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- PDB-9ll5: Crystal structure of the Helicobacter pylori copper resistance de... -

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基本情報

登録情報
データベース: PDB / ID: 9ll5
タイトルCrystal structure of the Helicobacter pylori copper resistance determinant CrdA in complex with silver ions in space group P1
要素Copper resistance protein
キーワードMETAL BINDING PROTEIN / CrdA / copper ion
機能・相同性SILVER ION / :
機能・相同性情報
生物種Helicobacter pylori (ピロリ菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.85 Å
データ登録者Ki, D.W. / Oh, H.B. / Cho, H.Y. / Song, W.S. / Yoon, S.I.
資金援助 韓国, 1件
組織認可番号国
National Research Foundation (NRF, Korea)RS-2023-00208153 韓国
引用ジャーナル: Febs J. / 年: 2025
タイトル: Structural basis of Cu(I) ion recognition by the Helicobacter pylori copper resistance determinant CrdA.
著者: Ki, D.U. / Oh, H.B. / Cho, H.Y. / Song, W.S. / Yoon, S.I.
履歴
登録2025年1月17日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02025年11月19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

ダウンロードとリンク

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集合体

登録構造単位
A: Copper resistance protein
B: Copper resistance protein
C: Copper resistance protein
D: Copper resistance protein
E: Copper resistance protein
F: Copper resistance protein
G: Copper resistance protein
H: Copper resistance protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,38029
ポリマ－98,1948
非ポリマー2,18621
水5,441302
1
A: Copper resistance protein
B: Copper resistance protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)24,9806
ポリマ－24,5492
非ポリマー4314
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-21 kcal/mol
Surface area11130 Å2
手法PISA
2
C: Copper resistance protein
D: Copper resistance protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,1648
ポリマ－24,5492
非ポリマー6166
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-22 kcal/mol
Surface area11280 Å2
手法PISA
3
E: Copper resistance protein
F: Copper resistance protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,1648
ポリマ－24,5492
非ポリマー6166
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-27 kcal/mol
Surface area10750 Å2
手法PISA
4
G: Copper resistance protein
H: Copper resistance protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,0727
ポリマ－24,5492
非ポリマー5245
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-21 kcal/mol
Surface area11020 Å2
手法PISA
単位格子
Length a, b, c (Å)42.928, 52.666, 104.112
Angle α, β, γ (deg.)86.496, 84.639, 66.646
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYS(chain 'A' and (resid 20 through 21 or (resid 22...AA20 - 265 - 11
12ASPASPPROPRO(chain 'A' and (resid 20 through 21 or (resid 22...AA29 - 4014 - 25
13LYSLYSVALVAL(chain 'A' and (resid 20 through 21 or (resid 22...AA42 - 6527 - 50
14PHEPHEPROPRO(chain 'A' and (resid 20 through 21 or (resid 22...AA67 - 7352 - 58
15PROPROMETMET(chain 'A' and (resid 20 through 21 or (resid 22...AA76 - 8161 - 66
16VALVALGLUGLU(chain 'A' and (resid 20 through 21 or (resid 22...AA84 - 8669 - 71
17ASNASNGLUGLU(chain 'A' and (resid 20 through 21 or (resid 22...AA88 - 9273 - 77
18THRTHRTYRTYR(chain 'A' and (resid 20 through 21 or (resid 22...AA95 - 11780 - 102
19ALAALALEULEU(chain 'A' and (resid 20 through 21 or (resid 22...AA119 - 125104 - 110
210PROPROLYSLYS(chain 'B' and (resid 20 through 21 or (resid 22...BB20 - 265 - 11
211ASPASPPROPRO(chain 'B' and (resid 20 through 21 or (resid 22...BB29 - 4014 - 25
212LYSLYSVALVAL(chain 'B' and (resid 20 through 21 or (resid 22...BB42 - 6527 - 50
