414-3.20550.30051920.235933083500100
3.2055-3.27510.30371900.223533523542100
3.2751-3.35120.27531940.21732883482100
3.3512-3.43480.28661690.219533963565100
3.4348-3.52760.24881750.219433113486100
3.5276-3.63120.25961640.215733933557100
3.6312-3.74820.24461490.194333633512100
3.7482-3.88190.24341790.178233333512100
3.8819-4.0370.21851770.168233633540100
4.037-4.22020.22621770.164633563533100
4.2202-4.4420.19011840.146633443528100
4.442-4.71930.1721790.138933523531100
4.7193-5.0820.17711600.139233703530100
5.082-5.59040.20241740.159433463520100
5.5904-6.39240.20941740.181233773551100
6.3924-8.02770.1931600.166733873547100
8.0277-29.81590.16861780.1363008318688
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.84772.1095-4.01473.1415-2.47428.1918-0.3070.0842-0.3984-0.12220.0855-0.11220.3935-0.16420.20380.2214-0.0439-0.03450.2175-0.00780.323416.413310.330792.9002
27.10252.76963.13468.2032.43157.98040.426-0.35910.36720.4002-0.2953-0.0056-0.55220.1089-0.03480.2654-0.03340.06420.37050.00350.371520.237726.834198.9148
35.03483.4353-1.77394.732-1.12973.4853-0.0414-0.0815-0.0349-0.08570.08570.28250.3704-0.3267-0.08320.28870.00480.0140.35930.03790.28827.46479.009198.3089
42.10820.2882-0.12673.57791.00682.63290.0182-0.4833-0.40890.2656-0.09740.0330.33040.0370.04760.3234-0.01540.0250.33810.07040.344114.07389.3906104.3631
50.57240.8738-0.06551.9078-0.26322.45890.1684-0.31430.19510.6259-0.08830.3111-0.3283-0.2682-0.0850.4553-0.0180.0810.5014-0.03480.37569.784620.6696120.1335
60.9866-1.4655-1.69713.38593.5673.8054-0.81230.8671-0.62410.91650.00860.25442.4869-0.52570.511.5518-0.2523-0.07831.43510.07770.6203-0.44546.3281137.9918
73.5353-0.2313-1.55572.8091.46622.3104-0.03150.4289-0.1976-0.17590.0463-0.01690.0137-0.2927-0.02660.3908-0.0483-0.03920.4282-0.0270.2115-22.146513.238527.7322
82.29830.3593-0.58452.36271.17433.78280.08240.11510.14330.0045-0.05210.0939-0.1768-0.0824-0.01970.3141-0.0148-0.00390.269-0.01780.256-23.804918.629237.8726
96.8363-1.1619-4.08680.14190.82353.37620.1965-0.58590.54140.23160.3223-0.13050.00560.2847-0.07410.3967-0.12570.01930.4603-0.08810.4601-46.770711.077750.2867
101.08640.7079-0.34853.18641.25792.4608-0.2819-0.0404-0.61330.3907-0.02570.40250.51060.26910.34860.40680.08530.08460.33090.06070.636510.4491-12.056859.1741
113.5598-2.2589-1.41697.5371.14292.5374-0.2387-0.1799-0.5158-0.07030.0380.32660.33080.08470.17810.2695-0.00020.00590.24240.01980.35457.1052-1.376559.2124
124.60283.1117-0.33573.35361.77073.5298-0.5910.0658-0.38791.03010.73560.76910.3886-0.3035-0.12250.34380.04010.06590.40920.0230.46972.6072.822970.9084
138.55053.0559-3.3536.4649-3.80496.3301-0.0074-0.745-0.9171.0345-0.15840.08250.82250.71340.2270.46270.10540.10870.41530.10140.49538.7797-7.119971.2863
144.0313-0.7987-1.7142.69882.71294.4352-0.0970.0778-0.1499-0.1180.1517-0.0388-0.33220.4142-0.06020.2711-0.0082-0.04620.22330.05680.296315.62162.756453.943
153.10532.7707-0.68988.5314-1.60888.7501-0.12011.16460.8047-0.42940.32330.2132-1.1638-0.5134-0.16270.34360.04350.07310.44120.05870.530922.25767.992441.4535
164.31443.05860.30435.91250.53073.0599-0.05770.1113-0.0227-0.0583-0.14490.4646-0.16120.04580.3170.16030.0151-0.05130.3275-0.01940.24718.133726.895779.512
170.8817-0.81080.98374.5713-3.71475.45870.06130.1476-0.3855-0.45880.16860.5740.2503-0.241-0.25450.3035-0.0175-0.02980.2567-0.03960.4056-1.401624.643865.9262
184.3409-2.0835-1.71197.68631.87724.4893-0.0731-0.20210.11130.0578-0.11430.4985-0.3241-0.2120.23570.2358-0.0012-0.02620.2632-0.03760.29861.918633.324578.6213
