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- PDB-5jmv: Crystal structure of mjKae1-pfuPcc1 complex -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 5jmv
タイトルCrystal structure of mjKae1-pfuPcc1 complex
要素
  • Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
  • Uncharacterized protein
キーワードTRANSFERASE / tRNA modification
機能・相同性
機能・相同性情報


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / protein serine kinase activity / protein serine/threonine kinase activity ...N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / protein serine kinase activity / protein serine/threonine kinase activity / zinc ion binding / ATP binding / cytoplasm
類似検索 - 分子機能
: / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / CTAG/Pcc1 family / Transcription factor Pcc1 / Gcp-like domain ...: / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / CTAG/Pcc1 family / Transcription factor Pcc1 / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / : / RIO domain / Alpha-D-phosphohexomutase, C-terminal domain / TATA-Binding Protein / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE MONOPHOSPHATE / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / KEOPS complex subunit Pcc1
類似検索 - 構成要素
生物種Methanocaldococcus jannaschii (メタン生成菌)
Pyrococcus furiosus (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.38646964319 Å
データ登録者Wan, L. / Sicheri, F.
資金援助 カナダ, 1件
組織認可番号国
CIHR Foundation GrantFDN 143277 カナダ
引用ジャーナル: Nucleic Acids Res. / 年: 2016
タイトル: Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t6A biosynthesis.
著者: Wan, L.C. / Pillon, M.C. / Thevakumaran, N. / Sun, Y. / Chakrabartty, A. / Guarne, A. / Kurinov, I. / Durocher, D. / Sicheri, F.
履歴
登録2016年4月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年7月6日Provider: repository / タイプ: Initial release
改定 1.12016年7月13日Group: Structure summary
改定 1.22016年8月31日Group: Database references
改定 1.32017年11月22日Group: Database references / Derived calculations / Refinement description
カテゴリ: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.name
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 / struct_ncs_dom_lim
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

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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: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
B: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
C: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,19414
ポリマ－165,0808
非ポリマー1,1156
水00
1
A: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
B: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)117,38410
ポリマ－116,6416
非ポリマー7434
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
H: Uncharacterized protein
ヘテロ分子

C: Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
H: Uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,6198
ポリマ－96,8764
非ポリマー7434
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
単位格子
Length a, b, c (Å)121.913, 121.913, 310.613
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22
32
42
52

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROMETMETchain 'A'AA0 - 315 - 36
121ASNASNILEILEchain 'A'AA40 - 32445 - 329
211PROPROMETMETchain 'B'BB0 - 315 - 36
221ASNASNILEILEchain 'B'BB40 - 32445 - 329
311PROPROMETMETchain 'C'CC0 - 315 - 36
321ASNASNILEILEchain 'C'CC40 - 32445 - 329
112ARGARGLEULEUchain 'D'DD5 - 3210 - 37
122GLUGLULYSLYSchain 'D'DD40 - 4445 - 49
132ILEILEILEILEchain 'D'DD50 - 8055 - 85
212ARGARGLEULEUchain 'E'EE5 - 3210 - 37
222GLUGLULYSLYSchain 'E'EE40 - 4445 - 49
232ILEILEILEILEchain 'E'EE50 - 8055 - 85
312ARGARGLEULEUchain 'F'FF5 - 3210 - 37
322GLUGLULYSLYSchain 'F'FF40 - 4445 - 49
332ILEILEILEILEchain 'F'FF50 - 8055 - 85
412ARGARGLEULEUchain 'G'GG5 - 3210 - 37
422GLUGLULYSLYSchain 'G'GG40 - 4445 - 49
432ILEILEILEILEchain 'G'GG50 - 8055 - 85
512ARGARGLEULEUchain 'H'HH5 - 3210 - 37
522GLUGLULYSLYSchain 'H'HH40 - 4445 - 49
532ILEILEILEILEchain 'H'HH50 - 8055 - 85

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein


分子量: 38555.711 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (メタン生成菌)
株: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
遺伝子: MJ1130 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q58530, N6-L-threonylcarbamoyladenine synthase, non-specific serine/threonine protein kinase
#2: タンパク質
Uncharacterized protein