213PHEPHEPROPRO(chain 'B' and (resid 20 through 21 or (resid 22...BB67 - 7352 - 58
214PROPROMETMET(chain 'B' and (resid 20 through 21 or (resid 22...BB76 - 8161 - 66
215VALVALGLUGLU(chain 'B' and (resid 20 through 21 or (resid 22...BB84 - 8669 - 71
216ASNASNGLUGLU(chain 'B' and (resid 20 through 21 or (resid 22...BB88 - 9273 - 77
217THRTHRTYRTYR(chain 'B' and (resid 20 through 21 or (resid 22...BB95 - 11780 - 102
218ALAALALEULEU(chain 'B' and (resid 20 through 21 or (resid 22...BB119 - 125104 - 110
319PROPROLYSLYS(chain 'C' and (resid 20 through 21 or (resid 22...CC20 - 265 - 11
320ASPASPPROPRO(chain 'C' and (resid 20 through 21 or (resid 22...CC29 - 4014 - 25
321LYSLYSVALVAL(chain 'C' and (resid 20 through 21 or (resid 22...CC42 - 6527 - 50
322PHEPHEPROPRO(chain 'C' and (resid 20 through 21 or (resid 22...CC67 - 7352 - 58
323PROPROMETMET(chain 'C' and (resid 20 through 21 or (resid 22...CC76 - 8161 - 66
324VALVALGLUGLU(chain 'C' and (resid 20 through 21 or (resid 22...CC84 - 8669 - 71
325ASNASNGLUGLU(chain 'C' and (resid 20 through 21 or (resid 22...CC88 - 9273 - 77
326THRTHRTYRTYR(chain 'C' and (resid 20 through 21 or (resid 22...CC95 - 11780 - 102
327ALAALALEULEU(chain 'C' and (resid 20 through 21 or (resid 22...CC119 - 125104 - 110
428PROPROLYSLYS(chain 'D' and (resid 20 through 21 or (resid 22...DD20 - 265 - 11
429ASPASPPROPRO(chain 'D' and (resid 20 through 21 or (resid 22...DD29 - 4014 - 25
430LYSLYSVALVAL(chain 'D' and (resid 20 through 21 or (resid 22...DD42 - 6527 - 50
431PHEPHEPROPRO(chain 'D' and (resid 20 through 21 or (resid 22...DD67 - 7352 - 58
432PROPROMETMET(chain 'D' and (resid 20 through 21 or (resid 22...DD76 - 8161 - 66
433VALVALGLUGLU(chain 'D' and (resid 20 through 21 or (resid 22...DD84 - 8669 - 71
434ASNASNGLUGLU(chain 'D' and (resid 20 through 21 or (resid 22...DD88 - 9273 - 77
435THRTHRTYRTYR(chain 'D' and (resid 20 through 21 or (resid 22...DD95 - 11780 - 102
436ALAALALEULEU(chain 'D' and (resid 20 through 21 or (resid 22...DD119 - 125104 - 110
537PROPROLYSLYS(chain 'E' and (resid 20 through 25 or (resid 26...EE20 - 265 - 11
538ASPASPPROPRO(chain 'E' and (resid 20 through 25 or (resid 26...EE29 - 4014 - 25
539LYSLYSVALVAL(chain 'E' and (resid 20 through 25 or (resid 26...EE42 - 6527 - 50
540PHEPHEPROPRO(chain 'E' and (resid 20 through 25 or (resid 26...EE67 - 7352 - 58
541PROPROMETMET(chain 'E' and (resid 20 through 25 or (resid 26...EE76 - 8161 - 66
542VALVALGLUGLU(chain 'E' and (resid 20 through 25 or (resid 26...EE84 - 8669 - 71
543ASNASNGLUGLU(chain 'E' and (resid 20 through 25 or (resid 26...EE88 - 9273 - 77
544THRTHRTYRTYR(chain 'E' and (resid 20 through 25 or (resid 26...EE95 - 11780 - 102
545ALAALALEULEU(chain 'E' and (resid 20 through 25 or (resid 26...EE119 - 125104 - 110
646PROPROLYSLYS(chain 'F' and (resid 20 through 27 or resid 29...FF20 - 265 - 11
647ASPASPPROPRO(chain 'F' and (resid 20 through 27 or resid 29...FF29 - 4014 - 25
648LYSLYSVALVAL(chain 'F' and (resid 20 through 27 or resid 29...FF42 - 6527 - 50
649PHEPHEPROPRO(chain 'F' and (resid 20 through 27 or resid 29...FF67 - 7352 - 58
650PROPROMETMET(chain 'F' and (resid 20 through 27 or resid 29...FF76 - 8161 - 66
651VALVALGLUGLU(chain 'F' and (resid 20 through 27 or resid 29...FF84 - 8669 - 71
652ASNASNGLUGLU(chain 'F' and (resid 20 through 27 or resid 29...FF88 - 9273 - 77
653THRTHRTYRTYR(chain 'F' and (resid 20 through 27 or resid 29...FF95 - 11780 - 102
654ALAALALEULEU(chain 'F' and (resid 20 through 27 or resid 29...FF119 - 125104 - 110
