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- PDB-2ypz: KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic... -

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基本情報

登録情報
データベース: PDB / ID: 2ypz
タイトルKSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form
要素KSHV LANA
キーワードVIRAL PROTEIN / LATENCY-ASSOCIATED NUCLEAR ANTIGEN / LANA-1 / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE / TUMOR VIRUS / CANCER / MURID HERPESVIRUS 4 / MUHV-4 / MURID HERPESVIRUS 68 / MHV-68
機能・相同性
機能・相同性情報


host cell nucleus / DNA binding
類似検索 - 分子機能
: / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
生物種HUMAN HERPESVIRUS 8 TYPE M (ヘルペスウイルス)
手法X線回折 / 分子置換 / 解像度: 3.199 Å
データ登録者Hellert, J. / Krausze, J. / Luhrs, T.
引用ジャーナル: Plos Pathog. / : 2013
タイトル: A Structural Basis for Brd2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Lana Proteins.
著者: Hellert, J. / Weidner-Glunde, M. / Krausze, J. / Richter, U. / Adler, H. / Fedorov, R. / Pietrek, M. / Ruckert, J. / Ritter, C. / Schulz, T.F. / Luhrs, T.
履歴
登録2012年11月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02013年11月13日Provider: repository / タイプ: Initial release
改定 1.12014年1月29日Group: Atomic model / Derived calculations / Other
改定 1.22019年5月8日Group: Data collection / Experimental preparation / Other
カテゴリ: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
改定 1.32019年5月22日Group: Data collection / Experimental preparation / カテゴリ: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
改定 1.42023年12月20日Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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: KSHV LANA
B: KSHV LANA
C: KSHV LANA
D: KSHV LANA
E: KSHV LANA
F: KSHV LANA
G: KSHV LANA
H: KSHV LANA
I: KSHV LANA
J: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)157,60210
ポリマ-157,60210
非ポリマー00
00
1
I: KSHV LANA
J: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)31,5202
ポリマ-31,5202
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-30.4 kcal/mol
Surface area13050 Å2
手法PISA
2
C: KSHV LANA
D: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)31,5202
ポリマ-31,5202
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-28.6 kcal/mol
Surface area13040 Å2
手法PISA
3
A: KSHV LANA
B: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)31,5202
ポリマ-31,5202
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-28.6 kcal/mol
Surface area13070 Å2
手法PISA
4
G: KSHV LANA
H: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)31,5202
ポリマ-31,5202
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-27.3 kcal/mol
Surface area13070 Å2
手法PISA
5
E: KSHV LANA
F: KSHV LANA


分子量 (理論値)分子数
合計 (水以外)31,5202
ポリマ-31,5202
非ポリマー00
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-28.4 kcal/mol
Surface area13200 Å2
手法PISA
単位格子
Length a, b, c (Å)76.790, 100.290, 214.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(-0.99757, 0.03583, 0.05983), (0.04177, -0.3801, 0.924), (0.05585, 0.92425, 0.37768)60.53185, -189.58101, 124.63594
2given(0.96999, -0.23561, -0.0601), (-0.20506, 0.65977, 0.72295), (-0.13068, 0.71357, -0.68828)80.22688, -144.99168, 359.20197
3given(0.95005, -0.03288, -0.31035), (0.29737, 0.39712, 0.86825), (0.0947, -0.91718, 0.38706)60.54406, -193.27036, 131.91946
4given(0.93546, 0.32243, 0.14473), (0.35107, -0.80055, -0.48566), (-0.04072, 0.50513, -0.86208)-35.31052, 93.23947, 389.81113
5given(-0.91296, 0.07138, 0.40176), (-0.40757, -0.11146, -0.90635), (-0.01991, -0.9912, 0.13085)-20.10275, 206.74512, 186.76468
6given(0.81914, 0.34501, -0.45823), (0.55757, -0.66645, 0.49493), (-0.13463, -0.66091, -0.73829)87.86293, -123.24555, 374.43887
7given(-0.8239, -0.53492, 0.18723), (-0.56114, 0.72364, -0.40182), (0.07946, -0.43612, -0.89637)15.62117, 99.15219, 399.28619
8given(0.99248, -0.09851, 0.07261), (0.0949, 0.24491, -0.96489), (0.07727, 0.96453, 0.25241)-25.54868, 198.31477, 152.46596
9given(-0.9893, 0.14457, 0.01988), (-0.14593, -0.98054, -0.1313), (0.00051, -0.13279, 0.99114)57.8303, 37.46007, 4.85199

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要素

#1: タンパク質
KSHV LANA


分子量: 15760.201 Da / 分子数: 10 / 断片: C-TERMINAL DOMAIN, RESIDUES 1013-1149 / 由来タイプ: 組換発現
由来: (組換発現) HUMAN HERPESVIRUS 8 TYPE M (ヘルペスウイルス)
発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q76SB0

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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: 2.63 Å3/Da / 溶媒含有率: 53.17 % / 解説: NONE
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.6
詳細: 1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. THE MIXTURE WAS INCUBATED AT 20 DEGREE ...詳細: 1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. THE MIXTURE WAS INCUBATED AT 20 DEGREE CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL.

