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- PDB-8xud: Crystal structure of adaptor NlpI in complex with endopeptidase M... -

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基本情報

登録情報
データベース: PDB / ID: 8xud
タイトルCrystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc
要素
  • (Substrate peptide) x 2
  • Lipoprotein NlpI
  • Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
  • Tail-specific protease
キーワードPROTEIN BINDING / hydrolases / lipoprotein / protease / protein complex / SUBSTRATE DEGRADATION
機能・相同性
機能・相同性情報


muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / C-terminal processing peptidase / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / cysteine-type peptidase activity / cell outer membrane / protein catabolic process ...muramoyltetrapeptide carboxypeptidase activity / muramoyltetrapeptide carboxypeptidase / C-terminal processing peptidase / capsule polysaccharide biosynthetic process / peptidoglycan metabolic process / peptidoglycan turnover / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素 / cysteine-type peptidase activity / cell outer membrane / protein catabolic process / cell wall organization / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / endopeptidase activity / receptor-mediated virion attachment to host cell / cell cycle / cell division / response to antibiotic / serine-type endopeptidase activity / signal transduction / protein homodimerization activity / proteolysis / plasma membrane
類似検索 - 分子機能
Tail specific protease, C-terminal / Lipoprotein NlpI / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / NlpC/P60 domain profile. / tail specific protease / Tail specific protease / Peptidase family S41 ...Tail specific protease, C-terminal / Lipoprotein NlpI / C-terminal domain of tail specific protease (DUF3340) / Tail specific protease, N-terminal domain / Tail specific protease N-terminal domain / C-terminal-processing peptidase S41A / NlpC/P60 domain profile. / tail specific protease / Tail specific protease / Peptidase family S41 / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / Tetratricopeptide repeat / ClpP/crotonase-like domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / Papain-like cysteine peptidase superfamily / PDZ domain / PDZ superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
PHOSPHATE ION / Lipoprotein NlpI / Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase / Tail-specific protease
類似検索 - 構成要素
生物種Escherichia coli K-12 (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.49 Å
データ登録者Tzeng, S.R. / Wang, S. / Huang, C.H.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: To Be Published
タイトル: Crystal structure of lipoprotein NlpI in complex with MepS
著者: Tzeng, S.R. / Wang, S. / Huang, C.H. / Lin, T.S.
履歴
登録2024年1月12日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年6月5日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Lipoprotein NlpI
B: Lipoprotein NlpI
C: Tail-specific protease
D: Tail-specific protease
I: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
J: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
K: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
L: Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase
M: Substrate peptide
N: Substrate peptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,61324
ポリマ－301,28310
非ポリマー1,33014
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)230.410, 230.410, 182.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2(chain "D" and resid 25 through 671)
d_1ens_3(chain "I" and resid 22 through 160)
d_2ens_3(chain "J" and resid 22 through 160)
d_3ens_3(chain "K" and resid 22 through 160)
d_4ens_3(chain "L" and resid 22 through 160)
d_1ens_4chain "M"
d_2ens_4(chain "N" and resid 3 through 10)

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ARGARGLEULEUAA25 - 28828 - 291
d_2ens_1ARGARGLEULEUBB25 - 28828 - 291
d_1ens_2ASPASPLYSLYSCC25 - 67125 - 671
d_2ens_2ASPASPLYSLYSDD25 - 67125 - 671
d_1ens_3SERSERSERSERIE22 - 16022 - 160
d_2ens_3SERSERSERSERJF22 - 16022 - 160
d_3ens_3SERSERSERSERKG22 - 16022 - 160
d_4ens_3SERSERSERSERLH22 - 16022 - 160
d_1ens_4UNKUNKUNKUNKMI1 - 81 - 8
d_2ens_4UNKUNKUNKUNKNJ3 - 102 - 9

