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- PDB-9e4w: Structure of Bacillus phage SPO1 anti-CBASS 4 (Acb4) in complex w... -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 9e4w
タイトルStructure of Bacillus phage SPO1 anti-CBASS 4 (Acb4) in complex with 3'3'-cGAMP
要素anti-CBASS 4 (Acb4)
キーワードVIRAL PROTEIN / anti-cbass / immune evasion / viral sponge
機能・相同性Phage protein (N4 Gp49/phage Sf6 gene 66) family / Phage protein (N4 Gp49/phage Sf6 gene 66) family / Chem-4BW / Gp1.3
機能・相同性情報
生物種Bacillus phage SPO1 (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.08 Å
データ登録者Chang, R.B. / Toyoda, H.C. / Hobbs, S.J. / Richmond-Buccola, D. / Wein, T. / Burger, N. / Chouchani, E.T. / Sorek, R. / Kranzusch, P.J.
資金援助 米国, 1件
組織認可番号
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250-01 米国
引用ジャーナル: Biorxiv / : 2024
タイトル: A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense.
著者: Chang, R.B. / Toyoda, H.C. / Hobbs, S.J. / Richmond-Buccola, D. / Wein, T. / Burger, N. / Chouchani, E.T. / Sorek, R. / Kranzusch, P.J.
履歴
登録2024年10月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年1月29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: anti-CBASS 4 (Acb4)
B: anti-CBASS 4 (Acb4)
C: anti-CBASS 4 (Acb4)
D: anti-CBASS 4 (Acb4)
E: anti-CBASS 4 (Acb4)
F: anti-CBASS 4 (Acb4)
G: anti-CBASS 4 (Acb4)
H: anti-CBASS 4 (Acb4)
I: anti-CBASS 4 (Acb4)
J: anti-CBASS 4 (Acb4)
K: anti-CBASS 4 (Acb4)
L: anti-CBASS 4 (Acb4)
M: anti-CBASS 4 (Acb4)
N: anti-CBASS 4 (Acb4)
O: anti-CBASS 4 (Acb4)
P: anti-CBASS 4 (Acb4)
Q: anti-CBASS 4 (Acb4)
R: anti-CBASS 4 (Acb4)
S: anti-CBASS 4 (Acb4)
T: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)232,91540
ポリマ-219,42720
非ポリマー13,48820
20,2131122
1
A: anti-CBASS 4 (Acb4)
B: anti-CBASS 4 (Acb4)
C: anti-CBASS 4 (Acb4)
D: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,5838
ポリマ-43,8854
非ポリマー2,6984
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-41 kcal/mol
Surface area17920 Å2
手法PISA
2
E: anti-CBASS 4 (Acb4)
F: anti-CBASS 4 (Acb4)
G: anti-CBASS 4 (Acb4)
H: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,5838
ポリマ-43,8854
非ポリマー2,6984
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-41 kcal/mol
Surface area17790 Å2
手法PISA
3
I: anti-CBASS 4 (Acb4)
J: anti-CBASS 4 (Acb4)
K: anti-CBASS 4 (Acb4)
L: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,5838
ポリマ-43,8854
非ポリマー2,6984
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-42 kcal/mol
Surface area17870 Å2
手法PISA
4
M: anti-CBASS 4 (Acb4)
N: anti-CBASS 4 (Acb4)
O: anti-CBASS 4 (Acb4)
P: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,5838
ポリマ-43,8854
非ポリマー2,6984
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-41 kcal/mol
Surface area17460 Å2
手法PISA
5
Q: anti-CBASS 4 (Acb4)
R: anti-CBASS 4 (Acb4)
S: anti-CBASS 4 (Acb4)
T: anti-CBASS 4 (Acb4)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,5838
ポリマ-43,8854
非ポリマー2,6984
724
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-42 kcal/mol
Surface area17740 Å2
手法PISA
単位格子
Length a, b, c (Å)54.284, 56.496, 167.581
Angle α, β, γ (deg.)87.529, 89.020, 81.580
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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要素