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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: 1.54181
検出器タイプ: RIGAKU-MSC SATURN 944 PLUS / 検出器: CCD / 日付: 2012年10月3日 / 詳細: MIRRORS
放射モノクロメーター: RIGAKU VARIMAX / 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: 1.54181 Å / 相対比: 1
反射解像度: 3.2→90 Å / Num. obs: 27442 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / 冗長度: 3.45 % / Biso Wilson estimate: 47.43 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 7.67
反射 シェル解像度: 3.2→3.39 Å / 冗長度: 3.37 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.03 / % possible all: 95.1

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)精密化
XDSデータ削減
XSCALE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 2YPY
解像度: 3.199→45.427 Å / SU ML: 0.4 / σ(F): 1.99 / 位相誤差: 24.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2651 1371 5 %
Rwork0.2177 --
obs0.2201 27435 97.56 %
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 mean: 50.7 Å2
精密化ステップサイクル: LAST / 解像度: 3.199→45.427 Å
タンパク質核酸リガンド溶媒全体
原子数10837 0 0 0 10837
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00311223
X-RAY DIFFRACTIONf_angle_d0.73415234
X-RAY DIFFRACTIONf_dihedral_angle_d11.2924282
X-RAY DIFFRACTIONf_chiral_restr0.0541508
X-RAY DIFFRACTIONf_plane_restr0.0041995
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1992-3.31350.33181280.29172419X-RAY DIFFRACTION93
3.3135-3.44610.29131370.25442600X-RAY DIFFRACTION99
3.4461-3.60290.26041380.25872627X-RAY DIFFRACTION100
3.6029-3.79280.29381370.2472600X-RAY DIFFRACTION99
3.7928-4.03030.29131380.23792641X-RAY DIFFRACTION99
4.0303-4.34120.26631370.2072601X-RAY DIFFRACTION98
4.3412-4.77770.26951380.18722632X-RAY DIFFRACTION98
4.7777-5.4680.23981390.19122631X-RAY DIFFRACTION99
5.468-6.88530.2451400.20012657X-RAY DIFFRACTION98
6.8853-45.4320.2181390.17642656X-RAY DIFFRACTION93
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.257-0.42771.42471.9121-0.71622.1033-0.0722-0.1269-0.08740.53980.25650.60020.4635-0.2265-0.1590.1158-0.0051-0.06320.3217-0.08940.517130.34-30.4542183.0035
21.3981-0.48760.44693.0871-0.13582.6479-0.18160.05930.3769-0.28190.1168-0.10050.0129-0.11670.06850.20070.0016-0.05520.3035-0.00230.308936.6828-23.4474182.8836
31.6006-0.54451.35952.289-0.00531.227-0.38840.24950.1163-0.6123-0.2271-0.65390.51060.63790.56890.5446-0.06860.19960.7268-0.00720.49144.4616-16.4008163.6105
40.635-1.45390.36843.7301-0.53781.83170.14740.35320.24330.0472-0.1477-0.9163-0.86061.37420.12350.449-0.09420.05610.7096-0.01560.419141.8392-7.6234155.9914
52.22270.4891-0.79021.44321.83866.0710.2463-0.2550.424-0.80110.2107-0.2966-0.39970.3110.13850.3940.1947-0.12030.3470.03230.433540.13460.5657165.4068
60.6432-0.8913-0.43464.3582-0.23310.4970.37030.24260.5998-0.2715-0.617-0.6464-0.27270.94650.36550.51020.0699-0.17730.91990.05080.381849.595-5.3309179.1412
71.0134-0.2033-1.01031.5816-0.02461.86180.0314-0.0712-0.2336-0.5194-0.3436-0.0744-0.2818-0.00390.15680.35270.006-0.12560.20040.0240.335234.5007-11.2805169.1172
80.3966-0.00230.26330.62690.32160.3894-0.0778-0.29830.02490.46-0.20450.55640.855-0.56240.11330.4266-0.06360.02420.4553-0.03290.300421.1375-24.4946175.1451