755PROPROLYSLYS(chain 'G' and (resid 20 through 25 or (resid 26...GG20 - 265 - 11
756ASPASPPROPRO(chain 'G' and (resid 20 through 25 or (resid 26...GG29 - 4014 - 25
757LYSLYSVALVAL(chain 'G' and (resid 20 through 25 or (resid 26...GG42 - 6527 - 50
758PHEPHEPROPRO(chain 'G' and (resid 20 through 25 or (resid 26...GG67 - 7352 - 58
759PROPROMETMET(chain 'G' and (resid 20 through 25 or (resid 26...GG76 - 8161 - 66
760VALVALGLUGLU(chain 'G' and (resid 20 through 25 or (resid 26...GG84 - 8669 - 71
761ASNASNGLUGLU(chain 'G' and (resid 20 through 25 or (resid 26...GG88 - 9273 - 77
762THRTHRTYRTYR(chain 'G' and (resid 20 through 25 or (resid 26...GG95 - 11780 - 102
763ALAALALEULEU(chain 'G' and (resid 20 through 25 or (resid 26...GG119 - 125104 - 110
864PROPROLYSLYS(chain 'H' and (resid 20 through 21 or (resid 22...HH20 - 265 - 11
865ASPASPPROPRO(chain 'H' and (resid 20 through 21 or (resid 22...HH29 - 4014 - 25
866LYSLYSVALVAL(chain 'H' and (resid 20 through 21 or (resid 22...HH42 - 6527 - 50
867PHEPHEPROPRO(chain 'H' and (resid 20 through 21 or (resid 22...HH67 - 7352 - 58
868PROPROMETMET(chain 'H' and (resid 20 through 21 or (resid 22...HH76 - 8161 - 66
869VALVALGLUGLU(chain 'H' and (resid 20 through 21 or (resid 22...HH84 - 8669 - 71
870ASNASNGLUGLU(chain 'H' and (resid 20 through 21 or (resid 22...HH88 - 9273 - 77
871THRTHRTYRTYR(chain 'H' and (resid 20 through 21 or (resid 22...HH95 - 11780 - 102
872ALAALALEULEU(chain 'H' and (resid 20 through 21 or (resid 22...HH119 - 125104 - 110

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要素

#1: タンパク質
Copper resistance protein


分子量: 12274.262 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Helicobacter pylori (ピロリ菌) / 遺伝子: B0X44_01495, B0X54_06630 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A2A6UQS9
#2: 化合物
ChemComp-AG / SILVER ION


分子量: 107.868 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Ag / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 302 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.19 Å3/Da / 溶媒含有率: 43.84 %
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 / pH: 4.8 / 詳細: PEG 600, phosphate 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: 0.9793 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2021年6月30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: 0.9793 Å / 相対比: 1
反射解像度: 1.85→30 Å / Num. obs: 67686 / % possible obs: 95.5 % / 冗長度: 3.7 % / Biso Wilson estimate: 20.38 Å2 / CC1/2: 0.995 / Net I/σ(I): 25.5
反射 シェル解像度: 1.85→1.88 Å / 冗長度: 3.6 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3263 / CC1/2: 0.803 / % possible all: 91.4

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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 / 解像度: 1.85→29.76 Å / SU ML: 0.215 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 24.6068
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2321 3274 4.84 %
Rwork0.1914 64395 -
obs0.1934 67669 95.13 %
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: 30.13 Å2
精密化ステップサイクル: LAST / 解像度: 1.85→29.76 Å
タンパク質核酸リガンド溶媒全体
原子数6332 0 30 302 6664
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00686445
X-RAY DIFFRACTIONf_angle_d0.94368731
X-RAY DIFFRACTIONf_chiral_restr0.05991014
X-RAY DIFFRACTIONf_plane_restr0.00671120
X-RAY DIFFRACTIONf_dihedral_angle_d16.86663968
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.2831360.25482484X-RAY DIFFRACTION84.43
1.88-1.910.33211430.23512663X-RAY DIFFRACTION91.7
1.91-1.940.31751240.21682719X-RAY DIFFRACTION91.01
1.94-1.970.2751370.21652699X-RAY DIFFRACTION91.25
