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- PDB-4jiw: c1882 PAAR-repeat protein from Escherichia coli in complex with a... -

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基本情報

登録情報
データベース: PDB / ID: 4jiw
タイトルc1882 PAAR-repeat protein from Escherichia coli in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5
要素
  • Putative uncharacterized protein
  • Tail-associated lysozyme
キーワードHYDROLASE/PROTEIN BINDING / PAAR-repeat motif / membrane piercing / type VI secretion system / T6SS spike / cell puncturing device / beta-helix / T4 gp5 / VgrG tip / CFT073 / VgrG protein / HYDROLASE-PROTEIN BINDING complex
機能・相同性
機能・相同性情報


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host / symbiont entry into host cell via disruption of host cell envelope / virus tail / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host / symbiont entry into host cell via disruption of host cell envelope / virus tail / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / metal ion binding / identical protein binding
類似検索 - 分子機能
Tumour Suppressor Smad4 - #60 / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme ...Tumour Suppressor Smad4 - #60 / Gp5, C-terminal / Gp5 C-terminal repeat (3 copies) / Protein Gp5, N-terminal OB-fold domain / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Type VI secretion system PAAR protein / Pre-baseplate central spike protein Gp5 / Uncharacterized protein
類似検索 - 構成要素
生物種Enterobacteria phage T4 (ファージ)
Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.402 Å
データ登録者Buth, S.A. / Leiman, P.G. / Shneider, M.M.
引用ジャーナル: Nature / : 2013
タイトル: PAAR-repeat proteins sharpen and diversify the type VI secretion system spike.
著者: Shneider, M.M. / Buth, S.A. / Ho, B.T. / Basler, M. / Mekalanos, J.J. / Leiman, P.G.
履歴
登録2013年3月7日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02013年8月14日Provider: repository / タイプ: Initial release
改定 1.12014年6月11日Group: Database references
改定 1.22017年11月15日Group: Refinement description / カテゴリ: software
改定 1.32024年3月20日Group: Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: Tail-associated lysozyme
B: Tail-associated lysozyme
C: Tail-associated lysozyme
D: Putative uncharacterized protein
E: Tail-associated lysozyme
F: Tail-associated lysozyme
G: Tail-associated lysozyme
H: Putative uncharacterized protein
I: Tail-associated lysozyme
J: Tail-associated lysozyme
K: Tail-associated lysozyme
L: Putative uncharacterized protein
M: Tail-associated lysozyme
N: Tail-associated lysozyme
O: Tail-associated lysozyme
P: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)157,56627
ポリマ-157,10116
非ポリマー46511
88349
1
A: Tail-associated lysozyme
B: Tail-associated lysozyme
C: Tail-associated lysozyme
D: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,4007
ポリマ-39,2754
非ポリマー1253
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22570 Å2
ΔGint-78 kcal/mol
Surface area15480 Å2
手法PISA
2
E: Tail-associated lysozyme
F: Tail-associated lysozyme
G: Tail-associated lysozyme
H: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,4007
ポリマ-39,2754
非ポリマー1253
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22580 Å2
ΔGint-73 kcal/mol
Surface area15570 Å2
手法PISA
3
I: Tail-associated lysozyme
J: Tail-associated lysozyme
K: Tail-associated lysozyme
L: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,3656
ポリマ-39,2754
非ポリマー902
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22550 Å2
ΔGint-72 kcal/mol
Surface area15610 Å2
手法PISA
4
M: Tail-associated lysozyme
N: Tail-associated lysozyme
O: Tail-associated lysozyme
P: Putative uncharacterized protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)39,4007
ポリマ-39,2754
非ポリマー1253
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area22630 Å2
ΔGint-72 kcal/mol
Surface area15860 Å2
手法PISA
単位格子
Length a, b, c (Å)184.157, 184.157, 238.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDモデル要素
11D-102-

CL

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要素

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タンパク質 , 2種, 16分子 ABCEFGIJKMNODHLP

#1: タンパク質
Tail-associated lysozyme / Protein Gp5 / Gp5* / Gp5C


分子量: 9896.807 Da / 分子数: 12 / 断片: gp5G484, UNP RESIDUES 484-575 / 変異: T566D, D568K, S570A, R571K, D573N, I574L, G575N / 由来タイプ: 組換発現
由来: (組換発現) Enterobacteria phage T4 (ファージ)
遺伝子: 5 / プラスミド: pEEva2, pET-23a derivative / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834 / 参照: UniProt: P16009, lysozyme
#2: タンパク質
Putative uncharacterized protein / c1882


