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- PDB-6vk8: Crystal Structure of Methylosinus trichosporium OB3b Soluble Meth... -

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基本情報

登録情報
データベース: PDB / ID: 6vk8
タイトルCrystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex with small organic carboxylate at active center
要素
  • (Methane monooxygenase ...) x 2
  • (Methane monooxygenase) x 2
キーワードOXIDOREDUCTASE / Methane Monooxygenase Hydroxylase
機能・相同性
機能・相同性情報


methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / one-carbon metabolic process / monooxygenase activity / metal ion binding
類似検索 - 分子機能
: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : ...: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
類似検索 - ドメイン・相同性
BENZOIC ACID / : / SUCCINIC ACID / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase / Methane monooxygenase component A alpha chain / Methane monooxygenase regulatory protein B
類似検索 - 構成要素
生物種Methylosinus trichosporium OB3b (バクテリア)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 2.03 Å
データ登録者Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
資金援助 米国, 2件
組織認可番号
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030, GM08347 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000, GM118047 米国
引用ジャーナル: Biochemistry / : 2020
タイトル: Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
著者: Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
履歴
登録2020年1月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年8月5日Provider: repository / タイプ: Initial release
改定 1.12020年8月26日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
改定 1.22020年9月2日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.32024年3月6日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Methane monooxygenase component A alpha chain
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase regulatory protein B
E: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase
H: Methane monooxygenase regulatory protein B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)281,28938
ポリマ-279,3368
非ポリマー1,95330
24,8971382
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area60300 Å2
ΔGint-186 kcal/mol
Surface area65640 Å2
手法PISA
単位格子
Length a, b, c (Å)101.866, 105.349, 297.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLY(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA12 - 31412 - 314
121TRPTRPPHEPHE(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA317 - 526317 - 526
211ASPASPGLYGLY(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE12 - 31412 - 314
221TRPTRPPHEPHE(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE317 - 526317 - 526
112PROPROLEULEU(chain 'B' and (resid 4 through 320 or resid 322 through 395))BB4 - 3204 - 320
122ALAALAASNASN(chain 'B' and (resid 4 through 320 or resid 322 through 395))BB322 - 395322 - 395
212PROPROLEULEU(chain 'F' and (resid 4 through 320 or resid 322 through 395))FF4 - 3204 - 320
222ALAALAASNASN(chain 'F' and (resid 4 through 320 or resid 322 through 395))FF322 - 395322 - 395
113ALAALAGLNGLNchain 'C'CC2 - 1682 - 168
213ALAALAGLNGLNchain 'G'GG2 - 1682 - 168
114SERSERARGARGchain 'D'DD2 - 1332 - 133
214SERSERARGARG(chain 'H' and resid 2 through 133)HH2 - 1332 - 133

NCSアンサンブル:
ID
1
2
3
4

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要素

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Methane monooxygenase ... , 2種, 4分子 AEDH

#1: タンパク質 Methane monooxygenase component A alpha chain


分子量: 60031.293 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Methylosinus trichosporium OB3b (バクテリア)
参照: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#4: タンパク質 Methane monooxygenase regulatory protein B


分子量: 14896.885 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Methylosinus trichosporium OB3b (バクテリア)
参照: UniProt: A0A2D2D0T8, UniProt: P27356*PLUS

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タンパク質 , 2種, 4分子 BFCG

#2: タンパク質 Methane monooxygenase


分子量: 45295.340 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Methylosinus trichosporium OB3b (バクテリア)
参照: UniProt: A0A2D2D5X7
#3: タンパク質 Methane monooxygenase


分子量: 19444.400 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Methylosinus trichosporium OB3b (バクテリア)
参照: UniProt: A0A2D2D0T0

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非ポリマー , 5種, 1412分子

#5: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 4 / 由来タイプ: 合成 / : Fe / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-SIN / SUCCINIC ACID / コハク酸


分子量: 118.088 Da / 分子数: 1 / 由来タイプ: 合成 / : C4H6O4
#7: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 24 / 由来タイプ: 合成 / : C2H6O2
#8: 化合物 ChemComp-BEZ / BENZOIC ACID / 安息香酸


