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- PDB-7x9s: Crystal structure of a complex between the antirepressor GmaR and... -

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基本情報

登録情報
データベース: PDB / ID: 7x9s
タイトルCrystal structure of a complex between the antirepressor GmaR and the transcriptional repressor MogR
要素
  • GmaR
  • Motility gene repressor MogR
キーワードPROTEIN BINDING/TRANSCRIPTION / Antirepressor / repressor / TRANSFERASE / PROTEIN BINDING-TRANSCRIPTION complex / PROTEIN BINDING
機能・相同性
機能・相同性情報


transferase activity
類似検索 - 分子機能
Motility repressor MogR, DNA-binding domain / Motility repressor MogR, DNA-binding domain / MogR, DNA-binding domain superfamily / DNA binding domain of the motility gene repressor (MogR) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / TPR repeat profile. / Tetratricopeptide repeats / Nucleotide-diphospho-sugar transferases / Tetratricopeptide repeat ...Motility repressor MogR, DNA-binding domain / Motility repressor MogR, DNA-binding domain / MogR, DNA-binding domain superfamily / DNA binding domain of the motility gene repressor (MogR) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / TPR repeat profile. / Tetratricopeptide repeats / Nucleotide-diphospho-sugar transferases / Tetratricopeptide repeat / Four Helix Bundle (Hemerythrin (Met), subunit A) / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
Glycosyl transferase family 2 / Motility gene repressor MogR
類似検索 - 構成要素
生物種Listeria monocytogenes (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.11 Å
データ登録者Cho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Yoon, S.I.
資金援助 韓国, 1件
組織認可番号国
National Research Foundation (NRF, Korea)2019R1A2C1002100 韓国
引用ジャーナル: Nucleic Acids Res. / 年: 2022
タイトル: Structural basis of flagellar motility regulation by the MogR repressor and the GmaR antirepressor in Listeria monocytogenes.
著者: Cho, S.Y. / Na, H.W. / Oh, H.B. / Kwak, Y.M. / Song, W.S. / Park, S.C. / Jeon, W.J. / Cho, H. / Oh, B.C. / Park, J. / Kang, S.G. / Lee, G.S. / Yoon, S.I.
履歴
登録2022年3月16日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年11月23日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: GmaR
B: Motility gene repressor MogR
C: GmaR
D: Motility gene repressor MogR
E: GmaR
F: Motility gene repressor MogR


分子量 (理論値)分子数
合計 (水以外)201,3586
ポリマ－201,3586
非ポリマー00
水00
1
A: GmaR
B: Motility gene repressor MogR


分子量 (理論値)分子数
合計 (水以外)67,1192
ポリマ－67,1192
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-8 kcal/mol
Surface area26220 Å2
手法PISA
2
C: GmaR
D: Motility gene repressor MogR


分子量 (理論値)分子数
合計 (水以外)67,1192
ポリマ－67,1192
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-9 kcal/mol
Surface area24240 Å2
手法PISA
3
E: GmaR
F: Motility gene repressor MogR


分子量 (理論値)分子数
合計 (水以外)67,1192
ポリマ－67,1192
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area25260 Å2
手法PISA
単位格子
Length a, b, c (Å)91.870, 91.992, 268.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
12
22

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
111HISHISALAALA(chain 'A' and (resid 233 through 300 or (resid 301...AA233 - 3039 - 79
121TYRTYRPHEPHE(chain 'A' and (resid 233 through 300 or (resid 301...AA306 - 34082 - 116
131ALAALAASNASN(chain 'A' and (resid 233 through 300 or (resid 301...AA343 - 601119 - 377
141ALAALATHRTHR(chain 'A' and (resid 233 through 300 or (resid 301...AA603 - 627379 - 403
251HISHISALAALA(chain 'C' and (resid 233 through 250 or (resid 251...CC233 - 3039 - 79
261TYRTYRPHEPHE(chain 'C' and (resid 233 through 250 or (resid 251...CC306 - 34082 - 116
271ALAALAASNASN(chain 'C' and (resid 233 through 250 or (resid 251...CC343 - 601119 - 377
281ALAALATHRTHR(chain 'C' and (resid 233 through 250 or (resid 251...CC603 - 627379 - 403
391HISHISALAALA(chain 'E' and (resid 233 through 250 or (resid 251...EE233 - 3039 - 79
3101TYRTYRPHEPHE(chain 'E' and (resid 233 through 250 or (resid 251...EE306 - 34082 - 116
3111ALAALAASNASN(chain 'E' and (resid 233 through 250 or (resid 251...EE343 - 601119 - 377
3121ALAALATHRTHR(chain 'E' and (resid 233 through 250 or (resid 251...EE603 - 627379 - 403
1132GLUGLUGLNGLN(chain 'B' and (resid 5 through 62 or (resid 63...BB5 - 1611 - 22
1142THRTHRPROPRO(chain 'B' and (resid 5 through 62 or (resid 63...BB25 - 13431 - 140
1152THRTHRPHEPHE(chain 'B' and (resid 5 through 62 or (resid 63...BB153 - 156159 - 162
2162GLUGLUGLNGLN(chain 'F' and (resid 5 through 16 or (resid 17...FF5 - 1611 - 22
2172THRTHRPROPRO(chain 'F' and (resid 5 through 16 or (resid 17...FF25 - 13431 - 140
2182THRTHRPHEPHE(chain 'F' and (resid 5 through 16 or (resid 17...FF153 - 156159 - 162