196.2769-3.6498-4.35193.30724.58977.76980.0085-0.22880.49220.31610.0267-0.2959-0.73210.5669-0.29330.4285-0.0268-0.03420.23160.02650.32396.764138.660481.6683
207.04053.2588-1.34692.67881.25825.6826-0.4377-0.29070.20061.13120.22841.2882-0.0713-0.15240.24720.47370.10760.0620.42860.04710.38764.423330.861391.572
211.737-0.55850.70652.3251-0.94591.7078-0.07670.04110.2870.1364-0.1146-0.0176-0.29410.16410.1880.3073-0.0083-0.02530.3214-0.01670.36288.126336.143175.1766
225.2065.0582-0.47274.4705-0.82851.45140.5047-0.19381.08360.9782-0.54860.4948-0.35310.16060.16450.7343-0.05230.00210.48620.10290.665613.669555.727265.424
234.335-2.0098-2.03149.09544.18885.3924-0.14110.4494-0.1451-0.8910.3992-0.5027-0.0819-0.0916-0.28230.4319-0.18720.01640.29320.01110.3671-17.868942.633756.1199
248.42884.1963-5.40169.5058-4.85244.2895-0.5513-0.102-0.3116-0.00630.25180.29250.57650.03410.27490.5708-0.08920.04720.3904-0.00830.3435-24.495329.610167.0406
252.63881.263-0.54326.69021.5383.769-0.2670.27340.0072-0.43050.3636-0.18660.078-0.164-0.06810.3462-0.0102-0.02310.2446-0.00540.3461-16.840749.440362.5453
265.23220.6309-1.13066.2328-1.35364.5424-0.0818-0.37010.15390.51140.18980.88940.0006-0.6526-0.02330.3969-0.0180.05630.4238-0.06370.3716-30.801246.791773.3538
275.41131.5125-0.62823.0854-0.98270.1831-0.43960.4133-1.147-0.4190.2443-0.51130.20540.08560.05720.4045-0.0320.13330.4372-0.11480.5105-20.220313.672279.8011
287.6595-4.0001-3.8986.54251.14584.1173-0.13450.8369-0.1364-0.466-0.0192-0.09380.0555-0.1742-0.10770.2501-0.0578-0.02150.3968-0.00310.2279-29.699618.928478.541
296.7127-1.9106-1.69911.77760.13324.3435-0.2654-0.5056-0.5378-0.07580.52010.11450.01920.0796-0.07680.3276-0.05790.04580.32350.05670.3348-28.119917.858686.8883
307.14260.0106-2.30932.3813-0.02090.9172-0.3636-0.004-0.9928-0.18280.2113-0.21250.14770.11920.14790.2887-0.00480.07690.3980.01770.4172-35.355613.039185.3557
314.4319-1.89940.21725.9972-1.23625.7018-0.2331-1.05070.19820.49430.1814-0.6183-0.34890.56560.12710.2798-0.07830.00270.5869-0.03970.3125-20.116922.867594.4864
322.71682.7737-0.50793.58740.20912.27910.40.08180.4370.5151-0.174-0.0165-1.1024-0.0512-0.24230.88740.04590.04260.35680.02690.543916.822940.056418.9114
333.6860.7934-1.14676.5444-1.20643.4370.1432-0.22650.11170.38080.00750.0113-0.6458-0.2729-0.13510.420.03710.02880.40390.01290.248911.983627.474323.0209
342.67020.77210.58643.03650.38838.67650.15730.4490.0965-0.29580.1072-0.3331-0.16130.5197-0.33620.3812-0.05240.08950.44390.03750.395822.378724.74585.3293
353.4745-0.3282-0.58763.64380.36828.7033-0.0782-0.6904-0.20520.931-0.2750.6355-0.9623-0.5920.44170.87090.00330.02470.4618-0.00770.6579-28.2318-13.882390.1894
362.83913.83711.46665.26552.20219.43510.304-0.52980.41880.5154-0.68390.0060.2398-0.47090.25070.8452-0.0427-0.02710.62950.02950.8074-30.5305-32.454693.1482
373.12780.27821.59347.54540.10573.8420.0099-0.25930.10580.4221-0.11471.1491-0.5143-0.49690.11870.53260.09080.0710.4676-0.07910.7383-34.4764-15.160780.5922
381.8434-0.38280.60889.01023.55867.4902-0.1102-0.00280.18980.3853-0.33550.641-0.50870.03070.38260.5743-0.019-0.04120.3644-0.02510.6328-27.2173-14.554277.6832
392.0982-1.8886-2.55652.79793.06415.560.06140.2534-0.2439-0.0988-0.27810.4090.1264-0.60770.1650.61130.0317-0.06360.4598-0.04650.7468-28.0709-34.266372.3505
403.3892.5641-2.62695.0601-4.14377.7119-0.5053-0.4606-0.2945-0.4779-0.0647-0.53240.57390.49820.44350.5839-0.03720.09010.42080.14060.5862-7.4762-18.2095108.9522
414.8436-0.2351-5.31314.63190.05118.60120.08610.21010.56560.4439-0.06820.1213-0.0588-0.7314-0.18650.5951-0.2201-0.09160.48420.00390.692-12.7768-2.4725110.203