分子量: 122.121 Da / 分子数: 1 / 由来タイプ: 合成 / : C7H6O2
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1382 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.86 Å3/Da / 溶媒含有率: 56.98 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 / 詳細: Tacsimate, PEG3350

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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: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2018年12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: 0.9792 Å / 相対比: 1
反射解像度: 2.03→101.87 Å / Num. obs: 203307 / % possible obs: 98.5 % / 冗長度: 4.1 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.9
反射 シェル解像度: 2.03→2.1 Å / Num. unique obs: 19824 / CC1/2: 0.387 / Rpim(I) all: 1.105

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
XDSデータ削減
PHENIX位相決定
PHENIXデータスケーリング
PHENIXdata processing
精密化構造決定の手法: フーリエ合成 / 解像度: 2.03→85.99 Å / SU ML: 0.2706 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 22.4855
Rfactor反射数%反射
Rfree0.2075 10347 5.11 %
Rwork0.1667 --
obs0.1688 202365 97.85 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 36.59 Å2
精密化ステップサイクル: LAST / 解像度: 2.03→85.99 Å
タンパク質核酸リガンド溶媒全体
原子数19484 0 117 1382 20983
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.006920120
X-RAY DIFFRACTIONf_angle_d0.836327269
X-RAY DIFFRACTIONf_chiral_restr0.04922859
X-RAY DIFFRACTIONf_plane_restr0.00553517
X-RAY DIFFRACTIONf_dihedral_angle_d16.49987217
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.37043390.33136035X-RAY DIFFRACTION93.6
2.05-2.080.3523040.32416215X-RAY DIFFRACTION95.17
2.08-2.10.31333760.29366247X-RAY DIFFRACTION97.3
2.1-2.130.34573250.29996348X-RAY DIFFRACTION97.99
2.13-2.160.32263640.27946373X-RAY DIFFRACTION98.35
2.16-2.190.32543260.27316403X-RAY DIFFRACTION98.43
2.19-2.220.31553360.26016358X-RAY DIFFRACTION98.48
2.22-2.250.31143670.2626359X-RAY DIFFRACTION97.83
2.25-2.290.29643390.24086342X-RAY DIFFRACTION98.03
2.29-2.320.27523400.23516335X-RAY DIFFRACTION97.18
2.32-2.360.25973470.22056139X-RAY DIFFRACTION94.85
2.36-2.410.24523460.2066368X-RAY DIFFRACTION98.37
2.41-2.450.24883520.19286400X-RAY DIFFRACTION98.93
2.45-2.50.26533530.1956411X-RAY DIFFRACTION98.87
2.5-2.560.24663530.17696463X-RAY DIFFRACTION99
2.56-2.620.23583100.17836502X-RAY DIFFRACTION98.95
2.62-2.680.24363630.16766390X-RAY DIFFRACTION98.83
2.68-2.760.20433580.1616448X-RAY DIFFRACTION99.07
2.76-2.840.20013540.15576477X-RAY DIFFRACTION98.96
2.84-2.930.19323500.16246384X-RAY DIFFRACTION98.11
2.93-3.030.22033410.16326262X-RAY DIFFRACTION96.03
3.03-3.150.21053700.1656300X-RAY DIFFRACTION96.91
3.15-3.30.21283820.16366533X-RAY DIFFRACTION99.53
3.3-3.470.19863230.15816499X-RAY DIFFRACTION99.01
3.47-3.690.20563040.15026560X-RAY DIFFRACTION98.95
3.69-3.970.16273010.13566518X-RAY DIFFRACTION98.24
3.97-4.370.15473500.12046517X-RAY DIFFRACTION98.09
4.37-5.010.14663320.11496454X-RAY DIFFRACTION96.75
5.01-6.310.16563500.12876645X-RAY DIFFRACTION98.9
6.31-85.990.14923920.14326733X-RAY DIFFRACTION96.78
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)
11.86608035862-0.270524195362-1.174753536810.7800644212590.189296941731.83272298892-0.0862901565338-0.269729585734-0.3441907967-0.05595243333180.0003798011202010.011720768460.25918554830.1967137050420.08105630608230.2914493861830.0265417303083-0.04450400085840.2288438482660.0550325672670.297209705795-0.423060483051-5.6776407128737.2631343069
20.6689564499970.146933919861-0.4114106602440.06131220369120.005547795062040.936019525339-0.0224259740421-0.00671653235359-0.09703578004060.1470913675380.009610804341250.02577714563420.175835820989-0.00125770644098-0.003890775067640.243663877180.0306316485421-0.02757548119840.23288357479-0.002816965278040.22234638348910.949179405515.543571042231.2563817259