1.97-2.010.27161280.20592700X-RAY DIFFRACTION92.51
2.01-2.050.25671500.20082713X-RAY DIFFRACTION91.27
2.05-2.090.22881270.20022671X-RAY DIFFRACTION92.04
2.09-2.130.25591410.20242735X-RAY DIFFRACTION91.77
2.13-2.180.28041480.20182740X-RAY DIFFRACTION94.32
2.18-2.240.21371370.20012783X-RAY DIFFRACTION94.53
2.24-2.30.26521540.19952816X-RAY DIFFRACTION95.13
2.3-2.370.27881270.20722843X-RAY DIFFRACTION96.18
2.37-2.440.26541660.20652801X-RAY DIFFRACTION97.21
2.44-2.530.26911310.20582969X-RAY DIFFRACTION97.88
2.53-2.630.25591330.19882845X-RAY DIFFRACTION97.83
2.63-2.750.21621390.1952884X-RAY DIFFRACTION98.28
2.75-2.890.21921590.19632887X-RAY DIFFRACTION98.16
2.89-3.080.22541340.20382924X-RAY DIFFRACTION98.2
3.08-3.310.25251260.17822939X-RAY DIFFRACTION98.55
3.31-3.650.22081830.17872826X-RAY DIFFRACTION98.82
3.65-4.170.18271170.17532956X-RAY DIFFRACTION98.87
4.17-5.250.19571790.16232899X-RAY DIFFRACTION99.32
5.25-29.760.20871550.18812899X-RAY DIFFRACTION98.93
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)
13.523214647472.98379254802-4.068542794252.66437180806-3.517788075184.73362501223-0.242155292278-0.287509783976-0.4220498842010.1676943270930.3124365489420.1204616807620.4841058053770.112831106186-0.09568930682050.2226276092530.01523434353420.05267786222960.2194387892880.03355333404090.245515193692-3.967291147620.842576874545-50.762848842
23.650974745941.30461416044-0.1301552796787.217806863941.253991043164.049843498450.3896789610840.1905309660310.325436865812-0.328763825772-0.473525538983-0.284940890985-0.5242829823790.21872598057-0.02694558114040.14860604288-0.06584304422490.02012250538190.19725716973-0.003231346675240.2834551052557.1131129559815.5379697061-55.9913658728
35.742246756761.756700368371.022357465424.806846880311.615093987663.34331711641-0.0467358944449-0.0963170457131-0.129222833588-0.2781647468140.00687713359613-0.0007760808589910.0894107184332-0.211323865221-0.01150677500330.12701118775-0.02622396149970.006682442412550.156994866040.008664076497010.064714960195-4.116320009597.19184615055-56.6319968935
43.711786623443.523798165472.09492960194.864920404580.9321204721171.89050558577-0.111363829915-0.9989655620440.1440232475330.226450503729-0.00982430874133-0.128234073261-0.236348060613-0.508014370731-0.08216625783950.140643657733-0.03553606811980.02406779360910.266987404596-0.04328715686820.152000362843-5.145165146899.09440293777-46.2434917303
53.51678560462.92062421631.016515731268.36595036323-0.1664827583350.4663973178150.426312810762-1.19905888270.4273554149770.762659996874-0.249926825586-0.71243621155-1.280725929011.15822427514-0.1070295825210.449375150529-0.167706204165-0.1119184680920.40883103521-0.09226861111870.40331659247810.419955453619.0645083168-39.9800409531
68.390007065624.844727727557.886620078844.070990851073.810525989248.230368430810.138998666722-0.2766207636140.1692230626510.390936534766-0.06756063401790.04791372246870.137351216885-0.468785840421-0.0692104921810.1791362185760.01580832213170.02649585300060.256690530779-0.05783181879820.161528796928-7.2556609305512.2475954843-45.6878816228
75.068117444181.57169913757-0.1795031998177.38882492791-4.815697356447.464915300420.155239607258-0.551329300632-0.5334120249050.357635856027-0.383725943105-0.7005604074740.6982036598841.04539949340.2763984526590.2842864549650.117760069842-0.06145483300830.3390071552490.04497790466150.321060501308-28.6535611395-11.1921472678-51.8624810418