424.39673.2682-0.96999.121-0.96173.97470.046-0.17780.09240.2978-0.17310.38350.24950.1160.09910.5008-0.07560.08210.3764-0.02330.3783-15.991-19.3323111.7638
435.47972.7827-2.0824.9694-3.19885.8316-0.73720.6594-0.7197-1.12570.3795-1.04911.0893-0.22080.21740.6968-0.06550.14020.3403-0.05480.4741-12.8942-29.1764103.4017
446.69224.9909-2.15519.7848-5.12398.5911-0.30780.2058-0.6676-0.8640.53080.33840.66920.75940.16730.54440.06060.12440.46970.1030.5567-4.3541-18.9105102.2912
453.6984-0.77091.23773.37191.66713.8355-0.1638-1.2269-0.13861.0727-0.1130.31220.2191-0.23860.28760.8426-0.13460.15190.7146-0.00060.4914-16.2465-17.2269124.7436
465.30720.19280.32827.7154-0.69213.36830.23560.1604-0.29880.0569-0.38270.6770.30590.19970.30420.4183-0.03860.06010.4126-0.06670.316-4.21434.423428.4275
472.0541-2.2027-0.70239.2644-3.26654.3962-0.6183-0.85180.1460.8907-0.5522-0.4376-0.44830.76430.42420.508-0.1572-0.07980.66240.11670.42876.163512.311736.8246
486.0786-1.1291-0.54998.14160.92354.37770.40320.8254-0.5906-0.3123-0.6339-1.44640.45881.02110.31680.52760.12060.15040.79930.20271.000415.2719-1.731227.2265
495.21643.197-1.18033.728-2.81833.267-0.4663-0.6641-1.1029-0.2064-0.2746-0.65190.86670.21690.75320.43970.01770.10770.47710.08010.6071-1.2826-3.164336.8653
506.1894-0.92260.81644.8561.02210.570.26450.2146-1.17070.069-0.6125-0.58060.53390.18480.17160.5454-0.03820.12690.4062-0.08850.6374-0.8983-7.290129.1998
516.62141.92910.34676.5806-0.81152.2271-0.15760.4811-1.7333-0.57740.11790.25450.7444-0.26360.02780.63460.0180.04880.3078-0.03140.7537-5.9338-9.506330.131
527.31715.52723.73214.54854.1445.38270.6934-0.5823-0.08391.1763-0.47520.8640.4502-0.7372-0.23990.4835-0.04320.12060.50090.08830.5704-13.4373-1.81437.7285
533.901-0.6112-0.36444.8531-0.1673.7687-0.06620.1839-1.0945-0.6278-0.1972-0.18060.8571-0.07560.2290.5725-0.02010.05810.39-0.10940.6023-8.5854-4.986626.354
543.69351.11840.48154.19061.95334.3705-0.15640.6602-1.2212-0.3348-0.0386-0.48540.33040.51510.10710.85420.21840.32990.6579-0.0070.97476.4118-6.895922.5785
552.5727-2.50780.91974.3511.43783.18540.62570.3893-1.1161-0.4872-0.424-0.30561.5871.32340.20791.15610.31620.26440.40960.21891.76357.7792-15.592228.8306
560.24050.24480.14620.8471-0.32670.48990.16270.2904-0.7761-0.4776-0.2907-0.60361.33020.4364-0.01511.48590.42960.88090.5685-0.37041.66179.7233-19.430519.1481
572.2903-0.4989-1.46292.5045-3.19057.63920.0757-0.0113-0.1157-0.4979-0.2314-0.33640.17960.2839-0.13790.75580.09650.01930.98140.00040.4103-23.248719.3115121.515
582.37570.4247-0.80143.3619-2.07726.1272-0.04170.7886-1.2454-0.9747-0.02770.3412.5229-1.304-0.55631.4915-0.4097-0.38291.495-0.11870.6663-33.15268.2151110.3139
591.02140.1661-0.83185.4066-3.78499.3606-0.06760.47480.0778-1.19880.170.0620.95-0.308-0.130.70260.0046-0.01111.0165-0.1380.3495-25.518411.0981126.4557
600.8269-0.62520.83152.941-2.89395.99550.08310.79950.2482-0.2908-0.16450.0193-0.3450.17910.09820.57680.04450.00420.9608-0.01870.3503-22.5817.8997132.1598
611.2992-0.65240.22162.5067-2.23443.6869-0.17491.2326-0.0224-0.83240.77281.08970.7059-2.1773-0.30590.7754-0.327-0.15441.79680.03830.5256-36.661610.0065127.927
622.76010.69212.32133.91372.36782.8425-0.1870.6648-0.61690.5399-0.30671.23231.1404-1.1442-0.25471.3999-1.1653-0.94442.27890.31781.1963-47.48982.1749124.7678