#1: タンパク質
anti-CBASS 4 (Acb4)


分子量: 10971.354 Da / 分子数: 20 / 由来タイプ: 組換発現 / 由来: (組換発現) Bacillus phage SPO1 (ファージ) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B6V2Y3
#2: 化合物
ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p] / cGAMP


分子量: 674.411 Da / 分子数: 20 / 由来タイプ: 合成 / : C20H24N10O13P2 / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1122 / 由来タイプ: 天然 / : 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: 2.31 Å3/Da / 溶媒含有率: 46.86 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 18% PEG-4000, Tris-HCl pH 8.80, and 0.1 M MgCl2

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データ収集

回折平均測定温度: 80 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.97934 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年2月3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: 0.97934 Å / 相対比: 1
反射解像度: 2.08→83.71 Å / Num. obs: 82527 / % possible obs: 98.4 % / 冗長度: 3.6 % / Biso Wilson estimate: 19.67 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.092 / Net I/σ(I): 4.2
反射 シェル解像度: 2.08→2.26 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4126 / CC1/2: 0.683 / Rpim(I) all: 0.388

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21_5207精密化
XDSデータ削減
Aimless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: 2.08→45.6 Å / SU ML: 0.265 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 28.7266
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2522 1409 1.71 %
Rwork0.2189 81091 -
obs0.2194 82500 69.37 %
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: 32.12 Å2
精密化ステップサイクル: LAST / 解像度: 2.08→45.6 Å
タンパク質核酸リガンド溶媒全体
原子数14517 0 900 1122 16539
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.001515731
X-RAY DIFFRACTIONf_angle_d0.402821425
X-RAY DIFFRACTIONf_chiral_restr0.04012477
X-RAY DIFFRACTIONf_plane_restr0.00332584
X-RAY DIFFRACTIONf_dihedral_angle_d10.68355496
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.150.44360.2584473X-RAY DIFFRACTION4.03
2.15-2.240.2843460.24712593X-RAY DIFFRACTION22.21
2.24-2.340.2694880.24155065X-RAY DIFFRACTION43.23
2.34-2.460.27231310.24597022X-RAY DIFFRACTION60.09
2.46-2.620.28061500.24368997X-RAY DIFFRACTION77.26
2.62-2.820.27831930.247811030X-RAY DIFFRACTION94.21
2.82-3.10.28462070.236811445X-RAY DIFFRACTION97.98
3.1-3.550.24091910.211811473X-RAY DIFFRACTION98.26
3.55-4.470.23941910.18611515X-RAY DIFFRACTION98.4
4.47-45.60.22292060.213811478X-RAY DIFFRACTION98.15
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)
10.01935374732280.02120547949020.01367750941260.02451966707240.0070663010602-0.002252914838170.002274325225170.04201598078640.00974511731799-0.0964776955991-0.01827606193490.157520393045-0.102722759983-0.115220514115-0.0136747058523-0.638617320815-0.0123975952566-0.2416386428150.151573962034-0.03115492353940.153123621354-6.586-2.007-1.809
20.0311516899136-0.0341135942196-0.02956582956890.04464583709520.04801501113670.06174912282940.003021488315930.01276720042920.02816800967260.0207963310079-0.01929949793120.05423233237040.0663507553139-0.0809150031223-0.0710067805546-0.06507143514490.0344768074207-0.06658804348870.00947736477862-0.000707097407110.2152665828624.7774.1661.696