30.3149631207970.335019889322-0.02797856580410.354641219330.002616895019610.5287775785270.01695417975220.00681320478757-0.0766547133144-0.005993260468850.00744523723315-0.05979782977040.08209058308980.0540294990886-0.02207608186330.2327328992950.03170813579610.001424623552490.247320152004-0.01769981019080.21888255580917.576961187618.90286412721.2296722439
40.971306263499-0.797147463316-0.1974151751562.67051175352-0.4392395639760.916745702352-0.08239783561560.00241850890805-0.243184813132-0.07841121978170.02196430845440.11741128280.3436729006740.1298915297990.04895084432940.3201906679680.00150451237076-0.007440640382740.368076316521-0.04131215719030.29891976408919.32679824029.9667249746731.3132180413
50.603436973333-0.01516250488010.1707888694513.19752826756-0.2555439470810.4549887184220.1511099004680.0484913144988-0.256217315638-0.0576071488753-0.3137068567930.2509923833870.1591593485240.2564250164020.1458456644630.2739747318140.05961728387380.03581360816150.293253442927-0.00683200787420.31691494271131.912316800512.100395222920.3276838869
60.4126935595220.282306020963-0.4073321202710.6300113879080.01306279443460.9685098989920.0468886121688-0.0681353028388-0.1381065866170.0518305708091-0.0860141276148-0.1243284306110.1668309992570.2189634807160.06380254966540.2487574018130.0444001419420.001667383231460.2923115355050.007946053469950.271788360536.239748711618.217628144626.4996975389
70.8346511338290.05304704687410.1058533794910.591233343565-0.1889136116311.23896767579-0.01634073513770.02542838358780.03593441384250.01884123512320.00434535480563-0.049267984874-0.1539376938760.1535139225436.02160649555E-50.2430859473770.01545155760940.02071679144610.255682673151-0.02022561588880.2393212507936.398384352838.478436540314.3434412252
80.4199446518250.080687316936-0.1363169479360.5297706163820.175656776810.119880815388-0.009684116707330.106812267086-0.06259321262690.004280641192960.0130396719502-0.02009422752950.0368026378618-0.00858488982351-0.006169898936040.2469457917910.01600760173120.02835497775570.258085582308-0.02190287974110.24525344560234.152759123918.5409046732.71796484545
91.48888792297-0.431991752399-0.765218642050.877944781856-0.1830060280030.9332900363730.05732698397790.2487240780780.00662424400630.0185365189142-0.0403526761975-0.0637874670576-0.235149375014-0.00857297583994-0.01005632146860.238689774814-0.018344059110.009538147182360.278358095625-0.0003120411364950.22316643836524.763316096737.36654921892.45759693723
100.9574993780110.41436988678-0.3212066336071.339822325170.5067677469510.9254280780620.146608519297-0.0443424038464-0.00340950243460.084865155833-0.0186330391226-0.02809925137510.01032907372370.135132251644-0.07989671861570.2411882334710.01454650678277.91815463381E-50.21960231989-0.01817762353980.22850975522321.998554127241.110909694729.7597420437
110.2700801822820.0289581726964-0.1311381308670.306034335183-0.08432318881710.459788318322-0.01600937333460.0337740170163-0.079598570529-0.03263847061960.02424517496820.008641032521010.122356243209-0.0369938106198-0.008541880531550.2338686749040.00399508215761-0.01769517144540.202420820564-0.01317445022880.2246132931-3.223996794134.337322957622.1167635414
120.8287648391620.587351753768-1.018073732020.750674364842-0.8292488327531.345777194410.003300527889760.195609269362-0.1127855329410.01352750398420.07967841809290.1123964122690.107017777035-0.269193528846-0.02792968427470.31875192867-0.0677975285391-0.02561649483510.271831402131-0.009991189200650.290742403245-10.7512907186-7.3545694240911.051195075
130.960774076830.190678988189-0.435855655171.01207186726-0.3173759702650.602370257391-0.2308106280160.323148403928-0.203663115138-0.1859202233730.1504948361190.06696683745070.249372250564-0.526715769350.06295714240720.33638585563-0.075347348531-0.02289111428020.343043215303-0.01741059461350.34069155534-22.3380751172-6.8808610962915.6767139593