分子量: 9882.477 Da / 分子数: 5 / 由来タイプ: 組換発現
由来: (組換発現) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (古細菌)
株: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / 遺伝子: PF2011 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8TZI1
#3: 化合物 ChemComp-AMP / ADENOSINE MONOPHOSPHATE


分子量: 347.221 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C10H14N5O7P / コメント: AMP*YM
#4: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg

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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: 3.5 Å3/Da / 溶媒含有率: 64.88 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 0.1 M Sodium Cacodylate pH 6.5 and 1.26 M Ammonium Sulfate

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データ収集

回折平均測定温度: 93.15 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年2月16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: 0.9792 Å / 相対比: 1
反射解像度: 3.4→50 Å / Num. obs: 33825 / % possible obs: 99.9 % / 冗長度: 8.4 % / Biso Wilson estimate: 63.0706493277 Å2 / CC1/2: 0.439 / Rsym value: 0.136 / Net I/σ(I): 13.6

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHASER位相決定
PHENIX1.9_1692精密化
HKL-2000データ削減
HKL-2000データスケーリング
PDB_EXTRACT3.2データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 2IVP for chains A-C and 3ENC for chains D-H

2ivp

3enc


解像度: 3.38646964319→48.241450813 Å / SU ML: 0.400943058682 / 交差検証法: FREE R-VALUE / σ(F): 1.33623300521 / 位相誤差: 23.679314769
Rfactor反射数%反射
Rfree0.243212133818 1419 5.03369989358 %
Rwork0.200425568412 26771 -
obs0.202641779643 28190 84.1090822294 %
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: 68.6947387896 Å2
精密化ステップサイクル: LAST / 解像度: 3.38646964319→48.241450813 Å
タンパク質核酸リガンド溶媒全体
原子数10363 0 72 0 10435
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0022447283584310619
X-RAY DIFFRACTIONf_angle_d0.67383271263114370
X-RAY DIFFRACTIONf_chiral_restr0.02436831734641659
X-RAY DIFFRACTIONf_plane_restr0.00265821530661807
X-RAY DIFFRACTIONf_dihedral_angle_d11.58697352393946
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3865-3.50750.391809242216420.301471723482721X-RAY DIFFRACTION23.4769230769
3.5075-3.64790.343578850612630.2776002335941322X-RAY DIFFRACTION42.4976986806
3.6479-3.81380.3165653681221270.2497074276472333X-RAY DIFFRACTION74.0963855422
3.8138-4.01480.2766613552221520.2185240935673075X-RAY DIFFRACTION97.7878787879
4.0148-4.26620.242778891151550.1987770109173138X-RAY DIFFRACTION99.9089805825
4.2662-4.59530.2135893484891840.165984300853144X-RAY DIFFRACTION99.9699609492
4.5953-5.05740.1941838188731620.1604416637743193X-RAY DIFFRACTION100
5.0574-5.78810.2624599929651800.2006919761843187X-RAY DIFFRACTION99.9406352033
5.7881-7.28840.289338007581710.2312844124943237X-RAY DIFFRACTION100
7.2884-48.24630.1995817568771830.1868425959213421X-RAY DIFFRACTION99.5305164319
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)
11.10501682464-0.4664605179590.3721290053140.423315519583-0.3966968134960.386882688927-0.109327828104-0.04094599136480.152067053685-0.221033889276-0.1365116192450.540702719117-0.348309819765-0.4291136037750.04639880781090.302665421610.546476468225-0.3863515159750.590766115459-0.1643598454520.494800743268152.280308677139.67643411522.0554927072
21.092235486970.3475215897860.4731771621742.02841512681-0.2044181489320.368812214573-0.1717923222560.1749442680760.5940724882150.1362505186590.03966962817330.375878200394-0.340757386037-0.2866402859330.1378312285670.6948937630980.270534101675-0.2857312196150.3895887498530.09677630038240.416327288728167.427454572153.87568364519.4611681833
