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- PDB-5jj3: Refined Structure of the Mature Virion Conformation of P22 Portal... -

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基本情報

登録情報
データベース: PDB / ID: 5jj3
タイトルRefined Structure of the Mature Virion Conformation of P22 Portal Protein
要素Portal protein
キーワードVIRAL PROTEIN / portal protein / dodecamer / packaging motor / procapsid
機能・相同性viral DNA genome packaging, headful / Phage P22-like portal protein / Phage P22-like portal protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / virion assembly / Portal protein
機能・相同性情報
生物種Enterobacteria phage P22 (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 7 Å
データ登録者Lokareddy, R.K. / Sankhala, R.S. / Cingolani, G.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100888 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA56036 米国
引用ジャーナル: Nat Commun / 年: 2017
タイトル: Portal protein functions akin to a DNA-sensor that couples genome-packaging to icosahedral capsid maturation.
著者: Lokareddy, R.K. / Sankhala, R.S. / Roy, A. / Afonine, P.V. / Motwani, T. / Teschke, C.M. / Parent, K.N. / Cingolani, G.
履歴
登録2016年4月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年2月8日Provider: repository / タイプ: Initial release
改定 1.12017年2月15日Group: Database references
改定 1.22017年9月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月4日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年9月27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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Portal protein
B: Portal protein
C: Portal protein
D: Portal protein
E: Portal protein
F: Portal protein
G: Portal protein
H: Portal protein
I: Portal protein
J: Portal protein
K: Portal protein
L: Portal protein


分子量 (理論値)分子数
合計 (水以外)993,95312
ポリマ－993,95312
非ポリマー00
水00
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 area149200 Å2
ΔGint-558 kcal/mol
Surface area378100 Å2
手法PISA
単位格子
Length a, b, c (Å)409.043, 409.043, 260.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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要素

#1: タンパク質
Portal protein / Gene product 1 / Gp1 / Head-to-tail connector


分子量: 82829.375 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage P22 (ファージ)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P26744

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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: 5.47 Å3/Da / 溶媒含有率: 77.52 %
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: 5.6
詳細: 30% tert-butanol, 70 mM sodium chloride, 2.5% PEG400 in 0.1 M sodium acetate

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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: SSRL / ビームライン: BL14-1 / 波長: 0.9 Å
検出器タイプ: RAYONIX MX325HE / 検出器: CCD / 日付: 2015年2月14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: 0.9 Å / 相対比: 1
反射解像度: 7→15 Å / Num. obs: 33729 / % possible obs: 98.8 % / 冗長度: 3.9 % / Net I/σ(I): 19.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
HKL-2000データ削減
HKL-2000データスケーリング
PHENIX(1.10.1_2155: ???)位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3LJ5