30.1057762876450.0142615952931-0.09129010247470.0264183051382-0.001221416981910.0624795360206-0.01698258843360.197143969161-0.0863095166095-0.07755270456370.0004231875793260.006423628279-0.0169152786327-0.00853040319677-0.018074264990.0640242804232-0.0177261478322-0.0322721819730.1173126785840.008964430072640.101256452941.69-3.91-2.599
40.00957004417962-0.002225336981120.002349930041160.007339390980030.001219610984420.00263211188576-0.02936354992830.0144021421954-0.04498751558230.0700319529508-0.06956511040940.0658761957035-0.0133629660507-0.0928669228266-0.0001291228960.1714976523450.00698759839375-0.008561714538350.1737083121520.000380069689210.16853892022-6.483-17.683-6.735
50.00728178738089-0.00502020787927-0.005695697982280.01376041388540.009962315498490.0074401567154-0.0195993562704-0.0205846273927-0.0001265154140.033107155538-0.0247706177465-0.01037831459590.02346725966970.00885581267073-0.04335685607860.06174394239250.00724623047567-0.1541105161410.3348788765780.08651181519440.18254611958425.7896.26416.721
60.0118930169169-0.02238409903490.02176119029630.0403141752367-0.0411375518030.03969123820480.0128103463985-0.00896990935876-0.044026671830.00391882430963-0.01975719285550.02152239513110.0384057978148-0.0115942067399-0.0228575062119-0.002916313299460.10140876849-0.06429127706170.2109147579080.006307699419120.1503132360328.849-1.12812.974
70.0463423890853-0.007419550570290.03418692023130.00417636423447-0.008506215081370.0296165328808-0.0523590431874-0.0005346768936430.021664967570.039671234537-0.0409912211456-0.0214888072997-0.1323370752520.0453198368021-0.02323713326510.0880543493022-0.0134309340617-0.008715716905770.254723058189-0.01519989677740.19717506958130.5796.4687.312
80.18414537888-0.0882555612073-0.17890221260.08497751354440.1020041468440.1804516616470.0702425405433-0.2140228018240.255345494264-0.1647028999290.1591174826080.0343889837359-0.179155391255-0.03065908599380.1013659539210.03864501656-0.0214176600816-0.025325915180.09897209475360.002132975662270.065751205558815.1486.4066.87
90.1380364085820.06349605670140.02356595076110.109310472557-0.002113043749830.0100163954282-0.00294861418673-0.0467553021641-0.020980688050.00476755159471-0.0450620929689-0.0222122019670.0492735653183-0.0480448878791-0.06884854731540.0954867507939-0.120236387307-0.03602781728320.203058414480.07159414364970.10682845350610.348-9.85817.687
100.2062069671650.04105162002370.07427056203970.01016933106980.004017391256510.03035655992950.00955982776983-0.0912571459487-0.0659084605390.009039257309350.0756718865546-0.08407342506680.05193731561360.0279556102050.0727211527499-0.335056311215-0.104232557915-0.2473512742330.125632163504-0.1479892846610.2299028516621.331.534.855
110.01326981122130.004294336113920.008381286114870.00609821395427-0.002214479918780.0350119765274-0.0268538970821-0.02969346284240.03455768128590.02101684714840.0693554412117-0.0350519106441-0.04337846856090.06980791765210.007674580539420.0904841758989-0.0446098500460.007336386822260.20298843610.01200575054550.24495302403934.9417.532-2.419