90.1405-0.3006-0.13261.10990.14850.19040.15070.09760.1469-0.35140.2079-0.2298-0.341-0.00950.09010.56050.1161-0.24270.1433-0.26210.420134.6091-4.3906173.7479
102.2972-1.560.65762.1028-1.78511.909-0.2734-0.3268-0.2990.14550.23610.5299-0.51490.0461-0.07950.4339-0.0893-0.18180.1766-0.09170.480935.6823-9.2373176.2976
110.14990.06470.52520.05460.06144.11930.18510.19080.03840.69160.17950.0323-0.00951.2174-0.17950.72820.23820.13090.8329-0.16430.357752.9543-45.2453211.3298
120.1920.21750.07323.12350.21055.32750.00050.204-0.0005-0.00580.3202-0.53360.99380.29260.22170.17810.07950.12350.49370.07450.321147.4038-38.9282199.651
132.36610.9124-0.98750.4736-0.60262.0339-0.27340.00550.0197-0.29770.4578-0.29220.03510.5323-0.17740.4539-0.16890.05960.4079-0.10470.790452.9916-25.1358211.394
140.5244-0.78630.81032.1293-0.44721.97930.3862-0.1416-0.2351-0.2378-0.04650.07570.4922-0.32580.12620.2455-0.04930.0380.2366-0.05670.404738.4491-41.637210.4322
150.0669-0.0673-0.23810.10440.15630.9176-0.01730.0245-0.0740.24010.30480.00560.11910.40290.26520.55060.1013-0.15240.4307-0.04650.008745.7986-38.4583211.7775
161.64850.026-0.70772.0025-0.01132.0049-0.41260.16190.15990.4947-0.11240.16310.24320.09840.16280.3057-0.02740.00670.269-0.10640.242533.7691-39.5955218.679
172.1485-1.4726-1.37141.24041.09122.6260.0169-0.01930.0797-0.4457-0.30640.801-0.2287-0.41790.14870.3341-0.0173-0.01640.15860.010.266636.8863-35.9682201.8003
183.967-1.65540.26862.51431.41442.61220.3039-0.66380.69780.16160.4438-0.91380.03960.26970.16370.31820.0197-0.03170.54240.10820.289644.6944-28.3649217.2338
192.49030.10971.43471.5157-0.16042.82850.0486-0.64510.17460.7172-0.02210.08080.2832-0.43290.05370.97180.0024-0.17960.37210.0947-0.020231.3004-46.8251229.107
200.8157-0.09-0.45691.44590.74453.18970.2614-0.3175-0.23420.3323-0.1202-0.12520.6709-0.0613-0.1380.9971-0.0155-0.07470.5219-0.02310.006334.0754-45.2484241.2822
212.9389-0.01620.53913.38810.09674.1280.4213-0.03330.06340.2204-0.05590.41350.0735-0.2109-0.08920.55490.0278-0.02810.2695-0.08280.311931.5-33.4157240.7505
220.925-0.1453-0.29130.1028-0.1450.89940.119-0.07810.0334-0.12130.06490.12730.0722-0.3517-0.02930.17250.0317-0.15640.5045-0.16140.650422.3231-29.7283226.0448
232.72721.202-0.14082.01710.27692.9388-0.0381-0.11130.28460.1592-0.27090.111-0.23250.69360.26540.4085-0.0214-0.08060.37650.04650.22843.3693-32.2974227.386
240.5449-0.2742-0.19870.8350.90861.54970.0829-0.0734-0.15060.1899-0.33550.21050.3574-0.26060.02410.81990.1204-0.01970.0824-0.2335-0.005642.2041-41.1475234.2331
250.8712-0.0626-0.28010.77810.07750.7590.1936-0.0503-0.08180.15710.023-0.1593-0.316-0.31580.30160.42560.24960.1519-0.5367-0.4795-0.06334.5965-37.9885229.2837
261.23870.49220.4061.9336-0.47062.17360.13910.27420.1327-0.4548-0.037-0.13770.55480.7508-0.12420.37420.098-0.03720.4474-0.00920.232746.3537-36.4106221.995
270.95830.46650.14230.55040.89972.1282-0.29980.09870.12010.0848-0.12350.2765-0.10280.08180.13220.39240.0260.00420.2848-0.02660.289837.9599-26.7406235.5302