分子量: 9584.735 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / : CFT073 / 遺伝子: c1882 / プラスミド: pEEva2, pET-23a derivative / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): B834 / 参照: UniProt: Q8FHJ9, UniProt: A0A0H2V7J1*PLUS

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非ポリマー , 4種, 60分子

#3: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 4 / 由来タイプ: 合成 / : Mg
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / : Zn
#5: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / : Cl
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 49 / 由来タイプ: 天然 / : H2O

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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: 3.72 Å3/Da / 溶媒含有率: 66.95 %
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: 6.5
詳細: 100-150mM CaCl2, 13-15% PEG 3350, 100mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年9月22日 / 詳細: dynamically bendable mirror
放射モノクロメーター: Si(111) monochromator / 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: 3.4→48.6 Å / Num. all: 62214 / Num. obs: 62072 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / 冗長度: 7 % / Biso Wilson estimate: 79.75 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.56
反射 シェル解像度: 3.4→3.61 Å / 冗長度: 6.7 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 2.09 / % possible all: 98.9

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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
PHENIX(phenix.refine: 1.8.1_1168)精密化
XDSデータ削減
XDSデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.402→48.568 Å / SU ML: 0.51 / σ(F): 1.99 / 位相誤差: 25.48 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.243 3148 5.07 %
Rwork0.184 --
obs0.1869 62066 99.79 %
all-62214 -
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
精密化ステップサイクル: LAST / 解像度: 3.402→48.568 Å
タンパク質核酸リガンド溶媒全体
原子数10848 0 11 49 10908
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00211025
X-RAY DIFFRACTIONf_angle_d1.03915100
X-RAY DIFFRACTIONf_dihedral_angle_d9.4343876
X-RAY DIFFRACTIONf_chiral_restr0.0311772
X-RAY DIFFRACTIONf_plane_restr0.0021944
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4025-3.45560.411770.33832537X-RAY DIFFRACTION96
3.4556-3.51230.38011540.30142675X-RAY DIFFRACTION100
3.5123-3.57280.33171180.2822674X-RAY DIFFRACTION100
3.5728-3.63770.3411580.25732704X-RAY DIFFRACTION100
3.6377-3.70770.31811460.25212662X-RAY DIFFRACTION100
3.7077-3.78330.28371470.23972670X-RAY DIFFRACTION100
3.7833-3.86560.28241210.21632712X-RAY DIFFRACTION100
3.8656-3.95550.28531430.22622684X-RAY DIFFRACTION100
3.9555-4.05430.30111330.2382687X-RAY DIFFRACTION100
4.0543-4.16390.26561600.2182672X-RAY DIFFRACTION100
4.1639-4.28630.23121450.17732694X-RAY DIFFRACTION100
4.2863-4.42460.1891550.15472672X-RAY DIFFRACTION100
4.4246-4.58260.19931450.12512689X-RAY DIFFRACTION100
4.5826-4.7660.15311740.11062633X-RAY DIFFRACTION100
4.766-4.98270.18991170.1312738X-RAY DIFFRACTION100