3lj5


解像度: 7→14.993 Å / SU ML: 0.98 / 交差検証法: FREE R-VALUE / σ(F): 0.66 / 位相誤差: 28.1
Rfactor反射数%反射
Rfree0.2597 1561 5.19 %
Rwork0.239 --
obs0.2401 30078 99.05 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 7→14.993 Å
タンパク質核酸リガンド溶媒全体
原子数64536 0 0 0 64536
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00465784
X-RAY DIFFRACTIONf_angle_d1.01489148
X-RAY DIFFRACTIONf_dihedral_angle_d12.28540056
X-RAY DIFFRACTIONf_chiral_restr0.0579636
X-RAY DIFFRACTIONf_plane_restr0.00711928
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.0001-7.20170.39851310.40782588X-RAY DIFFRACTION98
7.2017-7.42880.41791300.3832563X-RAY DIFFRACTION99
7.4288-7.68750.36371310.35812605X-RAY DIFFRACTION99
7.6875-7.98640.34861310.30922581X-RAY DIFFRACTION99
7.9864-8.33810.29411290.28592622X-RAY DIFFRACTION99
8.3381-8.76120.25781320.23292587X-RAY DIFFRACTION99
8.7612-9.28580.231290.20712611X-RAY DIFFRACTION99
9.2858-9.9640.21881310.1912633X-RAY DIFFRACTION99
9.964-10.89710.21521430.1872576X-RAY DIFFRACTION99
10.8971-12.32010.19942450.15942496X-RAY DIFFRACTION99
12.3201-14.99320.24091290.19032655X-RAY DIFFRACTION99
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)
10.6712-0.12960.11580.3853-0.54672.2647-0.427-0.012-0.0767-1.25590.11310.69120.44420.0942-1.49140.7593-0.2579-0.44140.9952-0.20560.4338-119.1664-40.9141-120.1722
21.5867-0.54860.53990.9404-0.13132.627-0.3280.97030.0894-0.15680.30820.4051-0.407-0.70690.65361.1172-0.6872-0.34321.2014-0.43261.1022-114.325-29.3673-132.4508
32.383-0.4256-0.24614.013-1.26873.06790.3162-0.6424-1.32570.3796-0.6525-0.0831.0872-0.44010.0681.1854-0.27510.26721.2879-0.11961.428-132.6932-84.912-102.974
40.65350.29570.10860.2007-0.22390.7514-0.02320.6789-0.28220.2310.0481-0.4731-0.5564-0.00610.60761.243-0.8998-0.44261.5019-0.51960.5965-113.7152-20.7104-117.319
53.62240.84220.22431.7313-0.38080.9841-0.06660.37040.6392-0.42930.39610.17050.0356-0.5158-0.22390.5184-0.26780.02921.24450.2551.2822-126.5624-8.1735-93.4
61.79091.6030.3781.44910.41841.85740.6072-0.2626-0.1167-0.1244-0.2659-0.9786-0.58520.5583-0.09740.7912-0.0893-0.48572.1360.44791.0066-106.134482.2199-26.2849
70.6486-0.3099-0.71651.1869-0.94322.5050.23150.9387-1.3572-0.79131.1939-0.52640.86340.20483.25250.7451-0.7276-0.43610.4469-1.38121.2594-94.9557-57.0611-113.9344
80.48250.38010.31150.84280.87111.55170.14730.36270.3948-0.4670.10890.4894-1.27380.24650.52881.0398-0.2214-0.4760.61110.02920.2684-95.1421-29.1679-104.577
90.6963-0.14880.00890.6962-0.13830.6550.1198-0.39260.0035-0.2614-0.17960.15940.2216-0.0416-0.40510.474-0.58550.13111.0559-0.59280.6972-88.6345-37.4006-116.3219
101.53190.1365-0.9112.1444-1.39571.1451-0.16810.44780.5791-0.42761.06740.00690.1374-0.17440.20161.3188-0.26330.08811.0781-0.41780.6896-81.0293-32.7596-120.2409
112.2889-1.7628-0.40321.471102.47790.33440.7194-1.14290.78880.78730.67580.7387-0.41741.92680.7777-0.02570.63610.8931-0.58661.295-120.8609-84.4823-110.5161
122.698-1.1547-0.10571.70190.79642.80440.11120.2123-1.1294-0.128-0.88130.22410.87160.5393-0.9120.95130.75910.04991.90980.32441.5987-118.0394-83.0927-100.9355