280.4151-0.6875-0.77762.41640.38992.1159-0.3747-0.01920.04350.41210.3425-0.24920.20640.3079-0.00440.2757-0.1820.20060.6782-0.13870.28744.5119-29.7357233.1561
293.4196-0.4871.13123.35790.3673.94520.0050.1898-0.06040.06150.2630.65810.4028-1.0769-0.22340.2121-0.0581-0.03780.54490.16310.314726.39-33.0397218.1032
300.2915-0.1977-0.62690.9043-0.46912.33340.15640.2439-0.4546-0.18830.15440.70480.0531-0.99990.07350.3685-0.0699-0.17860.61410.18190.56656.468942.5916213.6297
310.13860.0940.01860.5572-1.00172.2344-0.28420.3382-0.0875-0.54670.35520.97390.3417-0.52590.00780.6363-0.1417-0.2280.7776-0.02481.33055.62225.0254214.5639
322.8646-1.0354-0.66213.25570.39183.10750.191-0.00080.16370.1842-0.11790.2010.3478-0.295-0.05750.3236-0.02110.0830.21140.00350.296217.864639.4244221.6804
331.2002-0.83310.51272.6295-1.22323.01960.010.3744-0.2523-0.208-0.00830.38290.2358-0.2408-0.09890.346-0.0217-0.01660.3994-0.00250.443417.334834.283214.2911
343.6085-4.62081.50256.4455-1.82251.77010.08110.5191-0.1926-0.1322-0.4572-0.39540.5631.09150.25480.5091-0.16010.05360.6289-0.06550.474221.031245.0941234.8923
354.2431-2.54912.20434.4029-2.25352.9956-0.3690.0807-0.1310.2498-0.3018-0.4136-0.12440.11680.36630.7557-0.0610.37440.6314-0.1550.542927.797238.4178249.1
362.7914-0.31680.2352.6548-0.76772.65030.00970.0322-0.35060.1229-0.3287-0.4469-0.33890.61350.0470.5176-0.06470.12560.5270.08140.356424.889227.2844246.5423
371.7674-0.4477-0.04390.9023-0.13650.22580.21250.1781-0.13850.19710.198-0.05250.17260.592-0.08110.4030.24230.1431.0040.14051.125135.238928.256231.3348
383.08221.033-0.33021.630.89711.7076-0.35290.3557-0.26470.0234-0.0487-0.10.1058-0.18210.20990.302-0.04350.07660.3569-0.0390.471817.483432.005236.928
390.61790.3431-1.21783.70090.79443.34440.03211.09870.054-0.5386-0.12480.12990.1952-0.81450.26020.5296-0.18610.03110.56560.03240.44710.814332.8705228.5002
400.24620.32970.23381.846-0.13522.54070.0123-0.17-0.8852-0.0044-0.03630.16090.2375-0.31280.06210.6639-0.01060.15020.38880.11030.53517.392121.6101240.8788
411.80660.3832-1.64392.6843-1.14692.6238-0.11770.1773-0.8373-0.2333-0.1691-0.23440.1419-0.33030.04750.4654-0.09430.07590.40760.10110.568626.006229.57225.976
420.0303-0.1746-0.14091.1140.38870.8445-0.1360.3446-0.8734-0.1468-0.3310.03720.0253-0.28280.23180.4546-0.00150.20790.25570.03120.516216.6987-0.1118263.5149
432.8602-0.6169-1.0451.63390.73672.8572-0.33360.08750.3176-0.1585-0.52150.0183-0.4552-0.61810.03310.37890.09060.05280.2750.02740.509714.540811.5643255.1151
441.07490.50840.99250.41930.37430.97170.0482-0.35090.0392-0.0244-0.39120.3167-0.2244-0.4419-0.1440.00960.1285-0.22250.9680.08820.468411.4072-3.316244.4886
451.8329-0.5194-1.09331.0310.09231.4631-0.0745-0.03170.26650.32070.22810.2357-0.2473-0.0446-0.11080.27190.01980.06690.2067-0.00750.368725.20284.133254.9341
464.5608-0.01471.56322.7330.43060.60470.06130.1790.2036-0.06630.1076-0.99470.2291.25720.15010.09890.17360.03950.6608-00.797642.6334-1.6947252.2585
470.40.9069-0.37092.0893-0.99530.9456-0.3446-0.0175-0.4124-0.28110.0899-0.71570.74030.8898-0.04360.56730.43790.24580.9285-0.35910.793945.72921.5858255.9416