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixベクター
1given(-0.0155532563466, -0.999878961522, 0.000398148202737), (-0.999866808629, 0.0155550344897, 0.00494023327092), (-0.00494582852163, -0.000321258458358, -0.999987717711)115.215756983, 113.030027543, 180.968679921
2given(-0.00148050887426, -0.999961567112, -0.0086413188728), (-0.999792701525, 0.00165562537876, -0.0202931732814), (0.020306700143, 0.00860948331745, -0.999756727772)114.9604216, 117.018727149, 178.267602202
3given(0.39475831688, 0.917843613681, -0.0415809100395), (-0.425343865652, 0.142448059484, -0.893751165762), (-0.814400679768, 0.370501890919, 0.446631706912)-25.0684763978, 156.142415425, 43.9804338684
4given(-0.0122274723944, -0.999862165342, -0.0112311725061), (-0.999843715089, 0.0120822776484, 0.0129059662422), (-0.0127684892082, 0.0113872245892, -0.999853637689)115.7800994, 112.899501466, 180.255407378
5given(0.424723916242, -0.145705903991, 0.893520780124), (-0.388009834453, -0.921018786579, 0.0342456294461), (0.817959634297, -0.361239787829, -0.447714029655)-41.411505315, 140.187048955, 135.985952892
6given(0.314563732173, -0.925545966626, -0.210747057072), (-0.866866521255, -0.189635896077, -0.461064703969), (0.386771370099, 0.327723802282, -0.861977387574)106.463300796, 174.739193105, 105.506557061

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要素

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タンパク質 , 3種, 8分子 ABCDIJKL

#1: タンパク質 Lipoprotein NlpI


分子量: 34082.734 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: nlpI, yhbM, b3163, JW3132 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P0AFB1
#2: タンパク質 Tail-specific protease / C-terminal-processing peptidase / PRC protein / Protease Re


分子量: 77520.758 Da / 分子数: 2 / Mutation: S452A/K477A / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: prc, tsp, b1830, JW1819 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P23865, C-terminal processing peptidase
#3: タンパク質
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase / Lipoprotein Spr / Murein hydrolase MepS


分子量: 19148.357 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 遺伝子: mepS, spr, yeiV, b2175, JW2163 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P0AFV4, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素, muramoyltetrapeptide carboxypeptidase

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タンパク質・ペプチド , 2種, 2分子 MN

#4: タンパク質・ペプチド Substrate peptide


分子量: 698.854 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: Chains M/N were supposed to be substrates peptides, but only the backbone orientation could be traced.
由来: (組換発現) Escherichia coli K-12 (大腸菌) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: タンパク質・ペプチド Substrate peptide


分子量: 783.958 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli K-12 (大腸菌) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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非ポリマー , 1種, 14分子

#6: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 14 / 由来タイプ: 合成 / 式: PO4

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詳細

研究の焦点であるリガンドがあるかN

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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: 4.03 Å3/Da / 溶媒含有率: 69.47 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 8% (w/v) PEG 4000, 1M sodium acetate pH 4.6