4.9827-5.24510.25361270.16442680X-RAY DIFFRACTION100
5.2451-5.57330.2221430.14932686X-RAY DIFFRACTION100
5.5733-6.00290.20431470.15072658X-RAY DIFFRACTION100
6.0029-6.60560.23291170.1622729X-RAY DIFFRACTION100
6.6056-7.55840.23831350.18092683X-RAY DIFFRACTION100
7.5584-9.5110.2221540.20242677X-RAY DIFFRACTION100
9.511-48.57340.2371320.17282702X-RAY DIFFRACTION100
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0153-0.0147-0.04850.02740.03110.0676-1.64640.18711.6741-0.3051-1.4325-1.33890.00840.0564-0.00393.0846-0.11010.58841.943-0.06572.559637.92318.08738.5133
20.7691-0.0067-0.64870.33620.03110.5531-1.38750.7944-1.39610.3745-0.0560.91180.3945-0.5712-0.07831.9295-0.15780.79981.1341-0.13592.122741.59810.7125-7.1946
30.2207-0.2383-0.64820.63470.40782.05750.05560.34950.860.4210.60850.69870.2547-0.06150.35161.9789-0.61821.05851.4758-0.56542.522234.016824.5877-10.1223
40.15140.1832-0.25810.2082-0.29340.4069-0.789-0.7561-0.2380.6682-0.1606-0.45750.32070.3638-0.0232.0919-0.48510.77351.3092-0.34871.766143.435328.54730.9425
50.5321.66810.71355.1392.27941.0287-0.00420.8698-1.64630.5520.5359-0.76470.8997-0.67920.33341.5589-0.06330.98821.5611-0.05512.463552.463319.6772-10.9215
61.2701-0.2810.45440.36580.07760.2549-0.9352-0.0068-0.86961.0292-0.55680.74031.6212-0.2917-0.79141.8185-0.33880.77031.2424-0.45381.946547.275734.3679-12.6505
70.0629-0.01430.01420.07550.03390.0354-0.6464-0.2793-1.11490.1085-0.01460.3945-0.2170.2214-0.00382.3616-0.26790.62261.1183-0.06191.783563.195129.0643-12.7122
80.0840.2387-0.05560.5162-0.15380.04650.14690.1689-1.26221.2252-0.73960.26940.108-0.1462-0.00081.6205-0.2910.36411.4778-0.39181.516957.157940.8371-19.9936
90.71250.581-0.16630.3482-0.21170.0925-0.23181.4382-1.70410.86160.26231.3194-0.26180.2234-0.0051.5753-0.23020.12681.172-0.15011.165366.740543.8527-26.4805
100.20430.1595-0.03710.6140.40430.41850.4859-0.9627-0.61270.1497-0.7191.1864-0.35310.4484-0.32452.0076-0.57870.88681.6703-0.73663.090127.243517.1597-7.0915
112.27780.88021.67350.34950.611.25130.033-0.33150.90060.2392-0.04820.6808-0.3214-0.1661-0.78592.9410.00651.67291.2260.11432.560738.616420.78854.9065
121.33910.97890.28870.77770.29280.2090.0062-0.1417-0.706-0.16810.4497-0.85990.38070.42542.52091.9492-0.92361.91540.7616-0.07832.836647.000412.571-7.6949
130.1855-0.0902-0.14050.0280.0220.5182-0.14140.62170.6307-0.36950.88261.0296-1.2852-0.51360.11271.8724-0.46190.37021.1423-0.41841.77936.682223.9168-15.6261
143.1643-0.8666-0.83831.43090.4330.891-0.8195-0.70120.79420.56320.8317-0.4756-0.45350.0121-0.18962.1425-0.51020.60421.1276-0.37351.734346.24331.0178-1.8166
150.43710.79010.34361.65110.78460.39670.57550.4387-0.21391.1221-0.2681-0.90690.3050.2440.07242.0793-0.28991.03371.2823-0.27322.059857.003222.4457-11.395
160.7427-0.3380.45110.6105-0.0240.2363-0.07930.1186-0.58561.3309-0.10490.86530.4681-0.02320.00891.4737-0.43780.63341.4318-0.3791.794951.050635.8794-15.1159