480.1684-0.3094-0.24891.88540.14250.340.16310.08280.0054-0.50540.0306-0.2543-0.1774-0.1819-0.05660.470.02120.1250.37490.01430.277522.49657.3202247.778
490.03960.02230.01350.00970.0122-0.00060.445-0.26670.65680.30890.3307-0.3564-0.410.0685-0.54150.4949-0.00830.1340.39390.0050.677229.139417.3736254.7605
503.8972.8222-0.18715.32380.38632.14190.24120.0722-0.0349-0.18240.06790.1118-0.1256-0.0830.02310.23720.10610.080.24280.15820.521421.6637-5.4547245.3909
510.8412-0.6613-0.6892.86840.55982.16010.07320.38290.05930.03820.5334-0.53460.1520.3327-0.05970.23770.0969-0.33810.726-0.24510.842545.4891-9.7044258.6342
521.9338-0.02520.19731.25090.39014.40880.01790.0275-0.4004-0.03490.1743-0.2870.3920.9199-0.22490.38980.030.01480.4825-0.0950.333244.4523-20.3109248.7937
531.16731.5512-0.54342.1221-1.05581.7088-0.03460.13130.0411-0.2335-0.3189-0.7309-0.23430.54690.00330.4291-0.04570.11040.98840.18220.384544.7719-4.3357239.1938
545.5726-0.3174-0.70061.55831.11160.9193-0.1062-0.46110.34290.09740.378-0.02170.5126-0.0007-0.180.21250.02930.00750.2364-0.01680.142834.992-13.3086252.274
550.5872-0.32410.2491.3461-0.00721.04370.0769-0.40810.03130.32870.42270.3276-0.1597-0.38330.81290.33230.04660.39870.8113-0.24690.054419.3014-8.6285258.219
566.71523.2432-1.9592.6382-0.86990.62890.2315-0.26420.40540.3203-0.19340.47780.0626-0.401-0.36350.35810.10250.27770.54510.1170.343717.0834-14.2774260.2976
571.1842-0.7377-0.30431.54631.20980.97120.1460.1536-0.2654-0.1628-0.3984-0.22290.1860.03340.19270.30110.01590.06510.3134-0.04670.232833.9647-17.5256246.3209
581.52421.6253-0.66225.7011-0.99471.97020.09260.0643-0.0625-0.1162-0.2615-0.44340.11380.41430.09730.2248-0.07570.09520.3878-0.09430.361432.716-3.5598242.7511
591.172-0.8023-1.16311.83440.35632.07870.1580.5018-0.5993-0.4566-0.40450.79240.3516-0.24130.34921.2428-0.1532-0.53320.5116-0.24930.556415.758723.3063166.4786
603.7108-0.45641.0094.37241.10052.9666-0.37430.2899-0.3525-0.6453-0.42590.99360.0797-0.38290.30780.70130.1875-0.14110.5459-0.17030.468222.559810.6972167.5531
610.81010.32140.96820.4063-0.14112.13970.33650.2107-0.50140.20390.21620.55970.221-0.7791-0.00410.3058-0.2160.27490.8111-0.25791.377311.450111.7995183.5627
621.0704-0.5820.8150.73260.30791.95570.0806-0.45850.1317-0.85950.1610.0482-0.2594-0.2485-0.09710.82630.1462-0.15050.3272-0.21460.401225.798521.2548174.0784
631.26630.536-0.43442.313-1.35280.82310.14550.0270.4525-0.01180.5039-0.8062-1.07211.036-0.39011.12890.0127-0.04290.7677-0.27940.631537.364735.1049181.872
641.8461-1.29210.67073.94361.55532.70370.12170.2343-0.1228-0.23030.35310.025-0.26710.1031-0.2380.47210.0352-0.04560.3268-0.02630.37528.624414.1104175.9958
656.6483-1.704-0.37443.62990.96474.12920.4594-0.393-0.27950.06750.04490.4609-0.0353-0.7239-0.17160.4415-0.02080.02510.3672-0.0050.496918.143319.5575185.7241
661.8676-0.8276-2.05982.47562.02184.1337-0.03070.0035-0.5533-0.95750.4411-0.41990.08030.8206-0.45770.6518-0.0194-0.05810.3519-0.09180.811831.482843.6572183.4169
671.45420.256-0.45081.7782-0.94451.1557-0.12780.3470.1254-0.2527-0.3455-0.1706-0.19420.08660.11740.5910.05390.01240.3586-0.14230.460224.507844.9803195.4086