130.43120.5156-0.17530.7071-0.2310.06180.62980.280.2331-0.0520.0715-0.3329-0.42070.83641.06120.826-0.5113-0.32531.3071-1.63710.8867-86.3638-23.8204-106.3023
142.90521.58380.74181.52740.01441.1606-0.10850.13011.0085-0.00360.28410.4717-0.5549-0.37720.99080.5983-0.5951-0.59130.512-0.33192.287-107.0404-8.672-90.8576
151.2761-0.0038-0.26481.62811.24151.10120.2657-0.10130.13420.3315-0.19630.214-0.20610.68290.02991.66970.01450.27760.9525-0.34020.7074-107.674679.6369-18.0717
161.56640.49390.14441.6233-0.56010.9323-0.1674-0.274-0.8190.38710.8899-0.77750.0802-0.05290.20370.4364-0.0174-0.3061.1242-0.3210.5479-74.2176-48.9957-92.983
171.74010.0530.57060.7167-1.25942.25720.70580.6964-0.4545-0.12010.0255-0.05150.65460.9710.33410.7816-0.2410.39471.3838-0.55270.7288-58.6647-40.9673-93.8613
184.3427-0.1032-0.53921.098-0.24860.723-0.57030.9964-0.9019-0.47410.52620.87960.9243-0.8147-0.1801-0.16440.691-0.11650.9367-0.51661.9693-105.6189-85.5624-106.5532
191.56580.3861-0.65421.0547-0.69941.2751-0.007-0.4584-0.27010.12220.05770.21310.33390.00090.75320.37530.4813-0.11480.7656-0.94290.6497-88.7588-58.4868-90.4608
202.70920.09130.86351.3694-0.051.188-0.15150.12280.8156-0.43630.1342-0.1615-0.1159-0.2258-0.00090.5978-0.1664-0.8670.62910.13330.9909-91.5448-12.1539-79.346
211.3847-0.6008-0.92860.27540.30530.21270.56030.374-0.5-0.5990.35550.71550.4980.13233.58311.0167-0.79490.74841.87891.86870.8284-113.345177.637-11.8528
220.65440.35210.13850.9623-0.28331.4894-0.31110.2527-0.0029-0.28930.3788-0.67860.53460.3918-0.25650.50450.24280.37031.644-0.5049-0.0961-68.1591-57.2151-67.3679
231.49940.9173-0.59661.6564-1.82381.94260.05960.3193-0.2696-0.6191-0.5704-0.57440.50230.16660.32911.06330.3955-0.08281.369-0.51381.3779-53.0521-51.6937-60.419
242.4369-0.4065-0.85980.9679-0.66563.0277-0.398-0.0101-1.2192-0.4411-1.0821-0.00431.02990.0522-4.00921.2310.1872-0.44450.3382-0.00061.0922-97.5194-88.082-91.858
252.2153-0.05071.02790.53080.28152.9965-1.1110.43530.89880.4252-0.0622-0.2657-0.59661.3179-4.65451.3705-0.66130.080.885-0.54370.2201-77.3899-25.4659-59.8825
260.0194-0.0629-0.03540.1344-0.29090.4051-0.05910.062-0.1617-0.25510.0847-0.2544-0.27010.2911-0.14631.1857-0.17210.59392.01920.49661.1422-121.661276.676-9.3846
271.5976-0.8342-0.71461.22620.70071.1642-0.6358-1.2767-0.20830.86540.58840.70670.28030.74120.19071.6560.9796-0.01451.1203-0.0071.5622-73.8258-79.7344-37.4092
286.00792.0581-0.40931.6628-0.95122.4632-0.40031.3515-1.8071-0.54180.047-0.64811.01191.20421.94660.13880.06420.5732.04790.60050.2378-83.8104-76.9818-59.4
291.50910.52630.86090.60240.44561.8567-0.5188-0.22860.36280.07760.465-0.0131-0.34750.7897-0.39061.05440.2911-0.09681.3226-0.3580.4168-74.995-57.1328-38.3847
301.7241-0.4445-0.18332.97422.14333.3915-0.3543-0.0479-0.26580.8337-0.35330.49890.79670.8181-0.12861.04540.5155-0.24052.0664-0.27581.0478-62.987-59.3009-27.646
311.2279-0.26750.25150.9173-0.44660.2683-0.08350.17940.027-0.24270.2521-0.15750.5898-0.15870.81041.80210.784-0.11410.5694-0.01180.6366-84.0574-84.0882-61.5339
