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- PDB-3k77: X-ray crystal structure of XRCC1 -

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基本情報

登録情報
データベース: PDB / ID: 3k77
タイトルX-ray crystal structure of XRCC1
要素DNA repair protein XRCC1DNA修復
キーワードPROTEIN BINDING (タンパク質) / xrcc1 / base excision repair (塩基除去修復) / scaffolding protein (足場タンパク質) / DNA damage (DNA修復) / DNA repair (DNA修復) / Nucleus (Nucleus) / Phosphoprotein / Polymorphism / Ubl conjugation
機能・相同性
機能・相同性情報


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / positive regulation of single strand break repair ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / poly-ADP-D-ribose binding / positive regulation of single strand break repair / voluntary musculoskeletal movement / cerebellum morphogenesis / single strand break repair / replication-born double-strand break repair via sister chromatid exchange / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Gap-filling DNA repair synthesis and ligation in GG-NER / response to organic substance / hippocampus development / 塩基除去修復 / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / chromosome, telomeric region / response to hypoxia / response to xenobiotic stimulus / クロマチン / 核小体 / enzyme binding / 核質 / 細胞核
類似検索 - 分子機能
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / Galactose-binding domain-like / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / BRCA1 C Terminus (BRCT) domain / Galactose-binding domain-like / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Jelly Rolls / サンドイッチ / Mainly Beta
類似検索 - ドメイン・相同性
DNA repair protein XRCC1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / 分子置換 / 解像度: 2.597 Å
データ登録者Cuneo, M.J. / London, R.E.
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2010
タイトル: Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.
著者: Cuneo, M.J. / London, R.E.
履歴
登録2009年10月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年4月28日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22017年11月1日Group: Refinement description / カテゴリ: software
改定 1.32023年9月6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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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: DNA repair protein XRCC1
B: DNA repair protein XRCC1
C: DNA repair protein XRCC1
D: DNA repair protein XRCC1
E: DNA repair protein XRCC1
F: DNA repair protein XRCC1
G: DNA repair protein XRCC1
H: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)143,7468
ポリマ－143,7468
非ポリマー00
水2,198122
1
A: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
B: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
5
E: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
6
F: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
7
G: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
8
H: DNA repair protein XRCC1


分子量 (理論値)分子数
合計 (水以外)17,9681
ポリマ－17,9681
非ポリマー00
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)64.451, 89.302, 93.178
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F
71G
81H

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 2 - 153 / Label seq-ID: 2 - 153

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:153 )AA
2chain B and (resseq 2:153 )BB
3chain C and (resseq 2:153 )CC
4chain D and (resseq 2:153 )DD
5chain E and (resseq 2:153 )EE
6chain F and (resseq 2:153 )FF
7chain G and (resseq 2:153 )GG
8chain H and (resseq 2:153 )HH

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要素

#1: タンパク質
DNA repair protein XRCC1 / DNA修復 / X-ray repair cross-complementing protein 1


分子量: 17968.193 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 株: Humanヒト / 遺伝子: XRCC1 / プラスミド: pET21a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-DE3 / 参照: UniProt: P18887
#2: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 122 / 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: 1.87 Å3/Da / 溶媒含有率: 34.06 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 25-30% PEG 3350, 0.2-0.3M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.5418 Å
検出器タイプ: RIGAKU SATURN 92 / 検出器: CCD / 日付: 2008年10月30日
放射モノクロメーター: MIRRORS / 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: 1.5418 Å / 相対比: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.394
反射解像度: 2.6→30 Å / Num. all: 89046 / Num. obs: 32158 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.8 / 冗長度: 2.8 % / Rmerge(I) obs: 0.11 / Χ2: 1.622 / Net I/σ(I): 11.9
反射 シェル解像度: 2.6→2.69 Å / 冗長度: 2.7 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3186 / Rsym value: 0.351 / Χ2: 2.15 / % possible all: 97.7

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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
PHENIX精密化
PDB_EXTRACT3.005データ抽出
HKL-2000データ収集
HKL-2000データ削減
HKL-2000データスケーリング
PHASER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 3K75