120.00293958178185-0.002881714206970.001809584165890.01774745873840.009427428255070.00311111825682-0.03140035379920.02459560919750.0072709932027-0.07585791449410.007417795944080.04608879348890.00918955598972-0.0642909334981-0.0188244273690.39937712658-0.00796418963197-0.09065710313180.2726209559160.07535272369230.05961431953918.396-0.433-26.632
130.02956114116070.02287810971230.01849288001350.051452529780.05002209656060.03621974244580.04178249837680.13603570058-0.00943693819249-0.1382045457040.0330585915557-0.0623485764455-0.06838636838770.08601573083260.03931658425450.152041372196-0.0308967591865-0.006516577156340.07762922966310.02765948762550.13915169203116.402-2.822-20.493
140.0572488403356-0.0239824631560.02166899045540.0535009539415-0.02468942738440.007712745887380.0108378493907-0.04298382448450.01377007131490.007347516901740.0741116156752-0.06955282926230.003270177949110.1216812288270.0429890306493-0.029260985054-0.157338859719-0.01653848119190.186601402313-0.01803524949140.22196352735121.115-2.222-15.202
150.01023451157760.00612515615786-0.007752536479180.01236597680330.0010939210360.0146131792329-0.03288923792950.04467598397820.006367178405040.02552485613040.004649206042310.051574843497-0.0178684170093-0.0131257517213-0.0077559704760.0932158176101-0.034720842268-0.002004411933770.163630709008-0.04477624003190.1915590173214.354-19.342-17.051
160.02737548480720.0195954347043-0.03819658146010.00550919076803-0.008337038109090.02676618964050.022472517255-0.0328277787007-0.007506158104220.01090437425320.0290220437693-0.0125656965780.0130527359037-0.0176110763141-0.00284129246640.1029713515190.01169738212530.008007783835280.1411930111660.02455830348560.15034580751113.567-0.57-15.665
170.00496281630165-0.0086261640348-0.001829052528760.01461566520890.002273096245290.0006935690798120.0237710000690.0437173832320.0214393660359-0.05405767232420.00495930348816-0.041822566524-0.0700185263744-0.004240111745920.01021262630.1554321453560.008795298419410.038258488880.1077872223550.06288801250760.20974677801614.76315.954-17.178
180.03397267797580.01699123252050.01977503166330.01191676123570.008061600305090.01555156619350.05226086433850.00428414259941-0.02472621180990.01648968349490.0129242053867-0.0422001025150.02800709752270.0386183585720.01879800317150.1860194837440.1315572068230.006197530339680.3151824363820.06002492804650.15414128533330.082-21.3832.18
190.00449989113389-0.0122737157048-0.04048880726370.008891954787360.0303037050540.1412556317060.01940126135490.0160241755551-0.17486349230.07637507902750.0818146858960.0872879475440.2103912809520.1836144318550.07436082142870.0402749356727-0.0343112839885-0.01387007755550.05483523739390.03780930562650.20304799074420.253-19.23-4.909
200.03272173753180.0330023665130.005878526927810.06022749347770.03345868410590.03072379832640.01175202250080.006370785768440.0398890550977-0.002248740156780.03291980995550.0112029663073-0.06824539733110.01427893541560.02881803709840.074703488337-0.0605712636490.0429306876838-0.0204413394008-0.06342785108460.33428356656135.281-5.021-10.691
210.01206759005930.01264021416-0.01893936665530.0286344272451-0.008263250046950.0221856438041-0.008124971448490.002714916519430.039176556345-0.0289876923480.02843430434880.0682587514207-0.03721250037490.01451881967580.0391736843142-0.00134463993635-0.0334730501405-0.06495850481470.0949759498431-0.04480609479230.22117544688419.913-15.384-0.731