322.5958-0.4034-0.62191.3537-1.46722.06360.3742-0.3036-1.043-0.4149-0.96620.53721.4801-0.67490.25011.24880.07280.04341.64290.5491.0358-99.2816-90.6062-77.2691
332.13621.14431.65771.2383-0.27363.2348-0.5887-0.55120.47350.5437-0.9789-0.0743-0.59730.2471-3.57991.74380.09340.62391.5693-0.39280.2507-76.6147-48.2819-29.9711
343.9899-0.78330.29462.49940.58753.7951-0.58580.35111.036-0.2780.4745-0.5804-0.35330.05680.28590.9635-0.194-0.06431.0732-0.27530.7189-86.8453-23.7073-43.591
351.9182-1.8652-0.15916.47861.65851.799-0.14110.11210.02440.02430.1070.0976-0.1828-1.23840.20470.13920.01720.71741.7431-0.2161.0062-130.100977.0811-11.0603
360.8425-0.1127-0.23890.42870.76882.29330.4297-0.03260.10040.39050.7085-0.72141.60420.16084.14040.66920.50910.87881.73290.39310.0837-96.8939-71.2706-24.7068
371.02681.2814-0.0541.31710.19792.1768-0.7688-0.8585-0.25270.46890.39330.69460.26750.90460.08471.56770.56170.45631.49870.20350.9782-93.6751-69.1316-7.6095
380.56840.2181.27991.5665-0.34523.13141.07070.7465-0.0616-0.38661.03110.31570.73190.60735.28451.2808-0.51190.92380.8320.95481.1186-94.7171-98.4117-66.7355
391.5994-1.1526-0.14674.57282.73734.54020.67220.4043-0.79910.6431-1.25440.31591.33740.1043-0.21351.7067-0.002-0.17061.39920.28710.6003-103.7033-93.8741-67.2963
400.17760.2198-0.19660.69450.64212.2865-0.3679-0.3941-0.40980.7848-0.89750.3831-0.0589-0.1888-3.0861.03840.85541.0821.9607-0.18010.68-100.3243-53.9598-13.0724
410.6214-0.2971-0.4810.53130.12451.7589-0.1731-0.30770.06610.55730.12820.0592-0.05850.1609-0.88390.7756-0.03730.86811.2573-0.84480.4266-98.8952-28.5814-28.84
420.8784-0.5342-0.59235.86880.70291.5089-0.6316-0.4303-0.04980.33380.8961-0.1301-0.58140.0579-0.21640.9119-0.4072-0.59892.8884-0.12090.7718-136.617478.7438-16.5286
430.91250.1674-0.36230.5438-0.27561.4862-0.3804-0.4866-0.51050.82510.2403-0.30490.73620.7887-0.34650.86440.33170.41221.5270.6511.1548-123.2928-73.8723-22.3904
440.7050.5011-0.48010.3223-0.36841.1924-0.1414-0.2377-0.37240.61490.17150.1710.3441-0.90991.08641.75750.38991.39751.65720.11860.8599-127.8006-71.1403-4.3933
450.99350.2872-0.15613.4628-0.27825.89010.91860.58070.4175-0.56570.7954-0.08741.06791.48274.0581.3823-0.47561.03541.11830.65151.0132-106.1368-101.8344-56.1319
461.0029-1.0068-0.04620.69190.64372.87750.09990.2423-0.2331-0.0667-0.2408-0.06820.3475-1.34780.30441.0567-0.37750.69591.29870.54341.4483-121.038-76.3097-36.0506
471.6548-0.9042-1.08041.49771.29272.33370.5079-0.02430.63720.15310.2029-0.3346-1.08490.4999-0.08540.5280.21610.87371.4529-1.20581.025-117.1552-30.9057-21.8056
481.3298-0.4836-0.02573.2796-0.57161.0825-0.4059-0.21720.1090.57260.7707-0.4958-0.54460.1347-0.25831.3796-0.7449-0.18062.5376-0.29940.4319-139.535981.2765-24.228
490.7575-0.03510.28080.1396-0.52011.7775-0.47950.4616-0.39950.8935-0.12860.97380.6385-0.43990.04280.9568-0.36960.54281.4054-0.0541.461-147.7992-72.2084-30.2796
501.06980.04060.37330.39620.31150.37070.2218-0.1957-0.2050.8841-0.19720.31070.74290.19941.45740.51660.43881.42891.64230.17172.3758-153.4967-75.2571-17.4247
510.49120.55270.35220.87660.6583.7945-0.99040.5842-0.426-0.789-0.1875-0.4412-0.4491-0.8923-3.71161.85930.0921.59961.02390.02141.3034-166.8578-59.2633-14.877