170.48180.0964-0.46560.3739-0.26580.4479-0.64060.6062-0.79171.28360.07911.06860.0316-0.2563-0.00021.5519-0.31820.35341.4745-0.3961.479960.345540.1681-20.9692
180.0860.01330.03580.36970.1320.18480.6848-0.4139-0.5364-0.1225-0.0007-0.42910.1368-0.7175-0.00031.2598-0.31160.12691.3979-0.11671.143870.194245.321-21.2661
190.1094-0.1896-0.16640.13030.21690.3483-0.7244-0.3524-0.88430.17430.21520.50011.4821-1.31430.00081.7356-0.49380.58991.5188-0.27022.57236.48929.8644-8.4254
200.61920.6291-0.20031.1168-0.26420.06990.713-0.1649-1.0221-0.42450.47950.714-0.153-0.1197-0.07682.1979-0.26661.04431.1793-0.3142.488633.824325.05320.0754
210.3685-0.5966-0.47282.06662.83144.5495-0.0025-0.7099-0.89220.205-0.9987-0.0045-0.10970.2342-0.24142.5161-0.73150.84921.2215-0.24611.618546.668421.48241.6593
220.146-0.0378-0.14960.02360.0440.1360.02650.327-0.1760.88650.8371-0.39420.5684-0.00791.00232.7004-0.08541.30870.9257-1.07922.345550.193415.7493-10.1578
230.483-0.08360.56230.79381.35863.3583-1.16091.60950.2027-0.2074-0.09081.6722-0.9915-0.33710.05251.9518-0.39710.75051.4479-0.37562.245240.406628.406-15.1512
240.4749-0.3608-0.42970.37140.54290.7779-0.87880.3615-1.25060.9362-0.2061.00751.3156-0.93350.00092.2283-0.34440.73471.3198-0.31642.01653.80830.1706-12.6177
250.153-0.10690.03140.09150.02520.00111.01211.3824-0.31960.9882-1.0307-0.03720.84150.73-0.00141.2633-0.19090.36681.1452-0.39481.494652.909442.8664-14.763
261.1809-0.07720.01670.0873-0.05640.2734-0.50220.83460.0960.3059-1.8423-0.04240.8577-0.2639-0.02621.3135-0.25880.3561.0991-0.19181.463864.525838.203-22.2438
270.25330.2008-0.17570.2774-0.19910.2440.88950.5787-0.98160.143-0.7068-0.0699-0.1172-1.0681-0.00031.1248-0.18030.13471.1709-0.27371.019163.511750.9768-21.9395
280.10330.0740.0870.2322-0.18270.28730.07571.31180.1346-0.70920.04620.70720.3744-1.3470.00051.3649-0.11580.01171.44840.04360.882377.269358.3213-37.06
293.41961.75662.33760.8721.15481.54960.79632.4566-0.2038-0.4743-0.2646-0.761-0.27230.24230.09651.75580.02270.12181.70410.06210.894784.961863.1846-38.54
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1150.12470.1256-0.04440.1039-0.03680.13320.33811.2192-0.11180.7024-0.78470.2989-0.71440.03870.00182.00290.45870.32082.6914-0.31683.228330.65741.6459-59.7402
1160.65160.83130.31642.7495-1.97243.5021-1.12090.54990.2576-0.0686-1.40090.9295-0.53580.6011-0.21191.79990.77490.54613.01080.39792.180135.594940.1489-77.0137
1170.3895-0.2070.3910.7369-0.53220.5593-0.2903-0.39010.31911.08890.45960.18350.06380.2514-0.40613.20192.08570.78253.54490.00852.461646.623946.9697-69.5774
1180.1148-0.0031-0.02170.01690.00780.04540.7848-0.51831.50250.41540.20960.1097-1.58150.12540.00062.58160.68220.55732.57060.31791.879845.600238.8239-57.9466
1190.23090.23010.19930.277-0.11882.4248-0.0351-0.12030.70330.30390.5544-0.58370.7587-0.26340.59062.06390.84660.91422.26080.42673.098243.322528.2417-71.9074