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 32 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 49 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 120 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 170 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 205 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 214 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 49 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 50 through 181 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 182 through 209 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 49 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 50 through 101 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 102 through 119 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 120 through 134 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 135 through 181 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 182 through 202 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 23 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 24 through 49 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 50 through 88 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 89 through 101 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 102 through 119 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 120 through 181 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 182 through 208 )D0
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 32 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 33 through 49 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 50 through 131 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 132 through 200 )E0
27X-RAY DIFFRACTION27chain 'F' and (resid 1 through 49 )F0
28X-RAY DIFFRACTION28chain 'F' and (resid 50 through 71 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 72 through 88 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 89 through 156 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 157 through 193 )F0
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 49 )G0
33X-RAY DIFFRACTION33chain 'G' and (resid 50 through 149 )G0
34X-RAY DIFFRACTION34chain 'G' and (resid 150 through 203 )G0
35X-RAY DIFFRACTION35chain 'H' and (resid 1 through 32 )H0
36X-RAY DIFFRACTION36chain 'H' and (resid 33 through 49 )H0
37X-RAY DIFFRACTION37chain 'H' and (resid 50 through 119 )H0
38X-RAY DIFFRACTION38chain 'H' and (resid 120 through 156 )H0
39X-RAY DIFFRACTION39chain 'H' and (resid 157 through 207 )H0
40X-RAY DIFFRACTION40chain 'I' and (resid 1 through 23 )I0
41X-RAY DIFFRACTION41chain 'I' and (resid 24 through 49 )I0
42X-RAY DIFFRACTION42chain 'I' and (resid 50 through 101 )I0
43X-RAY DIFFRACTION43chain 'I' and (resid 102 through 119 )I0
44X-RAY DIFFRACTION44chain 'I' and (resid 120 through 131 )I0
45X-RAY DIFFRACTION45chain 'I' and (resid 132 through 195 )I0
46X-RAY DIFFRACTION46chain 'J' and (resid 3 through 23 )J0
47X-RAY DIFFRACTION47chain 'J' and (resid 24 through 32 )J0
48X-RAY DIFFRACTION48chain 'J' and (resid 33 through 49 )J0
49X-RAY DIFFRACTION49chain 'J' and (resid 50 through 71 )J0
50X-RAY DIFFRACTION50chain 'J' and (resid 72 through 88 )J0
51X-RAY DIFFRACTION51chain 'J' and (resid 89 through 101 )J0
52X-RAY DIFFRACTION52chain 'J' and (resid 102 through 119 )J0
53X-RAY DIFFRACTION53chain 'J' and (resid 120 through 156 )J0
54X-RAY DIFFRACTION54chain 'J' and (resid 157 through 170 )J0
55X-RAY DIFFRACTION55chain 'J' and (resid 171 through 181 )J0
56X-RAY DIFFRACTION56chain 'J' and (resid 182 through 192 )J0
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 32 )K0
58X-RAY DIFFRACTION58chain 'K' and (resid 33 through 49 )K0
59X-RAY DIFFRACTION59chain 'K' and (resid 50 through 88 )K0
60X-RAY DIFFRACTION60chain 'K' and (resid 89 through 131 )K0
61X-RAY DIFFRACTION61chain 'K' and (resid 132 through 181 )K0
62X-RAY DIFFRACTION62chain 'K' and (resid 182 through 195 )K0

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る