3k75


解像度: 2.597→29.336 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.743 / σ(F): 1.34 / σ(I): 3.8 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射Selection details
Rfree0.237 1652 5.15 %RANDOM
Rwork0.2 ---
obs0.202 32108 98 %-
all-89046 --
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 / Bsol: 30.982 Å2 / ksol: 0.355 e/Å3
原子変位パラメータBiso max: 154.03 Å2 / Biso mean: 39.015 Å2 / Biso min: 1.43 Å2
Baniso -1Baniso -2Baniso -3
1--3.564 Å20 Å2-1.642 Å2
2--4.304 Å20 Å2
3----9.469 Å2
精密化ステップサイクル: LAST / 解像度: 2.597→29.336 Å
タンパク質核酸リガンド溶媒全体
原子数9355 0 0 122 9477
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0079564
X-RAY DIFFRACTIONf_angle_d0.97212915
X-RAY DIFFRACTIONf_chiral_restr0.0641411
X-RAY DIFFRACTIONf_plane_restr0.0051690
X-RAY DIFFRACTIONf_dihedral_angle_d23.5025965
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A1172X-RAY DIFFRACTIONPOSITIONAL0.045
12B1172X-RAY DIFFRACTIONPOSITIONAL0.045
13C1160X-RAY DIFFRACTIONPOSITIONAL0.038
14D1159X-RAY DIFFRACTIONPOSITIONAL0.042
15E1160X-RAY DIFFRACTIONPOSITIONAL0.041
16F1172X-RAY DIFFRACTIONPOSITIONAL0.044
17G1165X-RAY DIFFRACTIONPOSITIONAL0.043
18H1162X-RAY DIFFRACTIONPOSITIONAL0.041
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 98 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.597-2.6530.3751020.33617951897
2.653-2.7150.341950.29219322027
2.715-2.7830.3361090.28118962005
2.783-2.8580.3521070.29518771984
2.858-2.9420.317930.28219372030
2.942-3.0370.3461070.28218521959
3.037-3.1450.258940.22719602054
3.145-3.2710.2271130.19319022015
3.271-3.4190.215930.16619512044
3.419-3.5990.1821030.16319252028
3.599-3.8250.2051060.18519282034
3.825-4.1190.257920.17718571949
4.119-4.5320.204960.14218801976
4.532-5.1850.1991070.16919052012
5.185-6.5210.1991100.19319452055
6.521-29.3370.1791030.17719362039
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)
10.44360.1589-0.19990.76060.4123.5237-0.3665-0.04470.16340.25230.30590.00190.5952-0.33780.16780.03820.0478-0.01610.10350.01640.063420.427514.708716.461
20.0465-0.0475-0.0506-0.0898-0.0699-0.033-0.1454-0.15440.09520.3089-0.3337-0.0609-0.46660.07320.0010.1232-0.03180.05370.60220.13320.454421.177213.198526.5481
30.08910.09970.1304-0.0181-0.0503-0.02240.36960.6402-0.8217-0.23580.4012-0.16120.19540.510.00510.21560.0224-0.16070.3078-0.05240.532124.83821.80113.6849
40.63530.02910.08170.2652-0.38280.4591-0.14810.11060.41570.2379-0.1655-0.05070.1567-0.1471-0.00150.13440.0711-0.01190.2104-0.010.195429.749218.199914.0628
50.00450.0086-0.0103-0.0254-0.0151-0.0059-0.1885-0.0476-0.1047-0.0649-0.161-0.03230.1264-0.1175-0.00081.5573-0.09980.23430.1272-0.08571.515828.372920.6727-0.5288
6-0.1888-0.2868-0.1811.97750.04860.0592-0.06760.29450.00690.30830.0522-0.29530.0421-0.0088-0.05470.05320.1043-0.03570.4057-0.05620.165537.95677.812518.0649