83.890106769890.276207727985-0.1451786345766.371329555670.5611226544783.66433608464-0.2466402722610.570416371533-0.22295721443-1.01098541019-0.0772261407093-0.99051619070.02053515733580.7507409803340.1139185716720.212253343262-0.06233262817940.08221904954330.4232585425970.05381037078470.199459708944-26.34469635241.08909649204-62.748220096
95.331721406132.3229797389-1.003918098648.31992194456-4.067182938456.25483597254-0.0246630961287-0.0666103646111-0.287908993653-0.290970726370.249545848440.01371674975760.4384484758160.0597953998599-0.06453626201280.1081516306460.0181654409893-0.02131582663010.147810736367-0.03299540882040.127462844684-33.8419237537-6.1765464171-56.5470896501
104.50674605462-5.471045408020.149136400586.8375831386-1.128174833035.20081078897-0.6581126516710.0125270918464-1.76730056872-0.570466311339-0.183637604004-0.5892120287981.531618504140.273606168858-0.1627630034210.490162018931-0.02512676433880.1379841015540.3009501532160.160282941410.748839553195-41.8070066961-16.8720418794-50.0581107739
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588.27013944219-7.212232431495.535876706727.4866167271-5.381320591427.1607715572-0.823243045809-0.6350343796270.4579336757940.5454140429840.229878702959-0.624236610833-0.511981589033-0.275988008020.280287355850.2024806678690.00420531872237-0.01106628088750.22156646408-0.02429678710760.201827082289-38.2842432595-10.95200058555.02228231638
592.49955271948-0.956849638588-0.3858101560664.893697805871.786273499163.85095670196-0.09692525945550.1552638254-0.229959830820.186805404025-0.08922209877780.3405063761360.43252743079-0.2248252256810.15755554230.120980443655-0.04438186094880.007907652582880.100526441446-0.02675181458720.161706389388-2.83828109762-37.6991967879-22.3336393948
604.82639809051-1.78268351873-1.714533585944.566406500051.670255075433.03635825558-0.1064857763670.196071347598-0.09307189847160.2219654383510.101738238552-0.2421434763780.2571826757890.124364287438-0.02209701312560.141419041248-0.0156185093760.004962803483070.164920624014-0.01439671674510.1091411091724.5312655833-35.6098407318-27.3914746049
616.05583669971-1.1644514956-0.2093801082233.22535556874-1.069680747614.513327580260.2184531960630.1570981271161.040740521870.1412782848670.05995556415760.348849363244-0.562400648358-0.8310115835570.1496782519840.258752836290.0394103956891-0.0314911098960.2282096039690.03510371963380.310475292688-8.15725917271-18.9261257998-27.3022039295
626.23162024297-2.18622189344-1.256167559252.54095686861.083023732352.151389208640.001502684928330.1416114719660.07240896575250.111417845159-0.0293281076479-0.1226744444410.141958610991-0.07108898398760.05141848705520.1231966470560.00797777031215-0.007368533349510.122122676821-0.01661362402120.07741419082953.09033930791-31.5221969326-19.1030789387
634.54623811926-5.09537309487-3.275307042115.654751490643.01789788294.320134876830.247025026370.7283366065390.281533327942-0.26249014051-0.132623034975-0.299026051084-0.0368528162454-0.185243933805-0.1664094950810.1163766793980.00425526092538-0.01329703722450.210910762484-0.03382927245720.125188633121-1.72591129544-30.5538711734-29.4696043022
643.06666845908-2.43040411543-3.30032435323.297882077871.325887411024.6283182248-0.02148464739460.2863860763570.293174394612-0.1503199188390.10249116914-0.2470541281240.44522321333-0.1460110177930.06226573888350.203849794815-0.0002674613430330.004359481201710.185870883305-0.06344671157820.1387907728820.992798275721-35.7159077446-31.1473250921