220.01412852920330.005518120870880.001121725595940.0135360302093-0.009847004136320.01126750375970.00275502320104-0.0218715290059-0.0358204496460.0169072196634-0.01327714445890.02663601939510.0372637208544-0.0229495210965-0.00270008363720.097112458013-0.02601367631450.0524003647750.3056606934660.1143380681250.20293662988713.581-23.46212.133
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710.0373354674811-0.01125866682550.02097979600010.00415936350055-0.001989965280530.007803879807370.0760000615341-0.001660659176470.0701286703051-0.0984885188929-0.01892199844180.01774897062490.05616542518180.119385302910.06160663837170.600619060132-0.1227449729610.1637207559720.2228834842690.04243063990950.276614922082-12.27142.061-114.695
720.330623270220.0916573510953-0.04348134369920.161977751562-0.06934000562040.2867442104610.0758029463581-0.06017927563930.0165983482426-0.344732846964-0.1733329365750.01894108757750.1275312429170.19884929842-0.06685036819790.546921429040.03739399126320.02503539763680.239333285709-0.004390647122290.13819380215-20.41431.884-114.863
730.0976098808819-0.0602045239450.09135415143940.08866966981770.008300578014850.1849085471880.0998148025252-0.2078232371870.08329307483-0.135915336428-0.0718526596816-0.0377745592759-0.04915474386720.1209757016760.01680967316720.567638750372-0.03870431634290.105563366620.282922639246-0.0249925833091-0.0101623945588-16.24543.717-108.547
740.0019938708456-0.00019453248572-0.001620630952740.002239710295310.0003748286093420.00168108738441-0.02340683914370.01875165972460.00779565704463-0.0131576655705-0.01678963795420.0409352991917-0.0178239830223-0.02998280255460.00014603666560.6654478856350.143962192958-0.02423797415410.514638092744-0.07195061362580.498028464357-44.25450.865-103.452
75-1.9209675103E-50.000208467823050.0003020872088540.00682361951079-0.0003535400900250.001835059453840.0191301633870.02624380750060.00469595927636-0.00544530301092-0.0145423106117-0.02237111367-0.03155772856920.00689419950614-1.44087404969E-50.6583700469080.166372489546-0.07499399896950.5350920927910.04937110441630.378858086522-37.29450.609-109.95
760.0400570484501-0.0729248536965-0.03852853596190.1310413861890.08093389104690.034791508569-0.0488747260.130914574183-0.238710386443-0.105943715548-0.2038980129460.260361257308-0.0988647739969-0.208883622051-0.00727733186560.4275473966820.0627259450657-0.03008547330810.394251932399-0.06697884860710.30814440764-38.78241.431-99.882
770.001302763742630.000577409361160.0003920424933410.0003009784900640.000552756665433-0.000778018601572-0.02529000259450.01748458934480.0552833345947-0.00554934285820.01051076602260.0035847261818-0.05615104034510.0340237321782-1.12629758166E-50.6126262234660.02997670961210.01147127070750.243896170995-0.02343515984490.219369823289-22.854.854-95.414
780.0323073496312-0.00291779963283-0.03321224369410.0155461065659-0.01326467654810.03735054253930.05447064923210.0828516961301-0.1994714719770.012211248023-0.03597021664090.147059087177-0.115992040034-0.146637297429-4.51008523022E-50.4403835848220.00614349623729-0.01709984461290.365042166106-0.03188908369480.341827982386-36.59739.015-105.882