70.02750.0738-0.18540.27910.15680.9575-0.0370.0717-0.13350.17920.0021-0.09180.41230.3778-0.00430.063-0.0423-0.12660.26570.03940.523540.73421.556920.8683
80.7529-0.4332-0.33820.30260.29660.9177-0.0414-0.00050.30.09440.0965-0.05110.16680.14440.2384-0.0344-0.33120.1317-0.18960.34580.024333.201222.010111.1371
90.5565-0.33810.11581.07930.20610.4732-0.3011-0.23130.2051.12310.1734-0.18280.2796-0.15280.020.3259-0.075-0.05850.19210.02340.157431.224610.535818.6663
100.03140.06110.05450.141-0.0087-0.0277-0.1038-0.21140.31760.4961-0.2624-0.1431-0.0042-0.10650.00030.3832-0.2987-0.0860.69020.0840.165220.821126.747555.0878
11-0.022-0.05320.13850.23780.33930.16610.00020.05230.04550.0173-0.02580.07120.115-0.1721-0.16190.07380.1081-0.0525-0.53580.09930.116712.504412.990754.5076
120.03720.04670.10220.10980.03250.15420.2602-0.20830.29520.2821-0.0491-0.4588-0.48330.60380.00290.1746-0.1283-0.10950.3703-0.12660.43824.549613.614654.7591
130.6763-0.10550.00270.0779-0.19670.69480.06020.0615-0.07060.05580.0096-0.1612-0.11280.0723-0.00030.11560.06040.02380.152-0.04010.129214.337618.407645.911
14-0.2972-0.5277-0.11090.11710.7491.3416-0.0246-0.0687-0.0979-0.0008-0.05380.44290.238-0.0464-0.21531.19-0.0489-0.4212-0.17560.36511.20032.436628.642748.351
150.39060.2986-0.08780.2297-0.0268-0.0140.05110.3859-0.0735-0.1444-0.09490.48480.2133-0.10340.00030.21280.04580.0240.2965-0.01980.139715.359614.009136.2358
160.8446-0.3166-0.82880.06040.11330.68370.2015-0.47090.2491-0.03780.0533-0.1111-0.17420.37950.7904-0.4164-0.15330.08520.298-0.04950.188224.161216.042138.7639
17-0.04930.11460.17160.07890.1370.5493-0.21990.62960.1490.0834-0.1841-0.1125-0.44770.699-0.00420.50180.2786-0.03440.3777-0.07390.093317.472232.284837.3223
180.8454-1.441-0.66834.7027-0.05611.3820.07020.4056-0.00740.3402-0.1661-0.63960.08990.00330.00020.04930.00260.00280.05030.07070.064115.339117.768844.4804
190.1930.4027-0.12550.7639-0.17420.1481-0.27150.2840.0716-0.12920.3449-0.0952-0.045-0.1703-0.3085-0.4393-0.18560.4140.17780.0561-0.1421-4.169955.594829.8614
200.8791-1.0224-1.33731.11810.95511.4682-0.6106-0.189-0.343-0.1905-0.0843-0.01130.9094-0.1555-0.08390.37910.0652-0.00080.63830.08820.0158-3.340757.480219.8816
210.0883-0.3129-0.00951.4928-0.10720.3954-0.04970.07830.13460.188-0.2866-0.254-0.18210.2926-0.0074-0.1083-0.05720.31550.10040.02450.04491.242362.36634.8411
220.72490.1839-0.19911.8389-0.73861.43120.320.1895-0.11830.0413-0.09690.19840.13030.50540.00140.01560.1178-0.04170.1286-0.01010.13946.100650.303832.0894
230.4823-0.2243-0.39770.9368-0.55031.24020.0447-0.26720.21730.48390.3550.2296-0.19480.34630.08570.13520.02180.02620.22170.05390.143912.695460.426533.7598
240.04030.0486-0.0015-0.10460.0006-0.05640.07590.110.2432-0.6281-0.2012-0.3823-0.29850.30240.00020.2191-0.0215-0.05270.1544-0.00310.264812.125264.41921.6923
252.06170.65160.21770.6066-0.33120.20930.31360.5229-0.5156-0.2797-0.1813-0.44440.06720.4374-0.02830.46030.10320.06190.1376-0.02530.018916.687347.496528.308