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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: NSRRC / ビームライン: TPS 05A / 波長: 1 Å
検出器タイプ: RAYONIX MX300-HS / 検出器: CCD / 日付: 2022年11月7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: 1 Å / 相対比: 1
反射解像度: 3.49→30 Å / Num. obs: 61469 / % possible obs: 97.4 % / 冗長度: 7.6 % / Biso Wilson estimate: 118.59 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.048 / Χ2: 1.182 / Net I/σ(I): 19.76
反射 シェル解像度: 3.49→3.62 Å / 冗長度: 6.8 % / Num. unique obs: 6097 / CC1/2: 0.806 / CC star: 0.945 / Rpim(I) all: 0.414 / Χ2: 0.683 / % possible all: 99.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
HKL-2000データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.49→29.91 Å / SU ML: 0.4365 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.3829
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2718 1994 3.26 %
Rwork0.2346 59215 -
obs0.2358 61209 97.39 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 182.22 Å2
精密化ステップサイクル: LAST / 解像度: 3.49→29.91 Å
タンパク質核酸リガンド溶媒全体
原子数19307 0 70 0 19377
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002219712
X-RAY DIFFRACTIONf_angle_d0.585126615
X-RAY DIFFRACTIONf_chiral_restr0.04052895
X-RAY DIFFRACTIONf_plane_restr0.00413483
X-RAY DIFFRACTIONf_dihedral_angle_d3.9632682
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.632227751264
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS3.25018194626
ens_3d_2EIX-RAY DIFFRACTIONTorsion NCS6.59114842256
ens_3d_3EIX-RAY DIFFRACTIONTorsion NCS1.0339401101
ens_3d_4EIX-RAY DIFFRACTIONTorsion NCS6.64069698313
ens_4d_2IMX-RAY DIFFRACTIONTorsion NCS1.38098506858
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-3.580.32411380.31174123X-RAY DIFFRACTION96.62
3.58-3.670.31531430.31594252X-RAY DIFFRACTION98.96
3.67-3.780.30371430.28924220X-RAY DIFFRACTION98.84
3.78-3.90.32271420.26154246X-RAY DIFFRACTION98.7
3.9-4.040.31511430.24394231X-RAY DIFFRACTION98.87
4.04-4.20.29481410.22894258X-RAY DIFFRACTION98.7
4.2-4.390.26451430.2044243X-RAY DIFFRACTION98.52
4.39-4.620.19771430.18744243X-RAY DIFFRACTION98.67
4.63-4.910.22691440.18364264X-RAY DIFFRACTION98.15
4.91-5.290.22561430.22034236X-RAY DIFFRACTION98.14
5.29-5.820.2631440.23924262X-RAY DIFFRACTION97.61
5.82-6.650.35811430.25644261X-RAY DIFFRACTION97.09
6.65-8.350.28731430.244252X-RAY DIFFRACTION95.92
8.35-29.910.24691410.23024124X-RAY DIFFRACTION89.39
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)
12.089258024570.5133246990781.177539106722.91822305387-0.4796334382731.75673254427-0.2579664278210.218210674852-0.2514352456590.4146902940460.0343432021892-0.621623026703-0.03461847320430.262279325669-1.78205095605E-51.018239569890.03040571440060.143224643360.9562016912140.1829627268220.96450337514345.533860145288.94779264587.5825657592
25.39913204149-1.311281520230.1180693274055.06336561705-0.9483644598234.33968295454-0.1125798467540.1725962209850.3219547395610.0679135803309-0.0801452052527-0.298608312123-0.665841028013-0.0572634250686-1.3682890497E-51.03376106740.0708262074585-0.02534891528940.9024044427770.1682164614860.72720129832532.8180939946107.61211719985.6891135396
33.952866767231.6085372814-0.8300629384822.19555301421-1.482058990852.912378840580.01029751867970.0938796549955-0.848209722947-0.216200591064-0.05901053370580.05438716961970.408138745107-0.0645220086443-2.24965238811E-50.9243024908640.05914812895520.1135930175840.9311445356070.177297928210.9003241993230.609344054771.29071994893.9752204736
42.78572789922-0.484228564303-0.5845695128354.161672055011.822635275161.57835848338-0.0872649088670.166646497964-0.3997991133940.362016168006-0.3613253046230.5949824503050.115232874904-0.5432903871566.15456596649E-50.980356784609-0.01590272540550.2472220303781.130392327080.01730735433581.213015835284.8724287073972.988503336896.309608204
51.50183447873-0.44589128355-2.313095397342.285190633170.1287251665894.12424872963-0.185433258151-0.2951710097420.2401424008460.0472485077074-0.041809169455-0.116463811798-0.245640796361-0.628650658716-7.06678074598E-51.05557676624-0.03049408512740.1625856529031.06266284080.0006896236591980.81448528726312.654651465989.253446322395.2894733457
61.585921845051.00677503597-0.4907199997951.07586553911-0.02676838463070.306275668142-0.05425185615881.920257053120.789825980267-1.63090520918-0.793843165461-0.1299430273840.759614954159-0.205047694181-0.000640282992061.158957476780.1598855129450.1388186596021.311281045390.07254779881131.2697857492613.721161028481.853633845581.4015901802