655.43514104862-5.587843721216.113749926349.00793522713-7.861350368997.77747673324-0.009807922585740.2452849134350.3393875975310.441900865901-0.101843960775-0.522623553503-0.8994132232741.070799895290.241286260260.168119684225-0.0760099420410.03162434083890.298860406592-0.02517761031880.333442411374-23.4233509328-10.9226940478-22.3445996112
665.44633736716-2.919148298473.188500805373.516616967010.1654728613673.74320272430.06727704500240.1999734132790.45422434882-0.06652111274730.0243771470119-0.248173810455-0.9317681010790.4059594059650.1398746627990.23529907506-0.05882445965160.06103576440570.145639515330.009070252461240.245441512215-28.8058059149-8.4394143001-25.0136748023
673.13807214655-3.36068513977-0.865215049046.149504679891.343660552924.02504103836-0.174200857259-0.860329072413-0.1917878279740.6069852479320.239525303227-0.7767451620590.09700279228630.805017296482-0.1770156799290.1895985149120.0701605578382-0.002834017897940.328544472384-0.03477301726230.27064826468-22.7587284263-22.1065751104-12.7290998043
683.01425255026-1.451384605141.332643448581.29871232251-0.9836500492323.80332628387-0.01696932594590.008125432589110.3645932052880.117767840219-0.0427200990404-0.0641483557998-0.515423762654-0.0006158904383910.00757698055090.161858444079-2.07214148045E-50.02452796298120.0984697408091-0.0178068369370.200847056053-34.2622928946-10.8206204995-21.4177923538
692.008517993831.765869605810.2718326729842.00268452744-0.8021359884052.473532168680.161274747550.411235341188-0.0264538594251-0.152272651008-0.001418589528730.002597310936280.1856364069920.251513945266-0.2402758079680.1300989951650.0265756009018-0.01367253768070.164861323127-0.003107790215260.124015804696-30.774076859-21.8214828138-27.3792215682
705.56396865768-0.247465421003-2.090710470493.246580915762.146255836634.906173338870.470171422685-0.111109612758-1.121183914950.5442065163090.332349694417-0.5324939960550.3055211807941.44507786285-0.3584966578720.2754613075350.108718016424-0.1008815619670.387408358566-0.1417947730850.320115534866-18.0971222963-34.4120093417-29.455807711
717.83565044785-3.62425272406-3.04912312893.84339993222.101683819675.42620064668-0.1454639587180.135434620073-0.2694103543950.1634242579940.02385294336790.3447061814560.222771107699-0.1440142641380.07158061989270.103442168496-0.04190189062690.01001347643050.1078871297360.003206185877760.103671751622-35.7925924796-20.0793934391-21.2158953679
727.03344229085-3.88778679451-0.1583774761256.06446191858-1.440406763172.75858669709-0.184217770082-0.273342287125-0.3020547986880.2221270647470.1295881477960.094996319586-0.03506151499590.2361468254030.07646568879540.106350983839-0.0251352345605-0.00544775542810.10871919316-0.01515835035760.0803037711313-29.6434462408-22.8064894449-18.505610608
735.22760180287-1.311953266233.281728837513.74021464164-3.345998957534.925168405020.06810599398090.6136754790240.177403609139-0.0676260432783-0.1255162091620.121478672129-0.05257854749070.213715687072-0.1427203127910.1201290590960.001553383991820.03259552537040.108011905678-0.0313349851350.145767728947-28.4716981261-19.4174205445-28.5637407403
741.617496620841.084344130131.127373000434.406241468014.16342925013.947827476970.1654913968030.5326571159051.26866469345-0.7556299501380.2999704149760.283313685562-1.88455228745-0.553684834361-0.298910696940.3830830159950.1029811051340.03192490829730.2371199385080.09826451709120.350135462887-42.3978201998-7.54434076671-33.4307419108
755.04414021818-6.544392404166.496666035078.72081804183-8.51819887918.88535602292-0.0191177896234-0.02448551081750.200388360099-0.02581245610850.00647272489007-0.222222588298-0.04703186129090.0105049204814-0.08307969582650.183269999098-0.004676530254560.02934647918220.17430873054-0.02649195220580.215848454333-25.6182653287-16.5882219889-28.3709807688