790.0594675778124-0.00528122933101-0.004554890359020.113491747542-0.05781594681210.0305957360975-0.150444675212-0.15991444451-0.09402210889760.123687657123-0.036644146136-0.05455733105110.07779866842710.0151933530345-0.03087743286120.5808824342880.1782376749720.06588109862050.4129155361130.03448017885090.189649277776-18.81132.369-81.594
800.0371639184063-0.004926596908523.3258319442E-60.03588900097480.006796030352260.0340314355189-0.125754125719-0.0701868559542-0.1129332731450.2260954158960.06191785002290.09851488024820.0988166963758-0.0232872408717-0.06909254736070.4191913534240.04498710798030.1360691471130.3347573922980.003901552228140.277879946852-29.88235.069-88.919
810.01220384852120.01351896985870.0167687186330.040359089523-0.002884921827540.0309127299353-0.1065423923550.0434499932922-0.02333532568770.1060059811480.0813974301910.125651078655-0.01244797513930.01975180369910.01154066610280.511724249670.09620780595670.1140863255840.2544830913920.006161990579980.186083400421-20.96532.661-89.715
820.007215963318550.00251401322764-0.001780982171460.0107132496649-0.003072401545610.002096315054270.00686877218347-0.02624176874880.01004100284370.03465949807290.0287491002751-0.01158368791960.01222235219820.05721092932990.008599696698910.4069494586850.1362846590620.01373121564220.513391019584-0.1805081393270.266215916952-4.14732.566-89.644
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:32 )A2 - 32
2X-RAY DIFFRACTION2( CHAIN A AND RESID 33:63 )A33 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:86 )A64 - 86
4X-RAY DIFFRACTION4( CHAIN A AND RESID 87:96 )A87 - 96
5X-RAY DIFFRACTION5( CHAIN B AND RESID 3:8 )B3 - 8
6X-RAY DIFFRACTION6( CHAIN B AND RESID 9:14 )B9 - 14
7X-RAY DIFFRACTION7( CHAIN B AND RESID 15:23 )B15 - 23
8X-RAY DIFFRACTION8( CHAIN B AND RESID 24:55 )B24 - 55
9X-RAY DIFFRACTION9( CHAIN B AND RESID 56:63 )B56 - 63
10X-RAY DIFFRACTION10( CHAIN B AND RESID 64:85 )B64 - 85
11X-RAY DIFFRACTION11( CHAIN B AND RESID 86:96 )B86 - 96
12X-RAY DIFFRACTION12( CHAIN C AND RESID 3:14 )C3 - 14
13X-RAY DIFFRACTION13( CHAIN C AND RESID 15:44 )C15 - 44
14X-RAY DIFFRACTION14( CHAIN C AND RESID 45:55 )C45 - 55
15X-RAY DIFFRACTION15( CHAIN C AND RESID 56:63 )C56 - 63
16X-RAY DIFFRACTION16( CHAIN C AND RESID 64:86 )C64 - 86
17X-RAY DIFFRACTION17( CHAIN C AND RESID 87:95 )C87 - 95
18X-RAY DIFFRACTION18( CHAIN D AND RESID 4:14 )D4 - 14
19X-RAY DIFFRACTION19( CHAIN D AND RESID 15:55 )D15 - 55
20X-RAY DIFFRACTION20( CHAIN D AND RESID 56:63 )D56 - 63
21X-RAY DIFFRACTION21( CHAIN D AND RESID 64:86 )D64 - 86
22X-RAY DIFFRACTION22( CHAIN D AND RESID 87:96 )D87 - 96
23X-RAY DIFFRACTION23( CHAIN E AND RESID 3:24 )E3 - 24
24X-RAY DIFFRACTION24( CHAIN E AND RESID 25:32 )E25 - 32
25X-RAY DIFFRACTION25( CHAIN E AND RESID 33:63 )E33 - 63
26X-RAY DIFFRACTION26( CHAIN E AND RESID 64:86 )E64 - 86
27X-RAY DIFFRACTION27( CHAIN E AND RESID 87:95 )E87 - 95
28X-RAY DIFFRACTION28( CHAIN F AND RESID 3:14 )F3 - 14
29X-RAY DIFFRACTION29( CHAIN F AND RESID 15:55 )F15 - 55