680.28230.1283-0.29622.16420.31340.43190.410.51520.04150.1735-0.02890.01440.56310.2083-0.36910.28370.0832-0.22390.7331-0.28480.786936.333330.8338197.6075
690.9173-0.0727-0.28271.5860.37350.74970.44050.1080.3437-0.21880.10180.2609-0.1897-0.00960.47720.8310.3337-0.1290.0754-0.17810.471318.888835.6646186.6403
700.18930.2779-0.04650.51870.22980.8214-0.13450.13430.0397-0.07870.2617-0.2375-0.19110.3443-0.13850.71110.0604-0.14450.6468-0.27080.165629.330736.5395189.9383
710.26210.0207-0.2020.1626-0.11570.23390.18650.5218-0.4946-0.4996-0.03630.41940.3609-0.33210.20471.03810.1872-0.68820.6167-0.47220.574211.682626.5012175.5898
721.0305-0.02920.24891.09230.29921.9645-0.0439-0.00150.2314-0.09490.14690.0509-0.05090.5341-0.04640.37530.0752-0.01230.3862-0.01860.324121.512732.6759194.2654
731.0104-1.1083-0.91631.21280.99820.83090.0243-0.07490.0221-0.0527-0.00510.024-0.1402-0.01690.09180.40060.1447-0.14910.5451-0.06630.51610.51641.3663193.0489
744.2221-1.0223-1.19313.4033-0.03642.8580.0061-0.07660.3094-0.3399-0.0347-0.6973-0.26660.3172-0.07160.54630.0050.02640.3761-0.09470.453830.483724.8132189.5769
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1014 THROUGH 1074 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1075 THROUGH 1148 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 1014 THROUGH 1023 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 1024 THROUGH 1031 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1032 THROUGH 1046 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 1047 THROUGH 1055 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1056 THROUGH 1087 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 1088 THROUGH 1099 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 1100 THROUGH 1125 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 1126 THROUGH 1147 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 1014 THROUGH 1028 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 1029 THROUGH 1046 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 1047 THROUGH 1055 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 1056 THROUGH 1074 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 1075 THROUGH 1087 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 1088 THROUGH 1108 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 1109 THROUGH 1132 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 1133 THROUGH 1148 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 1014 THROUGH 1023 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 1024 THROUGH 1031 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 1032 THROUGH 1046 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 1047 THROUGH 1055 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 1056 THROUGH 1064 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 1065 THROUGH 1074 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 1075 THROUGH 1087 )
26X-RAY DIFFRACTION26CHAIN D AND (RESID 1088 THROUGH 1108 )
27X-RAY DIFFRACTION27CHAIN D AND (RESID 1109 THROUGH 1125 )