30.247304346090.2634080549850.1669811347860.4409576088870.4712542101420.586335303052-0.1117512811220.287811586640.274578598902-0.403694413990.1371564839130.263530883803-0.5155449483710.1034749172810.4026992707090.7352510152450.291449328814-0.402681501450.3707549171630.1287621847310.413255737173169.810816467155.54055377617.1036459835
42.42664152565-0.7495388800320.8363962657162.32427285782-0.6721054408182.5593589539-0.001509778447910.0602207697245-0.221081063679-0.0950721375704-0.2475969011840.8143056517320.313589014929-0.813586044950.1225028135690.2606837365070.00944389518347-0.07460786468620.521929447654-0.1758747753980.418512150285150.007890991110.0117261413.33366077781
53.777849539051.081328021451.502309598876.854185664644.25325621494.24421505127-0.3361026468490.700320269381-1.19397754655-0.7819347933020.01092730009850.2524383656540.707006741533-0.7819308460750.2108633575071.17299393944-0.2776139912190.163774838350.648673458917-0.1349537341260.785162315807159.48747664785.4592422099-2.89829965069
62.62146062579-1.060972910350.6396093221011.070016376690.1570716572071.3529523018-0.133661154366-0.107393931203-0.7343452857360.1387882705140.06573517676640.3855964307940.938281983352-0.4681929603190.04135104239860.784994184247-0.2440054227890.06507082963510.522333873983-0.07973231076230.461078557482157.07131879195.46356648759.23231223533
75.88783155733-5.852456146167.636223154159.216125720342.000005951791.999999914674.167683915392.41949544109-0.6202181369731.37048979332-1.317437103940.4534208249373.475540515562.2101663944-2.849625396551.304864333060.1763738788970.2064547435840.870064513276-0.425306774041.14138391513161.755435498106.24776166126.5819372181
81.760275890940.3851207290250.1482665991573.79380700961-1.244642735751.746030272440.1783945175330.1446266066180.336825275299-0.2747995977210.218933856839-0.5392497717960.0124685585687-0.161903994798-0.2778934393420.9452404023250.150869026144-0.01181249308890.2113016088740.08714415311680.698078356532186.84747080390.9736847115.3578498241
92.2755414123-0.5115914688660.511451807123.369917898672.499857792494.288212865450.06488111527260.04212024133120.0189718482625-0.3217147254350.0604188027919-0.437839331364-0.03318956099290.0917461924792-0.1120323663481.22748180040.2246220243290.0009528955779130.326974682475-0.001275701356470.309155786465183.59266781270.49536069821.7550733512
101.62577330164-0.843474992194-0.295524504543.19870861995-1.079025542671.055221045120.096827890515-0.2519086863380.133473705160.070840924011-0.0506861392278-0.347838047762-0.161870648351-0.0278047701306-0.0187345204050.9675290488130.185522514093-0.1455704679650.322984996930.02668140684880.287890510624182.53622849171.306461541625.0534568156
112.73502820218-1.548121358752.408040625373.007157938650.4205150600233.767493235010.330471626008-0.198853761826-0.9846096912970.218196964054-0.5159709259560.4976981824590.921604921436-0.9379210391410.03320589564840.363479948643-0.06100568701960.03793519315020.585934241344-0.07953213705820.428470223988154.401833298122.30453126435.8134850914
128.225585927681.318934036131.812605686385.434923113313.14917744872.93154698823-0.1045335428930.09565276169230.976148002608-0.0364394463182-0.220196162991-1.05655298124-0.02982665483151.074162016740.3914315421630.3146149457160.1118467474570.00547925659570.6645467118820.2518391163710.677453473377169.592700137128.9196763636.5905350542
134.433111846786.327190271962.582743336729.947887607215.085160117146.504954067950.568430484451-1.26108102045-0.6326092140780.381005060491-0.7338427063110.02068212823621.31529883964-0.1733387254160.1116218194850.939584082247-0.04180863556060.1125102368270.5335536081880.04861956291060.343261010703157.745480609118.78231215538.0615045094