260.6386-0.264-0.02931.1286-0.65450.88650.04920.1053-0.0127-0.118-0.2314-0.04130.17150.1241-0.19410.0624-0.0064-0.0327-0.03570.00730.18786.798857.481633.0003
270.9619-0.48371.1184-0.1503-0.12161.8703-0.08320.3761-0.1185-0.01270.0629-0.01570.4415-0.3310.23440.2251-0.29690.12190.38510.08860.03676.5844.832323.503
280.36340.81510.25164.02522.42052.19170.03830.20750.11720.32430.15810.4630.3877-0.1175-0.18940.0509-0.02440.0126-0.05960.2760.096927.40461.64121.0999
292.3453-0.58890.3550.1211-0.3396-0.18420.0121-0.64370.29030.45460.08650.2095-0.72570.2801-0.03760.3223-0.07960.020.1670.06120.191527.212456.393526.6376
300.9884-0.2841-0.88590.29050.2222.5043-0.0602-0.007-0.13160.1954-0.0757-0.0470.31960.444-0.25240.029-0.0958-0.0534-0.0838-0.00330.146635.304460.97320.4875
310.0145-0.03240.01570.04560.0079-0.00030.14810.10070.10570.060.32160.2066-0.112-0.03930.0021.35730.40370.10880.853-0.42011.269733.060969.57256.4973
320.94750.1912-0.09670.23280.45180.5101-0.37010.3676-0.61950.00750.289-0.1965-0.12530.4497-0.00090.195-0.0295-0.08510.15950.08560.284145.488556.098321.2184
332.2944-1.0703-1.01730.84480.93710.86290.21950.37070.02320.320.2063-0.33610.46130.32590.21680.08170.0061-0.1260.3973-0.166-0.044644.822362.07129.684
342.20990.5314-0.41160.3202-0.16880.39530.0435-0.30051.1220.38510.3403-0.1482-0.47470.07680.0330.5341-0.10660.00640.1756-0.13310.318941.291275.261320.8388
351.9577-2.4254-0.11514.8785-0.12610.1982-0.11020.2469-0.318-0.06380.03220.81630.15960.02590.01790.1856-0.0764-0.07170.148-0.07860.060640.504153.700416.6495
361.44340.10610.95740.0379-0.84640.5713-0.2462-0.0721-0.12370.42970.0071-0.477-0.2126-0.32260.18020.1456-0.4493-0.2299-0.1563-0.2753-0.10935.952662.568327.0825
370.06930.3066-0.9649-0.0489-0.12410.8910.1056-0.4981-0.16-0.0215-0.1199-0.20920.5054-0.6874-1.1479-0.2933-0.1872-0.34980.2133-0.08580.148218.151852.657412.7412
380.0022-0.0157-0.49220.14430.1876-0.3126-0.330.07050.14010.06880.12380.401-0.34250.11-0.21580.2041-0.2290.2576-0.00970.32430.939210.298350.510512.8835
390.96370.27272.13020.51060.48811.42280.0265-0.2710.1622-0.15630.1669-0.3458-0.7276-0.586-0.19560.26190.01710.04170.07140.13890.379718.102964.12598.0719
400.5196-0.08240.06150.23230.29090.83790.13930.0489-0.2130.20210.1237-0.19220.56850.07840.00380.2478-0.0579-0.0860.19160.00910.131819.241348.68973.2783
410.00580.00240.00980.0182-0.011-0.00440.0175-0.05090.15890.05410.00930.12420.00520.0544-0.00121.97640.73750.06730.82670.07921.225133.948646.48353.0012
421.610.1186-0.00530.7237-0.22950.25430.02020.69510.16630.13680.21270.0170.19050.2123-0.03130.1288-0.01050.00940.22030.03130.159217.643955.8421-5.5444
431.990.7427-1.7821.1635-0.64992.3170.38480.0750.24640.03350.34050.4928-0.0235-0.30010.3450.1113-0.0056-0.0706-0.00950.21160.17958.535663.0537-3.6562