70.787087533245-0.07346084114520.7057885342723.35342854355-0.3810401055433.585445313070.0755646173012-0.2579485576540.364683808675-0.0382106892454-0.0700340457576-1.28653535417-0.5243488862571.62568354781-0.003223887068731.38349062713-0.456062392012-0.322215084332.232871441680.2367401483862.1475262339182.9226208142113.595536038104.753262384
81.955492296281.674354185060.4622026194692.823890152432.525471714350.8985587118960.531776232670.425898171930.1309430993350.008744022438050.152266201520.1507574370390.02364413462690.229098485694-2.36852393133E-52.25783126370.365703227092-0.2755057468432.290649598340.5650399529482.2900788146579.489909635489.7282723171123.740215154
90.9448530969140.1194646917510.2877181146750.8047921282360.7541942294611.613157854290.104926861135-0.604136010025-0.1835406196610.815340196612-0.111119963511-0.42813800981-0.3227991404040.411356180821-1.10926953345E-52.30259557186-0.148385640772-0.2808359014052.032145000180.3254981563291.6709285299865.6387037646108.96634539129.677795611
101.864079827781.137013231561.75123258120.8401493865971.381845603371.141935673310.1777334959540.12370761864-0.632159560045-0.4803931971370.1803732837230.2820745212820.757096392395-0.468004395495-6.91909997334E-51.68284100783-0.3790928036850.1852938180491.52163126614-0.4029897603142.16061185509-6.546617980637.261460022181.5289724154
11-0.00582531991647-0.07892228548430.141464299799-0.0211906073341-0.2173676557010.270364172612-1.060388288341.99698958414-2.133240391021.322370254840.5422020433150.1335212142712.286860657740.4938352834310.0009947882836662.46087863157-0.2712740798080.1963323650232.9018352192-1.016727535992.96808743342-6.4741355530917.967154377867.5652412765
122.214691135150.5063999230520.5892039294430.8787183381370.712634073764-0.3065596980080.1027145339610.715580128885-0.96829074095-0.146915959655-0.382436956015-0.5030185048061.02827474992-0.110821845498-6.78821396081E-52.13250560810.06215541265950.4178060495721.85232009794-0.5123683355162.3642226785618.621170481530.858516480467.4022121888
130.04153876431020.0516738671515-0.2303933362330.061144323659-0.3926384569740.0632564847968-0.4216597461911.58281143381.244120771490.3480451763230.4808330983850.1574624208040.169371047897-2.84265855229-0.01677980846892.22010309944-0.3262357020710.607339083583.56053538746-0.4972374668561.8279328044320.28138905852.763363223250.1884071335
141.875055442120.474225095931.407556421654.394874959531.302492175012.54688378921-0.4716642171191.36195795915-0.310749722285-1.387045006180.083026973329-0.0858468888801-0.3032829002660.261267090028-5.46847730252E-51.78755110439-0.1147094567240.3321872655362.15836183317-0.25504057131.517854305812.866448567756.06158262463.282499905
150.379604344777-1.019671051890.4769967730092.538307507621.203295352692.16555599765-0.1889728091970.633393485761-0.260992866023-1.040220695710.189982770017-0.0445401116046-0.444181264537-0.237199835053-2.12931972242E-62.21308213259-0.3458945707980.1221903379062.55934422171-0.5443803905962.02941421509-1.5952813364743.83541473343.2848673503
160.3179625606660.813284504490.3145279478713.813908320260.9533409004333.52904799127-0.5127456946920.4503664744690.19387075746-0.4655200001020.4189827372751.065034786110.858509930931-0.864953425081-0.0001259725916220.9463947605080.1753418893190.1570875985421.04365116006-0.01763743372481.1503973647439.981100436970.74741154872.7504381878
172.17604068137-0.2387187061560.667789373281.92513685574-0.2786842254963.659711610130.2759634565160.959999765839-1.0219265507-0.634574672031-0.142126314267-0.32073123329-0.2608991457750.2910751979433.64024639435E-51.421897420270.1483711357750.2492192385881.09794035796-0.01671476398331.2630619516352.738209297163.233554623657.0026027084
181.368383640261.07798323131.137300118981.378422455041.506038697411.282600018050.4209354449380.7556036013810.643621683084-0.8200952022250.1680272054190.327236571506-0.215892347242-0.3136154831-7.16433810717E-51.364008210770.2605201729450.1881767552981.147186120860.1458102667061.161509148344.406623365272.938396986452.5624490697