148.77824384901-0.05804137351896.826952701720.08276899032-0.006724522400566.15176617599-0.0129787931772-1.179103361330.3214653794610.432794699458-0.4504795060930.01618744167730.807344091763-0.3967510264220.4690876651630.4459740862840.1064007285060.1055571456190.763621865759-0.05300367110460.446580563344160.745019006122.91918131244.5964798794
155.41832176026-1.873466180810.2725665478547.020983042520.3944872563615.52505912914-0.324365041373-0.3562611378930.3599400028260.0740276679204-0.205020124820.475544291098-0.605641712024-0.9855504094630.4170973860090.2826748632360.1579353657090.1210192828760.337365625603-0.07488160956210.250079119301155.219030369132.12275366837.8541870886
166.457843055741.88815849123.977715129367.075751503333.205929980956.017813975820.0824614712012-1.2439840855-0.4262640467841.25112880756-0.105510263627-0.2076706568480.574836806615-0.161734089347-0.03106161009250.668007379926-0.007821516182630.01802783353930.6862249455160.08310218756580.35384394399158.546366664127.97719226461.0222357331
177.23291937049-3.853263181813.941536063129.71177331394-4.235605719466.819024278530.100293048354-0.498011073719-0.04081105078890.9332083644210.0233027456460.8606956689990.696051581501-0.726434131862-0.1113582710940.745130815966-0.124423744660.2014514264490.973360005073-0.2649756461440.475996851365153.051431983129.1142802560.7633709014
184.45078917303-0.7596003509426.46517231161.63133092462-0.3177408333479.798681931520.5703227525150.1628397262020.368495230706-0.0959254620582-0.6203457517140.03603025221290.641941439661-0.7430246723160.09278219879820.756001776017-0.1002857249490.3488543564830.9389618779480.01810035869170.485396706956151.634923179126.25219341752.9262357948
196.185039277373.124907865825.240114455732.471874647232.772590237244.45662419352-0.6605275964260.5729091337280.8002307794630.00134326445535-0.1770599103390.274754711083-0.7900753817760.4532627179890.8571382004430.4516088234230.159202971358-0.1471287967820.779945709344-0.02376477019830.317570167367159.299640676136.06304795154.3017191931
206.38484766458-2.11287045333-5.887025657891.767832031442.70226926567.188816213250.03352210250030.1816687506420.381941628775-0.0742646832893-0.103719131752-0.11703247653-0.372858689676-0.5629946078310.03196379998750.9083179358870.0307076934544-0.4850426490950.8701909238940.1793159026630.597542793156158.193278539128.811387871-20.593089956
217.53570046663-0.799071528964.817996260651.0328896524-1.768084712688.2763247168-0.465823281535-0.7097434911610.5001875713560.06598265584540.488508703879-0.0358586989414-0.325793367445-0.06081896453060.04127794752620.462185241625-0.131155904621-0.2082462386390.4315831330330.03635634168330.229549307742161.390009625123.774556958-8.52144719465
222.31308028336-1.57182157888-1.983214369963.10096727053.934462397797.84821029106-0.04621217701630.1164753938420.110636182436-0.2541921631470.139787692115-0.00359215795235-0.7144490670820.5049395266320.005671536449150.839249532493-0.148755711262-0.3771301974820.538202193656-0.001327629394630.375118391038163.104082699127.917612019-17.5669329209
230.04958885785030.05411933119740.1682153540240.3485141448690.2441862497670.5854635341580.02071083394190.242965207195-0.115139487014-0.0645330957256-0.1501991802840.136747724822-0.0219958998231-0.2083820947030.07224238842670.440630719166-0.123734706617-0.3626126260860.632976511893-0.09413670947630.302725824506156.07656313118.478028039-15.7704370412
245.303684855080.6663831480471.101708468541.302864949242.589914860288.409449522170.05367096204050.889766388419-0.0387789399246-0.26428453937-0.1637081476230.00185586029958-0.6190341273530.03614629434960.0385658376181.09473183879-0.115838669808-0.4042339772510.593414548638-0.00663647716360.370797393935159.322671181121.482685921-37.5632812964