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質 GmaR / Glycosyltransferase


分子量: 47809.969 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Listeria monocytogenes (バクテリア)
遺伝子: B1O25_01135, B4X79_02990, B4X80_02895, B4X87_02980, B4X92_06885, B4Y36_05390, B4Y57_05390
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A3A6YDN3
#2: タンパク質 Motility gene repressor MogR / Motility genes transcriptional repressor MogR


分子量: 19309.281 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Listeria monocytogenes (バクテリア)
遺伝子: mogR, AF006_02860, APD94_05535, B1N38_01800, B1N40_07710, B1O10_02675, B1O25_01060, B4Y29_07380, B4Y40_02825, B4Y56_05470, B4Y57_05465, D4U00_09220, D4U23_03070, D6P18_12875, E1V33_14790, ...遺伝子: mogR, AF006_02860, APD94_05535, B1N38_01800, B1N40_07710, B1O10_02675, B1O25_01060, B4Y29_07380, B4Y40_02825, B4Y56_05470, B4Y57_05465, D4U00_09220, D4U23_03070, D6P18_12875, E1V33_14790, F3O35_02870, FC284_03505, FR217_11725, G3R95_001605, GEK29_05490, GFK29_02230, GON91_13840, GYP27_07090, GZK40_02265, I6I37_07885, JKV73_02241, JKV74_10915, JKX61_03425
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A3H0QY60

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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: 2.86 Å3/Da / 溶媒含有率: 56.93 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: PEG 4000, ammonium acetate, glycerol, sodium citrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: PAL/PLS / ビームライン: 7A (6B, 6C1) / 波長: 0.9794 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2018年9月19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: 0.9794 Å / 相対比: 1
反射解像度: 3.11→30 Å / Num. obs: 43043 / % possible obs: 99.9 % / 冗長度: 4.5 % / Biso Wilson estimate: 86.96 Å2 / CC1/2: 0.993 / Net I/σ(I): 16.7
反射 シェル解像度: 3.11→3.16 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2094 / CC1/2: 0.344 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
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: 3FDQ, 7X9R