440.09730.0343-0.05450.07190.0270.01260.3884-0.4179-0.53890.5792-0.29440.05390.78050.2586-0.00260.4098-0.0484-0.19340.3228-0.0720.45516.888640.7017-5.373
451.0907-0.09090.37860.7767-0.37211.59880.1463-0.3389-0.57340.1244-0.16680.1287-0.362-0.28580.78030.17020.042-0.09990.01230.0922-0.014117.628554.26842.3096
460.4357-0.34540.12353.3491.05140.94640.04660.25980.2353-0.41120.4289-0.302-0.04660.4461.1585-0.1055-0.10130.04860.14720.0632-0.0381-9.634952.607-8.082
472.31871.11722.92630.31621.23413.63990.3720.479-0.2095-0.06220.3665-0.35180.43040.7320.18430.2832-0.21220.08110.41950.2430.2060.072755.8011-8.0769
480.0310.1384-0.00750.0743-0.11190.45870.1901-0.14170.90730.06880.13290.25090.0405-0.30210.00350.21230.0712-0.04270.0963-0.01440.4372-14.484963.63330.1107
490.2357-0.28740.17880.5631-0.17670.40890.1623-0.2443-0.047-0.28420.04350.29080.2471-0.11420.03560.11890.14140.068-0.04410.00730.1224-14.296150.189-3.1316
500.1115-0.0006-0.0670.02780.09790.0508-0.39930.30210.1940.11040.4036-0.2750.84410.55370.00040.37840.1505-0.16530.2966-0.0360.3498-5.259739.0353-1.8273
510.2340.2655-0.2550.20510.02151.24640.03530.0386-0.5777-0.3949-0.0327-0.01660.110.4794-0.10150.19040.0320.04180.1134-0.06710.1797-9.526453.01355.5845
520.0247-0.0187-0.0386-0.01560.00530.00210.0932-0.13920.104-0.03740.00490.0541-0.0925-0.14390.00030.90090.3372-0.21850.9552-0.08960.8403-22.835741.1135-1.4963
530.2735-0.3218-0.1440.4442-0.13380.74290.0737-0.29970.08590.1809-0.1146-0.35580.1560.1724-0.00250.15120.016-0.00870.2175-0.05990.2093-6.096755.03919.9486
540.8288-0.18740.5375-0.07650.22051.2832-0.03080.1996-0.16090.28930.3274-0.38380.2293-0.0314-0.00050.2026-0.0191-0.03870.10660.0080.2582-9.022448.42043.8137
550.2065-0.6457-0.17340.57330.16930.1405-0.1465-0.1247-0.325-0.14390.15190.87-0.1945-0.1673-0.02870.3325-0.0959-0.03530.29360.02160.1685-12.40987.610625.4493
560.2070.36340.06520.43240.09070.02380.14880.17340.5180.27970.36740.46460.0111-0.1091-0.0020.30380.17490.12470.4247-0.03990.1172-12.954118.370823.2646
57-0.0232-0.0079-0.0096-0.01910.00540.02170.10560.11820.2165-0.01260.30440.3435-0.1371-0.047-0.0020.39450.0863-0.02470.3161-0.09040.1221-11.659410.340117.4639
582.97810.3917-0.16044.44412.57532.7696-0.32040.4443-0.2576-0.5595-0.27460.5956-0.17270.1149-0.28910.05420.0570.04950.26270.01690.0157-8.342118.895923.1964
590.0442-0.0508-0.0260.07610.01430.0152-0.03440.04240.17040.03060.12-0.1154-0.2117-0.27770.00090.5548-0.10670.11610.6068-0.00640.2303-1.678222.202433.508
600.5203-1.0804-0.05052.0417-0.46440.5691-0.3-0.0618-0.3654-0.19650.41110.49060.1962-0.38880.08940.1354-0.02390.00610.21310.0230.1272-4.51214.08125.6678
610.01170.01680.02470.02810.0217-0.0063-0.1620.01910.0307-0.0902-0.0290.09920.10920.07130.00020.90790.01440.23341.2602-0.49451.6022-6.16640.632840.2967
620.48310.41450.08855.2392-0.35320.5489-0.3259-0.1018-0.2472-0.52830.2869-0.78920.21830.03720.0230.09510.0152-0.05860.2431-0.0110.15445.891812.208522.9016