520.4705-0.06820.22280.7226-1.10071.7258-0.01670.5703-0.7285-0.3064-0.26511.16810.1398-0.38120.13310.5285-0.39660.2351.6153-0.0851.7176-133.7456-84.6096-44.5983
530.7807-0.0066-0.11591.1436-0.35320.7552-0.6608-0.71350.61111.3828-0.02060.5464-0.2897-0.2258-2.66190.20660.88731.2291.1647-1.4161.1974-136.5067-30.3854-24.4294
542.35211.4854-0.21282.0164-0.56360.81190.43990.24430.1866-0.011-0.12240.3478-0.2502-0.4753-0.09151.65460.1510.15942.88310.1552-0.0609-137.699983.7563-32.5178
552.4494-0.2909-0.10040.2252-0.78452.85990.1110.5353-0.52880.37790.11651.16440.62470.40480.19390.6503-0.23390.25051.46610.08351.7104-168.7424-65.1479-46.2647
561.67081.00850.42981.4851-0.26771.7650.1381-0.4302-0.9547-0.0559-0.20630.7899-0.01220.85680.27521.1898-0.19250.64832.4248-0.18762.596-186.2121-57.3622-37.7358
571.5291-0.1909-0.30020.6714-0.26211.1976-0.29750.2509-0.5770.19040.01240.46021.035-0.347-0.06821.1743-0.86310.22551.1504-0.35862.5988-146.6326-90.4168-57.5516
581.1389-0.14190.57590.4025-0.36581.3580.0121-1.2457-0.34160.1780.50030.83280.1476-0.92962.13750.70791.13520.36011.21-0.28362.113-160.2253-33.8974-38.5545
591.6689-0.96270.0991.6016-0.32161.2372-0.163-0.18370.73680.90240.34170.4556-0.109-0.4328-0.29021.61820.07670.00961.6948-0.2970.6379-132.523184.2408-38.5668
601.8443-1.35071.04861.0239-0.58271.3297-0.04390.0918-0.83350.0241-0.11951.2820.1189-0.52620.27450.87060.1712-0.16010.9367-0.84832.7064-181.4864-66.7888-81.8553
614.6793-1.6224-0.49892.748-0.413.4775-0.1060.2859-1.8021-0.1126-0.0711.03271.0957-0.79591.06280.65550.13830.69791.3336-0.31991.6083-161.6911-73.8344-69.6603
621.809-0.1217-0.83950.3299-0.73232.22720.26480.51010.39720.04150.21190.5229-0.5271-0.86210.53250.6990.0556-0.28342.0988-0.38711.5634-177.0921-48.3775-69.4615
632.7509-0.8006-0.06190.5581-0.10211.1524-0.1098-0.8808-0.38290.07570.1737-0.20590.10760.0193-0.2340.66120.4268-0.29681.6481-0.28643.2507-192.7441-46.4267-72.3538
641.07130.3790.00390.7244-0.17620.0742-0.0840.35350.0397-0.09610.2320.6448-0.24290.20951.26871.3706-0.9368-1.04061.3759-0.8492.3248-181.9702-55.8796-80.2771
652.87311.2344-1.220.68010.15353.4129-0.2770.8239-1.6588-1.0339-0.18-0.37811.20471.20070.83011.28610.1054-0.091.17330.05742.0671-147.7934-99.0233-66.9201
660.93850.2294-0.68270.0929-0.3441.55280.4289-0.07530.5142-0.27620.0297-0.56520.3866-0.38960.50810.606-0.7085-0.06781.2594-0.13832.0855-159.3782-65.5556-71.7027
670.6286-0.1343-0.34640.3518-0.13010.6228-0.01-0.5353-0.04680.1149-0.07791.41140.1068-0.05690.30640.77981.12330.07111.4682-0.20631.5852-159.4954-21.5401-53.233
681.0973-0.08280.26661.9197-0.63070.1346-0.322-0.37410.18260.55060.64870.2345-0.251-0.4589-0.24611.86881.01891.28662.65410.02660.8784-123.813686.5568-41.5065
692.4186-0.8587-0.32750.2674-0.06682.1608-0.0075-0.559-0.2842-1.0647-0.52871.3320.0889-0.49920.26670.94430.0041-0.64691.2654-0.27521.7883-171.2798-44.3708-100.8707
702.5865-0.409-0.05831.5594-0.67850.72840.22790.3598-0.0046-0.2986-0.9054-1.55070.3709-0.0914-0.10471.1926-0.3208-0.37161.4966-0.3890.5174-153.5362-71.3317-86.9273