3fdq

7x9r


解像度: 3.11→29.49 Å / SU ML: 0.4625 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.6119
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2411 2127 5.09 %
Rwork0.195 39674 -
obs0.1974 41801 99.92 %
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: 87.53 Å2
精密化ステップサイクル: LAST / 解像度: 3.11→29.49 Å
タンパク質核酸リガンド溶媒全体
原子数12093 0 0 0 12093
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007312360
X-RAY DIFFRACTIONf_angle_d0.888116862
X-RAY DIFFRACTIONf_chiral_restr0.05161953
X-RAY DIFFRACTIONf_plane_restr0.00612164
X-RAY DIFFRACTIONf_dihedral_angle_d16.68924260
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.180.43441520.34632592X-RAY DIFFRACTION99.89
3.18-3.260.36421410.29772609X-RAY DIFFRACTION99.82
3.26-3.350.31071170.26232625X-RAY DIFFRACTION100
3.35-3.450.29371490.24522575X-RAY DIFFRACTION99.93
3.45-3.560.32421130.21642665X-RAY DIFFRACTION99.96
3.56-3.690.25371600.19832602X-RAY DIFFRACTION99.93
3.69-3.830.25081400.19162632X-RAY DIFFRACTION99.96
3.83-4.010.23841220.18432613X-RAY DIFFRACTION99.93
4.01-4.220.21641540.16642623X-RAY DIFFRACTION100
4.22-4.480.18511430.15682622X-RAY DIFFRACTION100
4.48-4.830.20331430.16342663X-RAY DIFFRACTION99.96
4.83-5.310.24841310.19042641X-RAY DIFFRACTION99.96
5.31-6.070.27541150.22222727X-RAY DIFFRACTION99.96
6.07-7.630.26681580.20292703X-RAY DIFFRACTION99.9
7.63-29.490.19721890.16872782X-RAY DIFFRACTION99.63
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)
11.83730222934-2.135504438571.10218386851.97719077467-1.257875103626.744746997880.0650596683897-0.218819409806-0.2060163657880.0379376513318-0.0595095978825-0.1599596410610.2717489822280.615412584568-0.001270513103470.6048129782120.01971090608240.09506747310780.260480815421-0.02355585031620.66461145887810.4341027137-1.40148247752-18.7211247203
28.320021806020.270643499436-1.238377762690.6531512597370.9135567445271.420087569860.106596772233-0.185053918705-0.057901534003-0.0849793727401-0.1854714103630.1342800581310.01452157306930.04033773841310.1191299284750.9266649673310.0563750288888-0.009539164802210.327942688578-0.0101754239930.623156599351-8.487064234629.190525884963.88451385107
34.87634893467-2.76662934226-2.038320214162.385814553971.720994159321.619309378970.06739472014070.0710049464289-0.4490178034250.00235772918429-0.3052317872990.4028956125970.0420345296619-0.1629546911510.2753032801470.592705948677-0.097285918792-0.0378078177640.3381670064680.02888237384350.770608042371-8.59844388023-17.1777870484-5.87164391226
40.01896401792810.02537185739910.2773398709165.07958954752.992461219496.644870879430.3330181353770.152340707919-0.261009175775-1.11288464861.17171083511-2.03663863208-1.291345587061.57466393276-0.5890286217361.47183983834-0.3697923261480.7616740876840.5687164893670.0981789869182.221079588936.4441600975-22.2023059288-38.9984698497
53.849266546361.81235485909-3.243542926956.531087735621.047386940473.84807133002-0.4303106200531.12234016319-0.0964749299936-1.011512429930.3393087654240.2824660916180.273819610482-0.1411766461810.2266244967861.279746316190.0692888167142-0.1193758417681.01250862087-0.08865879564611.0197312066519.0675073204-27.0164461105-41.1186376906
67.56664145785-3.928423863680.2388404035254.15762149486-3.758545079366.305485049580.0682110192520.802223009716-0.269134612044-0.85084148391-0.132601208871-1.494195880390.2950283259350.9440114463110.09341597947360.949279161747-0.04655607825510.01770799671120.528286130298-0.07449790506671.1352852334227.3033872203-29.9222194916-31.5806817193
77.3224039519-0.585010596422-0.9647916236024.808960558541.74667961327.260094362390.03331583593520.341028680043-0.560044682637-0.4911377353070.134544325811-0.2695103948260.07335061382390.123010484214-0.1308714186370.7857622544160.03841423090740.1079546664810.326147948676-0.0386880413530.92987523516120.6420295731-25.9682639516-27.8699049481
82.250074703862.24670243836-4.372123561793.28012957108-3.134396343919.794177811110.199781218472-0.02245651340.3493180239930.509662597798-0.6901640541720.9576620439160.335940807338-0.178962203012-0.3503639097570.652526625835-0.2386533995860.1307568782820.587355164561-0.0313802893781.14121857086-10.992661053-32.3151614003-9.05607996747
93.92999461398-3.629883821570.1888225422047.7561628997-1.145785954721.088747602880.3133470459020.4117290120710.252465230789-0.520177789556-0.33666691843-0.277432704617-0.133345443950.01879677917730.02726119821250.4705832111220.02941890450620.04762250697430.410235293704-0.03385995089550.442344636374-0.045793042663923.4954929933-40.4893398325