764.639981870554.482776805985.103451315517.8550526643.763874483476.206937728920.0590902379713-0.4525044992290.247939633134-0.0814912250645-0.5968043700580.645834692042-0.628065869985-0.716941473010.4822357851310.2387610064920.0005583338419860.04056257325350.305717342329-0.0745125075250.22176378204-9.2832649992318.6012712087-50.3280097818
773.514467600251.586559258812.862190106463.85630400782.245328896753.29948951344-0.0900311499605-0.1423575679360.9572723144370.1562540637150.2996362861910.144099179416-1.13595253675-0.137684864790.1643097908740.342901858223-0.01940736740710.04698774738740.217083835071-0.1215273716820.310736938957-3.916367222520.7244281971-48.2299262489
785.880405445583.174877936692.909288904186.925724127083.637007779147.13897012666-0.220973016506-0.04556546449180.178561199088-0.4154098440550.220778753529-0.202749197806-0.50752407186-0.2815344186760.03795754363420.1272989828640.01494242272150.01491580743850.1469584845150.02895414243410.1479353562-5.0476995464613.2065310974-56.9614038805
791.855305885120.130220121364-0.9103699817072.03916903295-0.9129488163484.05631724360.390668876202-0.2924703506021.030951732450.2585399756420.06414705453720.0659792609757-0.8514669442730.2071098369140.8450496284480.347596815136-0.482024597938-0.168306129159-0.178897492837-0.2627629534220.4525050439096.8988894746623.8282228276-48.0050840516
804.547331549212.441344016933.214429526532.738128990652.577946030563.675308022510.239336641727-1.38933982205-0.7627969518890.10439718519-0.447425663705-0.3763083815320.075478422767-0.05437695510670.03921767715270.156997334945-0.0654701663565-0.009839086109110.2733394267130.0163496407490.205162478425-2.596053044896.77249316562-47.7544211685
816.24695875283.177803008540.3597969685682.05810917846-0.1316328480493.8510344732-0.11925207468-0.594538922626-1.194439193480.002833432440930.228395706882-0.8084816675350.0951565481739-0.363722091647-0.1323195467860.267964504972-0.08463886645650.02436634856030.3989710221880.140984626980.490115454392-16.3048889862-4.21403162198-46.6315246658
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 78 through 82 )
2X-RAY DIFFRACTION2chain 'E' and (resid 83 through 89 )
3X-RAY DIFFRACTION3chain 'E' and (resid 90 through 101 )
4X-RAY DIFFRACTION4chain 'E' and (resid 102 through 110 )
5X-RAY DIFFRACTION5chain 'E' and (resid 111 through 115 )
6X-RAY DIFFRACTION6chain 'E' and (resid 116 through 125 )
7X-RAY DIFFRACTION7chain 'F' and (resid 20 through 36 )
8X-RAY DIFFRACTION8chain 'F' and (resid 37 through 42 )
9X-RAY DIFFRACTION9chain 'F' and (resid 43 through 53 )
10X-RAY DIFFRACTION10chain 'F' and (resid 54 through 61 )
11X-RAY DIFFRACTION11chain 'F' and (resid 62 through 69 )
12X-RAY DIFFRACTION12chain 'F' and (resid 70 through 89 )
13X-RAY DIFFRACTION13chain 'F' and (resid 90 through 101 )
14X-RAY DIFFRACTION14chain 'F' and (resid 102 through 110 )
15X-RAY DIFFRACTION15chain 'F' and (resid 111 through 115 )
16X-RAY DIFFRACTION16chain 'F' and (resid 116 through 125 )
17X-RAY DIFFRACTION17chain 'G' and (resid 20 through 27 )
18X-RAY DIFFRACTION18chain 'G' and (resid 28 through 36 )
19X-RAY DIFFRACTION19chain 'G' and (resid 37 through 42 )
20X-RAY DIFFRACTION20chain 'G' and (resid 43 through 53 )
21X-RAY DIFFRACTION21chain 'G' and (resid 54 through 61 )
22X-RAY DIFFRACTION22chain 'G' and (resid 62 through 69 )