1200.59030.56790.32620.6281-0.04330.37740.4260.44890.06321.11010.65360.8814-1.1978-1.8551-0.00081.60110.59420.39792.310.2532.578956.214829.513-67.7882
1210.11490.1595-0.05640.2009-0.15390.1114-0.70450.2320.0849-0.04950.87820.896-0.37710.33580.00091.67910.38260.09642.1010.1921.66667.11728.086-73.4199
1220.5342-0.35750.50020.2288-0.32630.45291.4399-0.60650.00230.93311.21421.1805-1.1177-1.7350.05421.78170.35070.44422.22440.47232.230666.640814.4838-64.8595
1230.099-0.0987-0.01130.08170.0096-0.00710.06060.6703-0.0514-0.4309-0.3076-0.3543-0.7209-1.5540.00061.26970.27190.27871.57220.0711.376776.603417.7994-75.3592
1241.64391.16810.65360.77480.42890.25340.88581.6097-0.8022-1.30280.50120.0204-0.7358-0.12060.41012.93991.5248-0.13162.3693-0.21252.153238.091851.4418-66.1158
1250.7525-0.35570.88440.1811-0.41661.03270.2705-0.1291-0.2872-0.48860.78550.6169-0.0984-0.36790.03821.70810.54970.64713.17570.53412.029433.044335.4705-62.825
1260.05380.01660.08610.20490.00220.1659-0.5948-0.2044-0.22410.0865-0.1402-0.0064-0.325-1.27290.00071.8530.6058-0.10082.56370.54093.460539.658636.8767-77.0812
1270.0122-0.0124-0.00410.0519-0.01150.08150.0222-0.83970.38160.10360.1545-0.1910.07380.180702.89181.4970.77643.30640.33962.115350.644544.0155-69.2109
1280.80010.5285-0.1130.3593-0.01130.1571.7933-0.3384-0.39860.1613-0.0871-0.0807-0.90341.0533-0.02022.65270.73170.29151.94220.08712.302748.396733.6475-59.2306
1292.58851.47250.1630.95520.58231.6295-0.4970.56520.18461.5181.00322.4968-0.5477-0.8493-0.10271.98530.72820.53221.88240.2812.9255.461930.5266-70.9607
1300.1140.1409-0.02840.1139-0.08370.14760.3203-1.3691-0.02510.8840.10771.9845-1.5521-1.7426-0.00171.40030.40210.39262.27370.2242.04160.021619.707-69.1359
1310.1447-0.1319-0.06380.13230.08290.0390.7066-0.37761.20410.39850.60590.7019-0.9940.47270.00332.02330.39270.331.78370.15171.94373.909626.0228-67.7436
1320.3745-0.30330.31270.2186-0.24180.24771.3081-0.3333-0.3164-0.94530.61560.1896-2.2226-0.27670.0271.87150.25260.72971.2394-0.00952.071971.663412.0712-67.2388
1330.20590.18150.22380.18060.13750.12090.1324-0.73760.2435-0.00550.09420.81610.0630.36770.00151.57490.30650.04891.14550.10381.346192.99587.7024-66.9732
1341.3187-0.3661.4740.2256-0.21131.7576-1.0188-0.24011.2483-0.8341-0.2376-0.2553-0.75270.938-0.0841.0721-0.25650.06641.28380.07651.053899.56822.5432-70.6384
1350.0384-0.05290.04350.0963-0.1380.14060.24380.5479-0.1343-2.03340.15141.1589-0.29350.8883-0.00111.33770.13310.15271.27160.06211.198684.150113.3536-75.2851
1360.1307-0.21440.00550.31620.00870.049-1.12080.7703-1.2524-0.3871-0.38422.56610.2681-0.4635-0.00741.37520.09020.0481.7549-0.01971.42787.82121.5259-74.8597
1370.1323-0.1153-0.05190.10330.01260.0634-0.45170.6146-1.4583-0.23840.5162-1.93990.08470.57230.00111.50830.20170.17871.34820.23951.6231105.6157-2.9738-72.6236
1380.52431.92690.30527.0161.12766.89561.02060.3678-0.0018-0.12310.2574-0.22091.09010.82643.09371.41690.1704-0.06641.25540.07391.361395.7786-3.9223-72.5267