191.976295989520.218201506781-0.6821454873331.77390896888-2.267459422463.21026282544-1.310211439470.740544483344-0.280375977821-1.19260361547-0.073691567962-0.174600882051.81405074316-1.54407575694-0.05643821563321.336960304710.3382894355680.2572785302811.06360270994-0.1746133321371.6459613978139.277671514364.533578590656.813707901
201.3402883491-0.2310253208830.1680397727630.60587634502-0.7726354848180.808499044352-0.05391744356690.403306680941-0.911090968793-0.155494148764-0.151854948591-0.621262260071-0.343195452812-0.145581448893-0.0001291398292491.361429798470.1153682109920.1670560258971.111200745260.1492892767471.2205612858351.224079977282.332438480866.6841950858
211.990787035160.607127665001-0.1265690078631.254117309531.060185067281.186900273190.1448304123990.9139542434130.0843409707586-0.463876158508-0.2159647041350.810757604866-0.0910409439315-0.455129381076-1.267401685E-51.485498113190.2350436136660.3225016246311.110322379080.2549042849521.225432771651.6519850990.473274640351.4074373736
221.500003672831.339538221390.3946715449741.022982044320.4335517980840.0787958099938-0.04305844057111.098568193981.351121267340.5322866674470.4286809200110.268887495802-1.61845467427-1.025027814160.0002726255754161.753498853530.05911245686640.3954509592311.110839205360.08225211494361.9097410393951.1307199497102.24480666160.1067031918
231.24693274621-0.2493787456831.465653070820.746081407271-0.5301256161651.890934072450.0633651993605-0.3888444822820.674353050698-0.0220717044883-0.170788041391-0.272865463215-1.0523121030.473187794267-8.39804430099E-51.694006781150.03276017548570.4062320358621.066403311170.189004792451.5408953074158.4248619991101.34666187557.5076583662
240.391413162385-0.08592666955570.3969818117460.135039230212-0.2807609319140.549957895284-1.131344778662.97142912104-1.85491805982-1.61744585362-0.533239205574-0.348276032441-0.5871286914792.17642802201-0.03295334287972.183908231690.5172565835210.570336082642.087513905070.03228152565861.1817310965938.360828427794.120688845976.3164359333
253.18972011112-0.7636734806770.5241851491521.689348577630.0710913091280.5558868916570.184120121895-0.4758061407440.4698067499290.3903184676260.2676707381850.908015805316-1.52375778631-0.367649122859-2.184471003833.82129150946-0.3450328127370.0431267047571-1.086977730671.050304139581.2243345930540.489025873790.8162627219101.970264469
262.02499253-0.9538661858561.479143695610.509558661038-0.2592971120252.564516349730.167607415312-0.228330331649-0.65441412166-0.0701875528686-1.04158427417-1.59221836871-0.8019723381540.804175600673-0.0001103248809221.066882538330.2023924484740.05500674710131.078749582410.09248227108380.98680418943244.565968469270.9603291446109.313019974
270.1470135546150.0404644961308-0.11710123890.293813027945-0.08670254930830.07408873960670.494265922794-1.37124093515-1.567215821941.474025446161.482316585970.087468041837-0.0213442215092-0.2457587130150.001266333195921.160528053660.1592652170260.006237956719861.551898250930.2708004111880.92149761507345.493011354952.8819478094125.74773125
282.760975019870.2984144024451.315178363883.05456020604-0.9499501943381.83097282201-0.0615325636825-0.6719045084090.09267179071550.3791303019690.23274721026-0.032374284064-0.1445765389850.214068679978-1.22711416557E-51.158888661510.210654879152-0.005942179890051.219857659260.1163540914490.90867293236346.824920447969.1917516153125.754829611
296.77488159023-0.58813596051.68290428082.32515171049-0.1055407181690.4120719556030.367149309267-1.326464589630.9120834236141.54907917012-1.01331646027-0.8672856037590.429170737319-0.561668190568-0.3474222425551.306061854290.234948641590.3075211011821.427892772650.3400101454970.38303781738437.100145858874.5694172192109.539453719
300.696221652894-0.524067596789-0.31748542221.23046783928-0.1053266684240.194784337082-0.900578583879-0.129834643152-0.7163039401610.2495652074890.223336190864-0.6165065334270.0951855328371-0.5414689179241.69138909039E-50.9244998827970.003546251891980.07785091963361.299881810930.3614775505721.6317570615628.484571294555.3311414801117.651689058
314.05887829523-2.302571861930.5105487474581.3553185711-0.3643228461570.30768156487-0.589215556644-1.070413684130.0550050873574-0.04829031977281.316228350550.08487759269611.22334510416-0.0670036987491-0.1249037151571.489381531880.2474126941080.3617716526532.016300787930.546898100041.6161081109725.172969975357.0826460328136.040872663