23X-RAY DIFFRACTION23chain 'G' and (resid 70 through 77 )
24X-RAY DIFFRACTION24chain 'G' and (resid 78 through 82 )
25X-RAY DIFFRACTION25chain 'G' and (resid 83 through 89 )
26X-RAY DIFFRACTION26chain 'G' and (resid 90 through 101 )
27X-RAY DIFFRACTION27chain 'G' and (resid 102 through 110 )
28X-RAY DIFFRACTION28chain 'G' and (resid 111 through 115 )
29X-RAY DIFFRACTION29chain 'G' and (resid 116 through 125 )
30X-RAY DIFFRACTION30chain 'H' and (resid 20 through 53 )
31X-RAY DIFFRACTION31chain 'H' and (resid 54 through 69 )
32X-RAY DIFFRACTION32chain 'H' and (resid 70 through 82 )
33X-RAY DIFFRACTION33chain 'H' and (resid 83 through 101 )
34X-RAY DIFFRACTION34chain 'H' and (resid 102 through 125 )
35X-RAY DIFFRACTION35chain 'A' and (resid 20 through 27 )
36X-RAY DIFFRACTION36chain 'A' and (resid 28 through 36 )
37X-RAY DIFFRACTION37chain 'A' and (resid 37 through 53 )
38X-RAY DIFFRACTION38chain 'A' and (resid 54 through 61 )
39X-RAY DIFFRACTION39chain 'A' and (resid 62 through 69 )
40X-RAY DIFFRACTION40chain 'A' and (resid 70 through 77 )
41X-RAY DIFFRACTION41chain 'A' and (resid 78 through 82 )
42X-RAY DIFFRACTION42chain 'A' and (resid 83 through 89 )
43X-RAY DIFFRACTION43chain 'A' and (resid 90 through 101 )
44X-RAY DIFFRACTION44chain 'A' and (resid 102 through 110 )
45X-RAY DIFFRACTION45chain 'A' and (resid 111 through 115 )
46X-RAY DIFFRACTION46chain 'A' and (resid 116 through 125 )
47X-RAY DIFFRACTION47chain 'B' and (resid 20 through 36 )
48X-RAY DIFFRACTION48chain 'B' and (resid 37 through 42 )
49X-RAY DIFFRACTION49chain 'B' and (resid 43 through 53 )
50X-RAY DIFFRACTION50chain 'B' and (resid 54 through 61 )
51X-RAY DIFFRACTION51chain 'B' and (resid 62 through 69 )
52X-RAY DIFFRACTION52chain 'B' and (resid 70 through 77 )
53X-RAY DIFFRACTION53chain 'B' and (resid 78 through 82 )
54X-RAY DIFFRACTION54chain 'B' and (resid 83 through 89 )
55X-RAY DIFFRACTION55chain 'B' and (resid 90 through 101 )
56X-RAY DIFFRACTION56chain 'B' and (resid 102 through 110 )
57X-RAY DIFFRACTION57chain 'B' and (resid 111 through 115 )
58X-RAY DIFFRACTION58chain 'B' and (resid 116 through 125 )
59X-RAY DIFFRACTION59chain 'C' and (resid 20 through 53 )
60X-RAY DIFFRACTION60chain 'C' and (resid 54 through 69 )
61X-RAY DIFFRACTION61chain 'C' and (resid 70 through 82 )
62X-RAY DIFFRACTION62chain 'C' and (resid 83 through 101 )
63X-RAY DIFFRACTION63chain 'C' and (resid 102 through 110 )
64X-RAY DIFFRACTION64chain 'C' and (resid 111 through 125 )
65X-RAY DIFFRACTION65chain 'D' and (resid 20 through 27 )
66X-RAY DIFFRACTION66chain 'D' and (resid 28 through 36 )
67X-RAY DIFFRACTION67chain 'D' and (resid 37 through 42 )
68X-RAY DIFFRACTION68chain 'D' and (resid 43 through 61 )
69X-RAY DIFFRACTION69chain 'D' and (resid 62 through 69 )
70X-RAY DIFFRACTION70chain 'D' and (resid 70 through 77 )
71X-RAY DIFFRACTION71chain 'D' and (resid 78 through 89 )
72X-RAY DIFFRACTION72chain 'D' and (resid 90 through 101 )
73X-RAY DIFFRACTION73chain 'D' and (resid 102 through 110 )
74X-RAY DIFFRACTION74chain 'D' and (resid 111 through 115 )
75X-RAY DIFFRACTION75chain 'D' and (resid 116 through 125 )
76X-RAY DIFFRACTION76chain 'E' and (resid 20 through 27 )
77X-RAY DIFFRACTION77chain 'E' and (resid 28 through 36 )
78X-RAY DIFFRACTION78chain 'E' and (resid 37 through 53 )
79X-RAY DIFFRACTION79chain 'E' and (resid 54 through 61 )
80X-RAY DIFFRACTION80chain 'E' and (resid 62 through 69 )
81X-RAY DIFFRACTION81chain 'E' and (resid 70 through 77 )

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る