1390.14080.12920.03830.15730.08850.04410.0763-0.70980.40750.2128-0.03222.15140.5564-0.86670.00021.65520.31850.46721.6570.09991.392477.65354.6739-70.1332
1400.66370.59740.26750.46840.26040.09630.05530.0514-0.39970.31330.2073-0.2941-0.4875-0.2261-0.00011.46180.08190.12331.22360.08661.151787.82335.861-64.6601
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 483:488)A483 - 488
2X-RAY DIFFRACTION2(CHAIN A AND RESID 489:499)A489 - 499
3X-RAY DIFFRACTION3(CHAIN A AND RESID 500:505)A500 - 505
4X-RAY DIFFRACTION4(CHAIN A AND RESID 506:512)A506 - 512
5X-RAY DIFFRACTION5(CHAIN A AND RESID 513:522)A513 - 522
6X-RAY DIFFRACTION6(CHAIN A AND RESID 523:536)A523 - 536
7X-RAY DIFFRACTION7(CHAIN A AND RESID 537:543)A537 - 543
8X-RAY DIFFRACTION8(CHAIN A AND RESID 544:561)A544 - 561
9X-RAY DIFFRACTION9(CHAIN A AND RESID 562:575)A562 - 575
10X-RAY DIFFRACTION10(CHAIN B AND RESID 483:488)B483 - 488
11X-RAY DIFFRACTION11(CHAIN B AND RESID 489:497)B489 - 497
12X-RAY DIFFRACTION12(CHAIN B AND RESID 498:505)B498 - 505
13X-RAY DIFFRACTION13(CHAIN B AND RESID 506:512)B506 - 512
14X-RAY DIFFRACTION14(CHAIN B AND RESID 513:521)B513 - 521
15X-RAY DIFFRACTION15(CHAIN B AND RESID 522:528)B522 - 528
16X-RAY DIFFRACTION16(CHAIN B AND RESID 529:545)B529 - 545
17X-RAY DIFFRACTION17(CHAIN B AND RESID 546:564)B546 - 564
18X-RAY DIFFRACTION18(CHAIN B AND RESID 565:575)B565 - 575
19X-RAY DIFFRACTION19(CHAIN C AND RESID 483:494)C483 - 494
20X-RAY DIFFRACTION20(CHAIN C AND RESID 495:500)C495 - 500
21X-RAY DIFFRACTION21(CHAIN C AND RESID 501:506)C501 - 506
22X-RAY DIFFRACTION22(CHAIN C AND RESID 507:513)C507 - 513
23X-RAY DIFFRACTION23(CHAIN C AND RESID 514:522)C514 - 522
24X-RAY DIFFRACTION24(CHAIN C AND RESID 523:541)C523 - 541
25X-RAY DIFFRACTION25(CHAIN C AND RESID 542:551)C542 - 551
26X-RAY DIFFRACTION26(CHAIN C AND RESID 552:564)C552 - 564
27X-RAY DIFFRACTION27(CHAIN C AND RESID 565:575)C565 - 575
28X-RAY DIFFRACTION28(CHAIN D AND RESID 2:14)D2 - 14
29X-RAY DIFFRACTION29(CHAIN D AND RESID 15:24)D15 - 24
30X-RAY DIFFRACTION30(CHAIN D AND RESID 25:39)D25 - 39
31X-RAY DIFFRACTION31(CHAIN D AND RESID 40:45)D40 - 45
32X-RAY DIFFRACTION32(CHAIN D AND RESID 46:50)D46 - 50
33X-RAY DIFFRACTION33(CHAIN D AND RESID 51:60)D51 - 60
34X-RAY DIFFRACTION34(CHAIN D AND RESID 61:73)D61 - 73
35X-RAY DIFFRACTION35(CHAIN D AND RESID 74:94)D74 - 94
36X-RAY DIFFRACTION36(CHAIN E AND RESID 483:489)E483 - 489
37X-RAY DIFFRACTION37(CHAIN E AND RESID 490:497)E490 - 497
38X-RAY DIFFRACTION38(CHAIN E AND RESID 498:505)E498 - 505
39X-RAY DIFFRACTION39(CHAIN E AND RESID 506:512)E506 - 512
40X-RAY DIFFRACTION40(CHAIN E AND RESID 513:522)E513 - 522
41X-RAY DIFFRACTION41(CHAIN E AND RESID 523:545)E523 - 545
42X-RAY DIFFRACTION42(CHAIN E AND RESID 546:555)E546 - 555
43X-RAY DIFFRACTION43(CHAIN E AND RESID 556:564)E556 - 564
44X-RAY DIFFRACTION44(CHAIN E AND RESID 565:575)E565 - 575