107.504048592210.740335274349-6.106756693291.22793805666-0.5961719136247.37521390303-0.09361564549640.9330755734840.3245733783160.1202305627350.2193568944610.243785870019-0.115543074863-1.25995674178-0.1280616174520.5302179750620.072976903127-0.04035903297590.7592947909380.06499655108440.564632484697-29.778315360131.6501161273-35.8144459935
118.666665337021.15696859976-0.6863966810410.5448545871020.7209463388814.510001586970.481744249096-0.3596288170480.2495920276190.406967961109-0.2864119420510.07514995387150.306967488079-0.05943057084-0.2035426563220.735865916399-0.01272814284830.123458384220.365053912752-0.05443979681970.622594873337-25.229869505230.6364549753-12.9695638858
123.59317106906-0.248542542633-2.643793099072.41336998359-0.02775836072113.018113163050.567953487134-0.3343688036230.6360851935510.497115719401-0.189896409226-0.157597347069-0.5550116004660.291288560874-0.4104189041020.786146416673-0.1774273493740.01564178069120.432633663376-0.1073033149940.7361365722165.7186645616738.851599678-21.139933304
133.74825043871.82037284736-5.500290625555.72259513558-1.969331400158.66329869925-1.008269898850.0936204926991-1.655308598070.521641799409-0.780833528535-2.136351387732.112352416070.6061345378742.236954933310.328452525344-0.03655056332310.4453707615521.43036269436-0.2067217532841.4157949128935.168708520922.9704769815-38.373962377
149.42861939474-0.02012068525061.870712165772.831407508962.707029721812.97477311799-1.088284224791.06796794749-0.9084839729620.0365189531131.16514103189-0.724737485048-0.1783577784920.615207458932-0.194837055160.9707324980450.125875457087-0.08689326372991.166875618340.1940234897471.2372402823427.051612809918.2526207855-25.2636834402
156.87009579102-6.01959789465-1.485701331838.254463362440.809836591498.905971790.4882091048860.0288570015336-0.532490250489-0.6355177701240.232496064003-0.752096498965-0.7815402644740.374109824077-0.5572124113730.638837233542-0.2794883421410.101889231441.059729601110.1839037781530.98070117416429.028721861833.317861489-37.3959612047
163.63047085334-5.872470862710.3049264319789.701654063490.6920514950986.955169162910.7950010120730.0478304935959-1.61255945333-0.0994604605088-1.204415541940.4504084384760.5612601799110.8584469837810.7666558027990.482268786384-0.08993847017140.1820921378140.803297931439-0.01792218098141.1200128499123.777563675224.008356048-37.184789806
175.3462677756-0.2733838393041.313246181752.129512011270.8135833345353.699562602220.1140687833180.0143034791618-0.2939473615850.311779189259-0.580088982261-0.398727958673-0.9268068684580.7149454541220.5184733021780.760538090654-0.295291136423-0.1488623563220.6588755698830.1021481107750.94623097992618.321485779135.8125987454-20.1207368909
187.877588340640.2384272218962.557373441593.883635325961.904874551737.429902104730.3848154102480.575763092227-1.05565732544-0.500751414845-0.04932961438880.4253953460820.08022110102970.204292057011-0.2534376920540.5419455861420.06124922989590.06621752978910.387234156239-0.09632008732860.448107849992-1.85389721590.307664525135-44.464232309
196.871808487352.13517637111.689609412174.419287122490.01254481495165.512973146290.2423182954860.350836554914-1.085422530880.16717152473-0.2861521907450.1590074216461.23911511302-0.9010798165680.04005248886920.969951113113-0.1308224346380.08903191351730.623587492297-0.2575086523350.821291869128-11.2970048102-13.8917463896-48.1152257395
202.95258556366-0.770933381317-3.320633729731.27171663998-0.4073310944695.46013445681-0.2896045031640.151308909202-0.504739858831-0.0566685758925-0.1961841656060.4720350135771.01454643429-0.8302602480070.4764323253321.22203826644-0.3685153407440.1818450265250.811610598385-0.2417876783431.33525808338-29.8370063981-21.5369503753-33.7343082818
211.982289808131.13271802823-1.803868119428.39774406991-4.330417300418.721590299590.0209375003418-0.193216168837-0.3271579949210.940954437966-0.375471553154-0.209802737483-0.492846858304-1.509607993150.2973669643640.685679108672-0.1326136865150.06483945560411.20223039485-0.2452265865961.05743050937-42.3405610436-2.3086704787-28.4400672457
224.91596156481-1.4379774878-4.518282815952.293794215591.601829597375.383608338740.09511807865340.585667889784-0.0581892206232-0.194426486864-0.2031489975340.407806168633-0.486106572525-1.354238655360.1823382515310.7283629917650.147532016326-0.1675820559351.34654797568-0.3002794783920.752508058794-28.62020703620.0328849077169-60.3087309183