630.61760.3094-0.22371.4312-0.56620.7089-0.2266-0.1833-0.0874-0.2077-0.371-0.19020.61750.2316-0.2954-0.059-0.1557-0.20780.16430.00530.1057-0.78855.941925.3666
640.412-0.6919-0.22372.0081-0.18170.1409-0.3036-0.620.06720.21940.3353-0.8774-0.35870.90650.03530.1751-0.0862-0.00150.523-0.07610.177720.814863.596459.1357
650.39240.3650.42210.75370.39280.6987-0.0406-0.1356-0.204-0.35170.5507-1.5090.33450.79520.04020.0973-0.13840.11091.1665-0.16680.448428.170760.259659.7518
660.0742-0.08460.02750.2452-0.31930.082-0.21080.4779-0.6502-0.84320.25450.06720.73010.1307-0.00590.3645-0.13510.08530.92150.00190.266620.313350.15353.0841
670.0269-0.0581-0.01170.0472-0.05190.02860.2925-0.20450.8790.022-0.0581-0.0991-0.4234-0.4873-0.00310.4554-0.00170.12240.6357-0.14290.567318.220368.755755.2467
680.2008-0.08820.06130.60830.25930.37380.1638-0.22280.3057-0.4083-0.0014-0.4983-0.17630.00030.00750.30130.02710.01580.31580.04520.148222.21365.717847.2031
690.0019-0.0139-0.00970.05290.0241-0.0486-0.0288-0.09690.04930.32510.0337-0.0903-0.3188-0.1069-0.00090.8567-0.16320.09240.5675-0.15321.0985.836468.505349.6074
700.63740.08230.19251.3523-0.79890.99340.1131-0.45810.2646-0.0966-0.4002-0.4810.3783-0.2170.02220.1405-0.054-0.02460.16240.06750.249525.745556.436841.7904
710.9260.14870.6955-0.37460.15680.9271-0.17790.70540.6086-0.19830.0292-0.3778-0.8748-0.1686-0.04760.29360.07940.19280.35010.04020.480724.186473.265340.1632
721.03890.1042-0.30890.0674-0.02721.04330.0271-0.00460.00840.4914-0.1033-0.15310.0075-0.10450.00020.230.0193-0.10790.3488-0.06470.200822.014962.339548.9798
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:25)A2 - 25
2X-RAY DIFFRACTION2(chain A and resid 26:32)A26 - 32
3X-RAY DIFFRACTION3(chain A and resid 33:40)A33 - 40
4X-RAY DIFFRACTION4(chain A and resid 41:76)A41 - 76
5X-RAY DIFFRACTION5(chain A and resid 77:83)A77 - 83
6X-RAY DIFFRACTION6(chain A and resid 84:109)A84 - 109
7X-RAY DIFFRACTION7(chain A and resid 110:115)A110 - 115
8X-RAY DIFFRACTION8(chain A and resid 116:134)A116 - 134
9X-RAY DIFFRACTION9(chain A and resid 135:153)A135 - 153
10X-RAY DIFFRACTION10(chain B and resid 2:7)B2 - 7
11X-RAY DIFFRACTION11(chain B and resid 8:25)B8 - 25
12X-RAY DIFFRACTION12(chain B and resid 26:32)B26 - 32
13X-RAY DIFFRACTION13(chain B and resid 33:72)B33 - 72
14X-RAY DIFFRACTION14(chain B and resid 73:82)B73 - 82
15X-RAY DIFFRACTION15(chain B and resid 83:104)B83 - 104
16X-RAY DIFFRACTION16(chain B and resid 105:112)B105 - 112
17X-RAY DIFFRACTION17(chain B and resid 113:123)B113 - 123
18X-RAY DIFFRACTION18(chain B and resid 124:153)B124 - 153
19X-RAY DIFFRACTION19(chain C and resid 2:25)C2 - 25
20X-RAY DIFFRACTION20(chain C and resid 26:32)C26 - 32
21X-RAY DIFFRACTION21(chain C and resid 33:49)C33 - 49
22X-RAY DIFFRACTION22(chain C and resid 50:80)C50 - 80
23X-RAY DIFFRACTION23(chain C and resid 81:102)C81 - 102