45X-RAY DIFFRACTION45(CHAIN F AND RESID 483:489)F483 - 489
46X-RAY DIFFRACTION46(CHAIN F AND RESID 490:497)F490 - 497
47X-RAY DIFFRACTION47(CHAIN F AND RESID 498:505)F498 - 505
48X-RAY DIFFRACTION48(CHAIN F AND RESID 506:512)F506 - 512
49X-RAY DIFFRACTION49(CHAIN F AND RESID 513:522)F513 - 522
50X-RAY DIFFRACTION50(CHAIN F AND RESID 523:530)F523 - 530
51X-RAY DIFFRACTION51(CHAIN F AND RESID 531:544)F531 - 544
52X-RAY DIFFRACTION52(CHAIN F AND RESID 545:564)F545 - 564
53X-RAY DIFFRACTION53(CHAIN F AND RESID 565:575)F565 - 575
54X-RAY DIFFRACTION54(CHAIN G AND RESID 483:489)G483 - 489
55X-RAY DIFFRACTION55(CHAIN G AND RESID 490:499)G490 - 499
56X-RAY DIFFRACTION56(CHAIN G AND RESID 500:505)G500 - 505
57X-RAY DIFFRACTION57(CHAIN G AND RESID 506:512)G506 - 512
58X-RAY DIFFRACTION58(CHAIN G AND RESID 513:520)G513 - 520
59X-RAY DIFFRACTION59(CHAIN G AND RESID 521:529)G521 - 529
60X-RAY DIFFRACTION60(CHAIN G AND RESID 530:545)G530 - 545
61X-RAY DIFFRACTION61(CHAIN G AND RESID 546:564)G546 - 564
62X-RAY DIFFRACTION62(CHAIN G AND RESID 565:575)G565 - 575
63X-RAY DIFFRACTION63(CHAIN H AND RESID 2:8)H2 - 8
64X-RAY DIFFRACTION64(CHAIN H AND RESID 9:21)H9 - 21
65X-RAY DIFFRACTION65(CHAIN H AND RESID 22:37)H22 - 37
66X-RAY DIFFRACTION66(CHAIN H AND RESID 38:44)H38 - 44
67X-RAY DIFFRACTION67(CHAIN H AND RESID 45:50)H45 - 50
68X-RAY DIFFRACTION68(CHAIN H AND RESID 51:57)H51 - 57
69X-RAY DIFFRACTION69(CHAIN H AND RESID 58:64)H58 - 64
70X-RAY DIFFRACTION70(CHAIN H AND RESID 65:94)H65 - 94
71X-RAY DIFFRACTION71(CHAIN I AND RESID 483:490)I483 - 490
72X-RAY DIFFRACTION72(CHAIN I AND RESID 491:497)I491 - 497
73X-RAY DIFFRACTION73(CHAIN I AND RESID 498:505)I498 - 505
74X-RAY DIFFRACTION74(CHAIN I AND RESID 506:512)I506 - 512
75X-RAY DIFFRACTION75(CHAIN I AND RESID 513:522)I513 - 522
76X-RAY DIFFRACTION76(CHAIN I AND RESID 523:536)I523 - 536
77X-RAY DIFFRACTION77(CHAIN I AND RESID 537:543)I537 - 543
78X-RAY DIFFRACTION78(CHAIN I AND RESID 544:564)I544 - 564
79X-RAY DIFFRACTION79(CHAIN I AND RESID 565:575)I565 - 575
80X-RAY DIFFRACTION80(CHAIN J AND RESID 483:493)J483 - 493
81X-RAY DIFFRACTION81(CHAIN J AND RESID 494:499)J494 - 499
82X-RAY DIFFRACTION82(CHAIN J AND RESID 500:505)J500 - 505
83X-RAY DIFFRACTION83(CHAIN J AND RESID 506:512)J506 - 512
84X-RAY DIFFRACTION84(CHAIN J AND RESID 513:522)J513 - 522
85X-RAY DIFFRACTION85(CHAIN J AND RESID 523:536)J523 - 536
86X-RAY DIFFRACTION86(CHAIN J AND RESID 537:543)J537 - 543
87X-RAY DIFFRACTION87(CHAIN J AND RESID 544:559)J544 - 559
88X-RAY DIFFRACTION88(CHAIN J AND RESID 560:575)J560 - 575
89X-RAY DIFFRACTION89(CHAIN K AND RESID 483:490)K483 - 490
90X-RAY DIFFRACTION90(CHAIN K AND RESID 491:499)K491 - 499
91X-RAY DIFFRACTION91(CHAIN K AND RESID 500:508)K500 - 508
92X-RAY DIFFRACTION92(CHAIN K AND RESID 509:514)K509 - 514
93X-RAY DIFFRACTION93(CHAIN K AND RESID 515:522)K515 - 522
94X-RAY DIFFRACTION94(CHAIN K AND RESID 523:536)K523 - 536