235.00760848933-3.81204712991-0.773387023914.14410559632-1.332823160143.069564506530.0526387687413-0.704948109157-0.07636153863591.568835772350.799248870457-0.922822864701-1.158371250840.391027432948-0.6555190130991.0308476976-0.258479175748-0.07303806030560.928408238326-0.3411050974390.78578412019314.4000506144-2.25945277026-70.5877620727
245.88589722557-6.61690908127-0.8299653990448.36272814809-1.160281935124.835354667430.298965030257-0.6441182031741.27432703922-1.713043670550.288081098038-0.767581054290.04907166101080.329079947732-0.6489033829690.813227530414-0.2586666566530.192181368661.1389361494-0.3181275283930.81676548287719.8301558502-3.21932649085-78.3378119864
256.94437204469-6.9621281147-4.204565507837.041592168654.966348877287.71489052112-0.2843013305960.03405166439491.390159062680.3614648837850.591255517288-1.47601931356-1.029054328031.00153715024-0.4192031836661.31580003925-0.2425164079670.1823832788840.740683494589-0.3716989346740.93038592070511.7658621416.87892726987-76.5394755297
266.89521243677-6.33859853912-3.647857480067.459028191034.433151882352.684692153820.286563076771-0.3076614507451.47608758954-0.1518129813930.556413231074-0.914415111375-0.171559419584-0.015191701571-0.8370375457761.69940562444-0.02971585984770.3613325514720.794207990381-0.1524404591080.861635285710.79614813521314.2215884714-66.4200089591
278.021395924593.3174162209-1.601782240764.63353933095-5.027567373686.214426512680.1032840729740.1559930522190.32975943266-0.214615275274-0.005932545056540.2095548646240.1748089133960.229933956787-0.3846564702640.955546055517-0.1525473044960.03065503603440.746284424919-0.1086854176210.6877030878382.995959366170.470629263417-78.4148342272
283.284277216224.72405180004-3.462735937186.81297641361-5.125066731454.684642586870.05132162138630.0849706707228-1.095663357970.521780263729-0.291711484018-0.957774862983-0.349947901593-0.1882012184110.4354850987630.831278281882-0.04210597199850.04178586043380.783820478622-0.1091325332530.6257250458191.40477206631-8.17562075176-71.6152815049
294.18454432177-3.26948906477-3.045613456947.26302919631-0.3942711937033.843604375280.238669071421-0.9737150171560.2965976196060.712940724246-0.4779992287460.0430667408014-1.4393862101-0.5454457284280.1937439645170.933802880374-0.0554680543230.02945492143380.724466631766-0.2694875891750.5800442819243.469782393921.19237029788-65.1600793817
308.18401783431-1.53899382698-1.687004901060.7258729363280.04116828628410.32933082641-0.03023161258861.4032232690.243850056533-0.1643355048550.0653694256051-0.215002409265-0.344507164325-0.388474653554-0.08563318376731.073254234390.0403361774677-0.1142787229121.26884759740.0003010688142580.598096120989-12.53723069695.30909228011-73.1590874695
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 233 through 346 )
2X-RAY DIFFRACTION2chain 'A' and (resid 347 through 449 )
3X-RAY DIFFRACTION3chain 'A' and (resid 450 through 636 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 38 )
5X-RAY DIFFRACTION5chain 'B' and (resid 39 through 73 )
6X-RAY DIFFRACTION6chain 'B' and (resid 74 through 90 )
7X-RAY DIFFRACTION7chain 'B' and (resid 91 through 134 )
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 161 )
9X-RAY DIFFRACTION9chain 'C' and (resid 233 through 346 )
10X-RAY DIFFRACTION10chain 'C' and (resid 347 through 449 )
11X-RAY DIFFRACTION11chain 'C' and (resid 450 through 546 )
12X-RAY DIFFRACTION12chain 'C' and (resid 547 through 627 )
13X-RAY DIFFRACTION13chain 'D' and (resid 5 through 58 )
14X-RAY DIFFRACTION14chain 'D' and (resid 59 through 73 )
15X-RAY DIFFRACTION15chain 'D' and (resid 74 through 100 )
16X-RAY DIFFRACTION16chain 'D' and (resid 101 through 112 )
17X-RAY DIFFRACTION17chain 'D' and (resid 113 through 160 )
18X-RAY DIFFRACTION18chain 'E' and (resid 233 through 267 )
19X-RAY DIFFRACTION19chain 'E' and (resid 268 through 346 )
20X-RAY DIFFRACTION20chain 'E' and (resid 347 through 413 )
21X-RAY DIFFRACTION21chain 'E' and (resid 414 through 518 )
22X-RAY DIFFRACTION22chain 'E' and (resid 519 through 627 )
23X-RAY DIFFRACTION23chain 'F' and (resid 5 through 18 )
24X-RAY DIFFRACTION24chain 'F' and (resid 19 through 38 )
25X-RAY DIFFRACTION25chain 'F' and (resid 39 through 58 )
26X-RAY DIFFRACTION26chain 'F' and (resid 59 through 73 )
27X-RAY DIFFRACTION27chain 'F' and (resid 74 through 89 )
28X-RAY DIFFRACTION28chain 'F' and (resid 90 through 101 )
29X-RAY DIFFRACTION29chain 'F' and (resid 102 through 112 )
30X-RAY DIFFRACTION30chain 'F' and (resid 113 through 156 )

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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