28X-RAY DIFFRACTION28CHAIN D AND (RESID 1126 THROUGH 1138 )
29X-RAY DIFFRACTION29CHAIN D AND (RESID 1139 THROUGH 1148 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 1014 THROUGH 1045 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 1046 THROUGH 1055 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 1056 THROUGH 1108 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 1109 THROUGH 1148 )
34X-RAY DIFFRACTION34CHAIN F AND (RESID 1012 THROUGH 1021 )
35X-RAY DIFFRACTION35CHAIN F AND (RESID 1022 THROUGH 1028 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 1029 THROUGH 1046 )
37X-RAY DIFFRACTION37CHAIN F AND (RESID 1047 THROUGH 1055 )
38X-RAY DIFFRACTION38CHAIN F AND (RESID 1056 THROUGH 1087 )
39X-RAY DIFFRACTION39CHAIN F AND (RESID 1088 THROUGH 1108 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 1109 THROUGH 1132 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 1133 THROUGH 1148 )
42X-RAY DIFFRACTION42CHAIN G AND (RESID 1014 THROUGH 1028 )
43X-RAY DIFFRACTION43CHAIN G AND (RESID 1029 THROUGH 1045 )
44X-RAY DIFFRACTION44CHAIN G AND (RESID 1046 THROUGH 1055 )
45X-RAY DIFFRACTION45CHAIN G AND (RESID 1056 THROUGH 1087 )
46X-RAY DIFFRACTION46CHAIN G AND (RESID 1088 THROUGH 1092 )
47X-RAY DIFFRACTION47CHAIN G AND (RESID 1093 THROUGH 1099 )
48X-RAY DIFFRACTION48CHAIN G AND (RESID 1100 THROUGH 1125 )
49X-RAY DIFFRACTION49CHAIN G AND (RESID 1126 THROUGH 1132 )
50X-RAY DIFFRACTION50CHAIN G AND (RESID 1133 THROUGH 1148 )
51X-RAY DIFFRACTION51CHAIN H AND (RESID 1014 THROUGH 1028 )
52X-RAY DIFFRACTION52CHAIN H AND (RESID 1029 THROUGH 1045 )
53X-RAY DIFFRACTION53CHAIN H AND (RESID 1046 THROUGH 1055 )
54X-RAY DIFFRACTION54CHAIN H AND (RESID 1056 THROUGH 1084 )
55X-RAY DIFFRACTION55CHAIN H AND (RESID 1085 THROUGH 1094 )
56X-RAY DIFFRACTION56CHAIN H AND (RESID 1095 THROUGH 1099 )
57X-RAY DIFFRACTION57CHAIN H AND (RESID 1100 THROUGH 1132 )
58X-RAY DIFFRACTION58CHAIN H AND (RESID 1133 THROUGH 1146 )
59X-RAY DIFFRACTION59CHAIN I AND (RESID 1014 THROUGH 1028 )
60X-RAY DIFFRACTION60CHAIN I AND (RESID 1029 THROUGH 1046 )
61X-RAY DIFFRACTION61CHAIN I AND (RESID 1047 THROUGH 1055 )
62X-RAY DIFFRACTION62CHAIN I AND (RESID 1056 THROUGH 1087 )
63X-RAY DIFFRACTION63CHAIN I AND (RESID 1088 THROUGH 1099 )
64X-RAY DIFFRACTION64CHAIN I AND (RESID 1100 THROUGH 1132 )
65X-RAY DIFFRACTION65CHAIN I AND (RESID 1133 THROUGH 1148 )
66X-RAY DIFFRACTION66CHAIN J AND (RESID 1014 THROUGH 1028 )
67X-RAY DIFFRACTION67CHAIN J AND (RESID 1029 THROUGH 1042 )
68X-RAY DIFFRACTION68CHAIN J AND (RESID 1043 THROUGH 1055 )
69X-RAY DIFFRACTION69CHAIN J AND (RESID 1056 THROUGH 1074 )
70X-RAY DIFFRACTION70CHAIN J AND (RESID 1075 THROUGH 1084 )
71X-RAY DIFFRACTION71CHAIN J AND (RESID 1085 THROUGH 1098 )
72X-RAY DIFFRACTION72CHAIN J AND (RESID 1099 THROUGH 1125 )
73X-RAY DIFFRACTION73CHAIN J AND (RESID 1126 THROUGH 1132 )
74X-RAY DIFFRACTION74CHAIN J AND (RESID 1133 THROUGH 1148 )

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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://pdbjlvh1.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