713.9248-0.2481-0.30252.4085-1.67264.0449-0.1383-0.61020.32450.9238-0.35180.8769-0.43540.2589-0.28640.75620.24070.25281.04970.0190.9596-156.8212-15.554-71.6835
721.15031.510.87695.33490.26850.90950.2267-0.9548-0.093-0.2664-1.25380.0015-0.3388-0.35170.20410.5880.17260.70882.145-0.25210.9268-115.406686.2545-39.8015
732.5108-1.1864-0.17970.5427-0.06163.8759-0.5252-0.3865-0.353-1.17320.02750.97230.7940.2723-0.75261.4727-0.2184-0.37480.9298-0.77741.0597-144.8449-57.5232-115.9174
740.68980.20580.10190.6726-0.0250.37480.120.24550.5439-0.32020.15280.9145-0.71820.43160.40551.201-0.5855-0.20190.82520.00351.2379-147.0077-33.8209-113.6228
751.2710.04520.32531.14040.76870.57370.103-0.0857-0.3101-0.36870.4169-0.18620.3469-0.6730.57041.7149-0.3054-1.28071.90260.01371.5058-152.019-28.1412-128.0011
762.23480.33471.13371.1769-0.38652.2480.5273-1.4346-1.4750.001-0.7838-0.22070.2255-0.2007-0.27141.2779-0.36580.3331.4436-1.09390.3545-142.8533-76.0482-102.083
771.3103-0.9421-0.05380.69230.08543.0002-0.14120.3133-0.1667-0.53280.0332-1.0795-0.5769-1.2570.05750.6581-0.5383-0.23981.40250.18491.3197-143.1699-22.1353-113.9368
781.9184-0.3568-0.97120.8331-0.72121.75910.1175-0.19640.99670.57760.25010.1071-0.57710.12220.03270.84160.18040.23950.30790.16042.3374-144.8001-10.6351-86.387
791.23261.0098-0.22092.6097-0.51280.70740.3489-0.4079-0.3865-0.8864-0.5626-0.7396-0.8134-0.50420.40080.30870.32860.13211.807-0.13851.3618-108.921884.6419-34.1545
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 318 )
3X-RAY DIFFRACTION3chain 'A' and (resid 319 through 427 )
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 515 )
5X-RAY DIFFRACTION5chain 'A' and (resid 516 through 609 )
6X-RAY DIFFRACTION6chain 'A' and (resid 610 through 715 )
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 73 )
8X-RAY DIFFRACTION8chain 'B' and (resid 74 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 180 )
10X-RAY DIFFRACTION10chain 'B' and (resid 181 through 318 )
11X-RAY DIFFRACTION11chain 'B' and (resid 319 through 370 )
12X-RAY DIFFRACTION12chain 'B' and (resid 371 through 427 )
13X-RAY DIFFRACTION13chain 'B' and (resid 428 through 515 )
14X-RAY DIFFRACTION14chain 'B' and (resid 516 through 609 )
15X-RAY DIFFRACTION15chain 'B' and (resid 610 through 715 )
16X-RAY DIFFRACTION16chain 'C' and (resid 9 through 180 )
17X-RAY DIFFRACTION17chain 'C' and (resid 181 through 318 )
18X-RAY DIFFRACTION18chain 'C' and (resid 319 through 370 )
19X-RAY DIFFRACTION19chain 'C' and (resid 371 through 515 )
20X-RAY DIFFRACTION20chain 'C' and (resid 516 through 609 )
21X-RAY DIFFRACTION21chain 'C' and (resid 610 through 715 )
22X-RAY DIFFRACTION22chain 'D' and (resid 9 through 180 )
23X-RAY DIFFRACTION23chain 'D' and (resid 181 through 318 )
24X-RAY DIFFRACTION24chain 'D' and (resid 319 through 427 )
25X-RAY DIFFRACTION25chain 'D' and (resid 428 through 609 )
26X-RAY DIFFRACTION26chain 'D' and (resid 610 through 715 )
27X-RAY DIFFRACTION27chain 'E' and (resid 9 through 40 )
28X-RAY DIFFRACTION28chain 'E' and (resid 41 through 72 )
29X-RAY DIFFRACTION29chain 'E' and (resid 73 through 180 )