321.505026406371.1630931804-0.9172855262970.793674620485-0.6271265218920.7254200632890.0313696254465-0.1019682456641.565456457730.316272612289-0.1593127623311.15149616417-1.800568612240.388371412262-0.04029792840371.182013437220.263446216650.1820460386081.395541517060.3296650660081.2802837242422.207798988667.1362820929124.287405732
330.004148694317390.02733541015410.06755137929210.7809338782980.9420453383191.059624064930.233236092476-0.0750943731094-1.01123785576-1.44071707020.5327897309791.33542493766-0.9259667517382.040601100860.01701120713040.924096362507-0.126109419702-0.08371327303752.24889139760.2151756669331.9029638042212.91908646860.1181290313112.569898953
341.36974953389-0.0341330181227-1.166195890941.55690188891-0.1851733265372.04672530469-0.350899901114-0.1975597700330.1485693255380.654040235802-0.2325667255750.549624317588-0.625723644565-0.745452958197-0.0001673288183021.195286553890.1468321643520.3199234428541.765077710260.4633016044751.7436530491112.093421429857.2300458366125.002457871
35-0.00974155966328-0.1674721221310.1361617369610.324042325471-0.3860074851180.2958034835930.4122132541790.7371117487070.659179286957-2.25471719419-0.505946429454-1.05504486074-0.116504338764-2.006047932380.003458396148671.733040081590.3024565452320.398421354832.078308994740.6502563849521.0132016016921.044908841774.1485233396106.846420583
360.04644212894870.2234378780990.261255152841.095418658451.155603144871.19080776518-1.300077174490.350970788271-0.4937463573920.367114763946-0.8380411352540.1219873421771.09685578044-1.56179035922-0.03108179831671.29451635273-0.07017243979030.1384454944331.530886256710.0425689458011.1088233352962.2795938573100.203149441112.527521708
370.02435798746420.02157101575290.0632732792330.0649699317648-0.02984726981640.0766666822070.226879296083-0.302223019039-1.27113959252-0.517381192564-0.3864892704720.794862106982.333433773041.008567290680.001163561564581.75663429083-0.3246883724630.0647144507841.50135653774-0.329903886641.254513168810.713357922450.371560313466.2549181385
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 143 )AA25 - 1431 - 119
22chain 'A' and (resid 144 through 288 )AA144 - 288120 - 264
33chain 'B' and (resid 25 through 109 )BB25 - 1091 - 85
44chain 'B' and (resid 110 through 211 )BB110 - 21186 - 187
55chain 'B' and (resid 212 through 268 )BB212 - 268188 - 244
66chain 'B' and (resid 269 through 288 )BB269 - 288245 - 264
77chain 'C' and (resid 25 through 299 )CC25 - 2991 - 275
88chain 'C' and (resid 300 through 387 )CC300 - 387276 - 363
99chain 'C' and (resid 388 through 671 )CC388 - 671364 - 647
1010chain 'D' and (resid 25 through 159 )DD25 - 1591 - 135
1111chain 'D' and (resid 160 through 204 )DD160 - 204136 - 180
1212chain 'D' and (resid 205 through 361 )DD205 - 361181 - 337
1313chain 'D' and (resid 362 through 416 )DD362 - 416338 - 392
1414chain 'D' and (resid 417 through 512 )DD417 - 512393 - 488
1515chain 'D' and (resid 513 through 675 )DD513 - 675489 - 651
1616chain 'I' and (resid 21 through 51 )IE21 - 511 - 31
1717chain 'I' and (resid 52 through 98 )IE52 - 9832 - 78
1818chain 'I' and (resid 99 through 150 )IE99 - 15079 - 130
1919chain 'I' and (resid 151 through 162 )IE151 - 162131 - 142
2020chain 'J' and (resid 22 through 51 )JF22 - 511 - 30
2121chain 'J' and (resid 52 through 93 )JF52 - 9331 - 72
2222chain 'J' and (resid 94 through 118 )JF94 - 11873 - 97
2323chain 'J' and (resid 119 through 160 )JF119 - 16098 - 139
2424chain 'J' and (resid 161 through 168 )JF161 - 168140 - 147
2525chain 'K' and (resid 21 through 27 )KG21 - 271 - 7
2626chain 'K' and (resid 28 through 51 )KG28 - 518 - 31
2727chain 'K' and (resid 52 through 67 )KG52 - 6732 - 47
2828chain 'K' and (resid 68 through 160 )KG68 - 16048 - 140
2929chain 'L' and (resid 21 through 35 )LH21 - 351 - 15
3030chain 'L' and (resid 36 through 51 )LH36 - 5116 - 31
3131chain 'L' and (resid 52 through 67 )LH52 - 6732 - 47
3232chain 'L' and (resid 68 through 98 )LH68 - 9848 - 78
3333chain 'L' and (resid 99 through 107 )LH99 - 10779 - 87
3434chain 'L' and (resid 108 through 157 )LH108 - 15788 - 137
3535chain 'L' and (resid 158 through 168 )LH158 - 168138 - 148
3636chain 'M' and (resid 1 through 8 )MI1 - 81 - 8
3737chain 'N' and (resid 2 through 10 )NJ2 - 101 - 9

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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://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