24X-RAY DIFFRACTION24(chain C and resid 103:109)C103 - 109
25X-RAY DIFFRACTION25(chain C and resid 110:119)C110 - 119
26X-RAY DIFFRACTION26(chain C and resid 120:147)C120 - 147
27X-RAY DIFFRACTION27(chain C and resid 148:153)C148 - 153
28X-RAY DIFFRACTION28(chain D and resid 2:17)D2 - 17
29X-RAY DIFFRACTION29(chain D and resid 18:29)D18 - 29
30X-RAY DIFFRACTION30(chain D and resid 31:75)D31 - 75
31X-RAY DIFFRACTION31(chain D and resid 76:82)D76 - 82
32X-RAY DIFFRACTION32(chain D and resid 83:106)D83 - 106
33X-RAY DIFFRACTION33(chain D and resid 107:112)D107 - 112
34X-RAY DIFFRACTION34(chain D and resid 113:126)D113 - 126
35X-RAY DIFFRACTION35(chain D and resid 127:140)D127 - 140
36X-RAY DIFFRACTION36(chain D and resid 141:153)D141 - 153
37X-RAY DIFFRACTION37(chain E and resid 2:23)E2 - 23
38X-RAY DIFFRACTION38(chain E and resid 24:29)E24 - 29
39X-RAY DIFFRACTION39(chain E and resid 31:40)E31 - 40
40X-RAY DIFFRACTION40(chain E and resid 41:76)E41 - 76
41X-RAY DIFFRACTION41(chain E and resid 77:83)E77 - 83
42X-RAY DIFFRACTION42(chain E and resid 84:99)E84 - 99
43X-RAY DIFFRACTION43(chain E and resid 100:109)E100 - 109
44X-RAY DIFFRACTION44(chain E and resid 110:124)E110 - 124
45X-RAY DIFFRACTION45(chain E and resid 125:153)E125 - 153
46X-RAY DIFFRACTION46(chain F and resid 2:25)F2 - 25
47X-RAY DIFFRACTION47(chain F and resid 26:32)F26 - 32
48X-RAY DIFFRACTION48(chain F and resid 33:41)F33 - 41
49X-RAY DIFFRACTION49(chain F and resid 42:49)F42 - 49
50X-RAY DIFFRACTION50(chain F and resid 50:59)F50 - 59
51X-RAY DIFFRACTION51(chain F and resid 60:73)F60 - 73
52X-RAY DIFFRACTION52(chain F and resid 74:83)F74 - 83
53X-RAY DIFFRACTION53(chain F and resid 84:113)F84 - 113
54X-RAY DIFFRACTION54(chain F and resid 114:153)F114 - 153
55X-RAY DIFFRACTION55(chain G and resid 2:16)G2 - 16
56X-RAY DIFFRACTION56(chain G and resid 17:23)G17 - 23
57X-RAY DIFFRACTION57(chain G and resid 24:29)G24 - 29
58X-RAY DIFFRACTION58(chain G and resid 31:36)G31 - 36
59X-RAY DIFFRACTION59(chain G and resid 37:42)G37 - 42
60X-RAY DIFFRACTION60(chain G and resid 43:76)G43 - 76
61X-RAY DIFFRACTION61(chain G and resid 77:83)G77 - 83
62X-RAY DIFFRACTION62(chain G and resid 84:113)G84 - 113
63X-RAY DIFFRACTION63(chain G and resid 114:153)G114 - 153
64X-RAY DIFFRACTION64(chain H and resid 2:18)H2 - 18
65X-RAY DIFFRACTION65(chain H and resid 19:31)H19 - 31
66X-RAY DIFFRACTION66(chain H and resid 32:41)H32 - 41
67X-RAY DIFFRACTION67(chain H and resid 42:53)H42 - 53
68X-RAY DIFFRACTION68(chain H and resid 54:76)H54 - 76
69X-RAY DIFFRACTION69(chain H and resid 77:83)H77 - 83
70X-RAY DIFFRACTION70(chain H and resid 84:109)H84 - 109
71X-RAY DIFFRACTION71(chain H and resid 110:122)H110 - 122
72X-RAY DIFFRACTION72(chain H and resid 123:153)H123 - 153

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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