257.710140569310.679385814288-4.367357823410.748780700081.247756221876.346115538310.24572891903-0.5735749803230.132358337571-0.0552486315795-0.2518764377070.021577258861-0.9412424244320.1714095761830.04452891433341.19951318388-0.0068641236144-0.5663596763140.869536216121-0.02541267319980.610468015265156.073689103126.651388123-33.4453812877
266.07266540707-2.31986645483-5.115622704263.251373982544.038496139067.49406819946-0.55018785909-0.3633865798280.04229150961040.3787785862580.2907024460960.01472578965210.614367891392-0.1609714835750.1265316596180.59277004542-0.0315102688975-0.2013548507590.630733366107-0.2402821414960.394862437533157.833471716114.732910377-30.8084400054
272.44778971615-0.381050912722-3.041402236741.094896044782.008448297856.052412368270.5751604715540.6421278808572.31264678157-0.195086289379-0.0633745148301-1.78119585626-1.505602966350.614732779135-0.4859367094650.953009729811-0.2147513958760.3997866347630.7463330044540.08995260110291.70389039544212.74977060697.33579251752.55937769878
283.751691392510.846194280563-2.259784448891.717341998732.380655910776.834876745930.294331475317-0.1096108036541.669825289740.838815661079-0.0504238933612-1.39720892169-1.783105928110.759454385082-0.2060728872090.969538501328-0.227439266201-0.09829148887950.615846385507-0.007390474655331.46203150799203.24335882100.01898651613.3299639902
292.175176126821.849537470970.3253958351591.95682066643-1.57441629888.974699885160.243508134391-0.5268294181821.38552457511-0.7046878660740.127969374727-2.99682750258-0.5989953350171.80924523559-0.3424067140620.71214100064-0.09543251381480.06153223919990.87586017355-0.05602419131091.65735835279215.42627371592.73151481758.94923264113
302.4725824768-0.329834987990.09620816962624.75601880456-0.2549435695031.600809504090.4039654531150.0606528139573-0.381476523213-0.5752710093150.0464079350727-0.323955917206-0.3533563769480.169108261294-0.4451404381950.70343172676-0.03738000260410.03615032631290.322320217305-0.008317736883911.33415325815203.43314086190.77082135475.2215787488
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 132 )
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 215 )
6X-RAY DIFFRACTION6chain 'B' and (resid 216 through 324 )
7X-RAY DIFFRACTION7chain 'B' and (resid 325 through 325 )
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 115 )
9X-RAY DIFFRACTION9chain 'C' and (resid 116 through 182 )
10X-RAY DIFFRACTION10chain 'C' and (resid 183 through 324 )
11X-RAY DIFFRACTION11chain 'D' and (resid 5 through 31 )
12X-RAY DIFFRACTION12chain 'D' and (resid 32 through 39 )
13X-RAY DIFFRACTION13chain 'D' and (resid 40 through 48 )
14X-RAY DIFFRACTION14chain 'D' and (resid 49 through 58 )
15X-RAY DIFFRACTION15chain 'D' and (resid 59 through 82 )
16X-RAY DIFFRACTION16chain 'E' and (resid 5 through 29 )
17X-RAY DIFFRACTION17chain 'E' and (resid 30 through 48 )
18X-RAY DIFFRACTION18chain 'E' and (resid 49 through 58 )
19X-RAY DIFFRACTION19chain 'E' and (resid 59 through 82 )
20X-RAY DIFFRACTION20chain 'F' and (resid 5 through 16 )
21X-RAY DIFFRACTION21chain 'F' and (resid 17 through 39 )
22X-RAY DIFFRACTION22chain 'F' and (resid 40 through 58 )
23X-RAY DIFFRACTION23chain 'F' and (resid 59 through 80 )
24X-RAY DIFFRACTION24chain 'G' and (resid 5 through 39 )
25X-RAY DIFFRACTION25chain 'G' and (resid 40 through 58 )
26X-RAY DIFFRACTION26chain 'G' and (resid 59 through 81 )
27X-RAY DIFFRACTION27chain 'H' and (resid 5 through 16 )
28X-RAY DIFFRACTION28chain 'H' and (resid 17 through 32 )
29X-RAY DIFFRACTION29chain 'H' and (resid 40 through 58 )
30X-RAY DIFFRACTION30chain 'H' and (resid 59 through 81 )

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万見について

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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