30X-RAY DIFFRACTION30chain 'E' and (resid 181 through 281 )
31X-RAY DIFFRACTION31chain 'E' and (resid 282 through 370 )
32X-RAY DIFFRACTION32chain 'E' and (resid 371 through 427 )
33X-RAY DIFFRACTION33chain 'E' and (resid 428 through 515 )
34X-RAY DIFFRACTION34chain 'E' and (resid 516 through 609 )
35X-RAY DIFFRACTION35chain 'E' and (resid 610 through 715 )
36X-RAY DIFFRACTION36chain 'F' and (resid 9 through 180 )
37X-RAY DIFFRACTION37chain 'F' and (resid 181 through 318 )
38X-RAY DIFFRACTION38chain 'F' and (resid 319 through 370 )
39X-RAY DIFFRACTION39chain 'F' and (resid 371 through 427 )
40X-RAY DIFFRACTION40chain 'F' and (resid 428 through 515 )
41X-RAY DIFFRACTION41chain 'F' and (resid 516 through 609 )
42X-RAY DIFFRACTION42chain 'F' and (resid 610 through 715 )
43X-RAY DIFFRACTION43chain 'G' and (resid 9 through 131 )
44X-RAY DIFFRACTION44chain 'G' and (resid 132 through 318 )
45X-RAY DIFFRACTION45chain 'G' and (resid 319 through 370 )
46X-RAY DIFFRACTION46chain 'G' and (resid 371 through 515 )
47X-RAY DIFFRACTION47chain 'G' and (resid 516 through 609 )
48X-RAY DIFFRACTION48chain 'G' and (resid 610 through 715 )
49X-RAY DIFFRACTION49chain 'H' and (resid 9 through 119 )
50X-RAY DIFFRACTION50chain 'H' and (resid 120 through 226 )
51X-RAY DIFFRACTION51chain 'H' and (resid 227 through 318 )
52X-RAY DIFFRACTION52chain 'H' and (resid 319 through 515 )
53X-RAY DIFFRACTION53chain 'H' and (resid 516 through 609 )
54X-RAY DIFFRACTION54chain 'H' and (resid 610 through 715 )
55X-RAY DIFFRACTION55chain 'I' and (resid 9 through 180 )
56X-RAY DIFFRACTION56chain 'I' and (resid 181 through 281 )
57X-RAY DIFFRACTION57chain 'I' and (resid 282 through 427 )
58X-RAY DIFFRACTION58chain 'I' and (resid 428 through 607 )
59X-RAY DIFFRACTION59chain 'I' and (resid 608 through 715 )
60X-RAY DIFFRACTION60chain 'J' and (resid 9 through 40 )
61X-RAY DIFFRACTION61chain 'J' and (resid 41 through 73 )
62X-RAY DIFFRACTION62chain 'J' and (resid 74 through 180 )
63X-RAY DIFFRACTION63chain 'J' and (resid 181 through 281 )
64X-RAY DIFFRACTION64chain 'J' and (resid 282 through 318 )
65X-RAY DIFFRACTION65chain 'J' and (resid 319 through 370 )
66X-RAY DIFFRACTION66chain 'J' and (resid 371 through 515 )
67X-RAY DIFFRACTION67chain 'J' and (resid 516 through 609 )
68X-RAY DIFFRACTION68chain 'J' and (resid 610 through 715 )
69X-RAY DIFFRACTION69chain 'K' and (resid 9 through 318 )
70X-RAY DIFFRACTION70chain 'K' and (resid 319 through 515 )
71X-RAY DIFFRACTION71chain 'K' and (resid 516 through 609 )
72X-RAY DIFFRACTION72chain 'K' and (resid 610 through 715 )
73X-RAY DIFFRACTION73chain 'L' and (resid 9 through 72 )
74X-RAY DIFFRACTION74chain 'L' and (resid 73 through 180 )
75X-RAY DIFFRACTION75chain 'L' and (resid 181 through 281 )
76X-RAY DIFFRACTION76chain 'L' and (resid 282 through 427 )
77X-RAY DIFFRACTION77chain 'L' and (resid 428 through 515 )
78X-RAY DIFFRACTION78chain 'L' and (resid 516 through 609 )
79X-RAY DIFFRACTION79chain 'L' and (resid 610 through 715 )

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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