95X-RAY DIFFRACTION95(CHAIN K AND RESID 537:549)K537 - 549
96X-RAY DIFFRACTION96(CHAIN K AND RESID 550:564)K550 - 564
97X-RAY DIFFRACTION97(CHAIN K AND RESID 565:575)K565 - 575
98X-RAY DIFFRACTION98(CHAIN L AND RESID 2:14)L2 - 14
99X-RAY DIFFRACTION99(CHAIN L AND RESID 15:21)L15 - 21
100X-RAY DIFFRACTION100(CHAIN L AND RESID 22:38)L22 - 38
101X-RAY DIFFRACTION101(CHAIN L AND RESID 39:44)L39 - 44
102X-RAY DIFFRACTION102(CHAIN L AND RESID 45:50)L45 - 50
103X-RAY DIFFRACTION103(CHAIN L AND RESID 51:59)L51 - 59
104X-RAY DIFFRACTION104(CHAIN L AND RESID 60:65)L60 - 65
105X-RAY DIFFRACTION105(CHAIN L AND RESID 66:94)L66 - 94
106X-RAY DIFFRACTION106(CHAIN M AND RESID 483:489)M483 - 489
107X-RAY DIFFRACTION107(CHAIN M AND RESID 490:499)M490 - 499
108X-RAY DIFFRACTION108(CHAIN M AND RESID 500:506)M500 - 506
109X-RAY DIFFRACTION109(CHAIN M AND RESID 507:514)M507 - 514
110X-RAY DIFFRACTION110(CHAIN M AND RESID 515:522)M515 - 522
111X-RAY DIFFRACTION111(CHAIN M AND RESID 523:536)M523 - 536
112X-RAY DIFFRACTION112(CHAIN M AND RESID 537:548)M537 - 548
113X-RAY DIFFRACTION113(CHAIN M AND RESID 549:565)M549 - 565
114X-RAY DIFFRACTION114(CHAIN M AND RESID 566:575)M566 - 575
115X-RAY DIFFRACTION115(CHAIN N AND RESID 483:491)N483 - 491
116X-RAY DIFFRACTION116(CHAIN N AND RESID 492:499)N492 - 499
117X-RAY DIFFRACTION117(CHAIN N AND RESID 500:506)N500 - 506
118X-RAY DIFFRACTION118(CHAIN N AND RESID 507:512)N507 - 512
119X-RAY DIFFRACTION119(CHAIN N AND RESID 513:522)N513 - 522
120X-RAY DIFFRACTION120(CHAIN N AND RESID 523:544)N523 - 544
121X-RAY DIFFRACTION121(CHAIN N AND RESID 545:555)N545 - 555
122X-RAY DIFFRACTION122(CHAIN N AND RESID 556:566)N556 - 566
123X-RAY DIFFRACTION123(CHAIN N AND RESID 567:575)N567 - 575
124X-RAY DIFFRACTION124(CHAIN O AND RESID 483:493)O483 - 493
125X-RAY DIFFRACTION125(CHAIN O AND RESID 494:499)O494 - 499
126X-RAY DIFFRACTION126(CHAIN O AND RESID 500:508)O500 - 508
127X-RAY DIFFRACTION127(CHAIN O AND RESID 509:514)O509 - 514
128X-RAY DIFFRACTION128(CHAIN O AND RESID 515:522)O515 - 522
129X-RAY DIFFRACTION129(CHAIN O AND RESID 523:541)O523 - 541
130X-RAY DIFFRACTION130(CHAIN O AND RESID 542:555)O542 - 555
131X-RAY DIFFRACTION131(CHAIN O AND RESID 556:564)O556 - 564
132X-RAY DIFFRACTION132(CHAIN O AND RESID 565:575)O565 - 575
133X-RAY DIFFRACTION133(CHAIN P AND RESID 2:14)P2 - 14
134X-RAY DIFFRACTION134(CHAIN P AND RESID 15:24)P15 - 24
135X-RAY DIFFRACTION135(CHAIN P AND RESID 25:38)P25 - 38
136X-RAY DIFFRACTION136(CHAIN P AND RESID 39:43)P39 - 43
137X-RAY DIFFRACTION137(CHAIN P AND RESID 44:50)P44 - 50
138X-RAY DIFFRACTION138(CHAIN P AND RESID 51:60)P51 - 60
139X-RAY DIFFRACTION139(CHAIN P AND RESID 61:73)P61 - 73
140X-RAY DIFFRACTION140(CHAIN P AND RESID 74:94)P74 - 94

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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。

-
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