30X-RAY DIFFRACTION30( CHAIN F AND RESID 56:63 )F56 - 63
31X-RAY DIFFRACTION31( CHAIN F AND RESID 64:95 )F64 - 95
32X-RAY DIFFRACTION32( CHAIN G AND RESID 1:23 )G1 - 23
33X-RAY DIFFRACTION33( CHAIN G AND RESID 24:55 )G24 - 55
34X-RAY DIFFRACTION34( CHAIN G AND RESID 56:63 )G56 - 63
35X-RAY DIFFRACTION35( CHAIN G AND RESID 64:93 )G64 - 93
36X-RAY DIFFRACTION36( CHAIN H AND RESID 4:32 )H4 - 32
37X-RAY DIFFRACTION37( CHAIN H AND RESID 33:63 )H33 - 63
38X-RAY DIFFRACTION38( CHAIN H AND RESID 64:85 )H64 - 85
39X-RAY DIFFRACTION39( CHAIN H AND RESID 86:96 )H86 - 96
40X-RAY DIFFRACTION40( CHAIN I AND RESID 2:24 )I2 - 24
41X-RAY DIFFRACTION41( CHAIN I AND RESID 25:63 )I25 - 63
42X-RAY DIFFRACTION42( CHAIN I AND RESID 64:96 )I64 - 96
43X-RAY DIFFRACTION43( CHAIN J AND RESID 4:14 )J4 - 14
44X-RAY DIFFRACTION44( CHAIN J AND RESID 15:63 )J15 - 63
45X-RAY DIFFRACTION45( CHAIN J AND RESID 64:91 )J64 - 91
46X-RAY DIFFRACTION46( CHAIN K AND RESID 2:14 )K2 - 14
47X-RAY DIFFRACTION47( CHAIN K AND RESID 15:32 )K15 - 32
48X-RAY DIFFRACTION48( CHAIN K AND RESID 33:63 )K33 - 63
49X-RAY DIFFRACTION49( CHAIN K AND RESID 64:86 )K64 - 86
50X-RAY DIFFRACTION50( CHAIN K AND RESID 87:95 )K87 - 95
51X-RAY DIFFRACTION51( CHAIN L AND RESID 2:14 )L2 - 14
52X-RAY DIFFRACTION52( CHAIN L AND RESID 15:32 )L15 - 32
53X-RAY DIFFRACTION53( CHAIN L AND RESID 33:63 )L33 - 63
54X-RAY DIFFRACTION54( CHAIN L AND RESID 64:95 )L64 - 95
55X-RAY DIFFRACTION55( CHAIN M AND RESID 5:32 )M5 - 32
56X-RAY DIFFRACTION56( CHAIN M AND RESID 33:63 )M33 - 63
57X-RAY DIFFRACTION57( CHAIN M AND RESID 64:92 )M64 - 92
58X-RAY DIFFRACTION58( CHAIN N AND RESID 5:32 )N5 - 32
59X-RAY DIFFRACTION59( CHAIN N AND RESID 33:63 )N33 - 63
60X-RAY DIFFRACTION60( CHAIN N AND RESID 64:90 )N64 - 90
61X-RAY DIFFRACTION61( CHAIN O AND RESID 5:23 )O5 - 23
62X-RAY DIFFRACTION62( CHAIN O AND RESID 24:63 )O24 - 63
63X-RAY DIFFRACTION63( CHAIN O AND RESID 64:90 )O64 - 90
64X-RAY DIFFRACTION64( CHAIN P AND RESID 3:24 )P3 - 24
65X-RAY DIFFRACTION65( CHAIN P AND RESID 25:63 )P25 - 63
66X-RAY DIFFRACTION66( CHAIN P AND RESID 64:92 )P64 - 92
67X-RAY DIFFRACTION67( CHAIN Q AND RESID 3:44 )Q3 - 44
68X-RAY DIFFRACTION68( CHAIN Q AND RESID 45:63 )Q45 - 63
69X-RAY DIFFRACTION69( CHAIN Q AND RESID 64:92 )Q64 - 92
70X-RAY DIFFRACTION70( CHAIN R AND RESID 2:14 )R2 - 14
71X-RAY DIFFRACTION71( CHAIN R AND RESID 15:32 )R15 - 32
72X-RAY DIFFRACTION72( CHAIN R AND RESID 33:63 )R33 - 63
73X-RAY DIFFRACTION73( CHAIN R AND RESID 64:95 )R64 - 95
74X-RAY DIFFRACTION74( CHAIN S AND RESID 2:8 )S2 - 8
75X-RAY DIFFRACTION75( CHAIN S AND RESID 9:14 )S9 - 14
76X-RAY DIFFRACTION76( CHAIN S AND RESID 15:55 )S15 - 55
77X-RAY DIFFRACTION77( CHAIN S AND RESID 56:63 )S56 - 63
78X-RAY DIFFRACTION78( CHAIN S AND RESID 64:91 )S64 - 91
79X-RAY DIFFRACTION79( CHAIN T AND RESID 4:32 )T4 - 32
80X-RAY DIFFRACTION80( CHAIN T AND RESID 33:63 )T33 - 63
81X-RAY DIFFRACTION81( CHAIN T AND RESID 64:85 )T64 - 85
82X-RAY DIFFRACTION82( CHAIN T AND RESID 86:95 )T86 - 95

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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

+
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