144.93497900698-0.257088812727-0.5204323212683.82604416360.3199325509833.44203122703-0.08390532011990.322237863130.117309944691-0.5973215902630.07414627828960.092276925602-0.2894153752720.406938773392-0.001234022268370.327317552457-0.006674242771470.03007158077350.360405747041-0.00540151739430.21161251411619.370366827423.5778789343-9.5664921895
152.066536280652.330994784271.247082606934.49616952151.773049176221.288397177150.03012075278230.416694590224-0.0507561687409-0.381902393492-0.0126549026620.21337983273-0.015399824234-0.0299093874667-0.006051601418970.394740377917-0.0160447551636-0.04059591652730.46667310971-0.01070235511460.21896923135710.65477247311.7032965102-16.1889451773
162.629356801050.132456209057-0.2716487108810.716994990343-0.4757255268360.918592719066-0.05138000792140.432779009025-0.479966646749-0.3208461032240.0858587968306-0.08820657388230.0658775741273-0.008754619537680.005852493708030.3509210403810.02950712172710.05046558055480.344435646641-0.1001316784580.30365857133614.39235155060.731405915273-13.0247029622
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310.316629995994-0.07185264649950.3765756939560.826726183587-0.1422947054581.1767643742-0.0348241539001-0.01591677431920.101730033902-0.03707482436960.01381078279010.0313798824204-0.109275215787-0.06696105438560.04532233359370.2950789440280.01410236360460.04055383215710.198135430989-0.01420150996950.2345747941914.2205776113462.17055504956.4509231876
321.241701696770.240010139335-0.0830346729470.2700865166050.1357321752270.379856765588-0.00380038903495-0.05237660806440.1064281685960.07398870039980.02489091293630.023239631831-0.06690219155230.0269662518077-0.01970952222650.292235330620.0322202462020.01766793144090.190587500218-0.02624607972910.232388140952.4332631086862.459712553968.8954204903
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341.679951300360.0466516453455-0.5279357277130.6443805294660.3181244228450.345881228375-0.01379421210650.2799275342160.152041526403-0.07265495009040.01543998026150.00294919075817-0.06964653013660.06212659714380.02197940441760.206715311472-0.01241852283550.007352991062690.24084452074-0.01071570007030.2433890691615.216105352547.337563786544.977298418
350.5507180130340.249247822447-0.243069344610.7785445449160.07631405204660.406284829062-0.134279769435-0.0907963581486-0.1271395238080.1029887833650.07227229929730.09537407470760.0327170709805-0.03509613564710.05888646492610.2780259574930.01829904611450.02640683132780.2807696436230.01193574612060.221686571756-1.5577327747728.122666361163.3515275579
360.223558671409-0.0171121684028-0.04412742221220.2951108423960.21091179770.4539612218160.009957739024940.0136576817087-0.005453258098440.0180047273386-0.004054746090810.0888320558547-0.00646241334496-0.101137875842-0.01019199899380.19005395805-0.002419334404790.02005522900820.2351953451260.03903263455080.237806413709-22.956822831419.215160713149.9296375254
370.6603830953610.3870368790280.5373328062181.124129710050.7097636399531.274820447030.0730617677143-0.0656488357648-0.04734704857480.210618578768-0.02653154427210.2308316340090.134497665904-0.201046229026-0.01934833447280.252822803458-0.02981921759340.03999796150140.3054770260980.0436820067490.27837141479-31.831001038812.063252675762.5225048143
380.9603860047350.01640977341290.5483057546180.611781959440.2954748637661.101250988280.0781526839326-0.0954015412788-0.180389068310.132896874356-0.06571052671230.2157278286170.315592239453-0.26572042083-0.0198598810170.30833714919-0.05965917181810.01855619622830.2969733732080.02980525620370.330550313494-30.90690060780.54545027365157.4189964638
393.751362243250.35417142140.1109192889782.260753729260.2142725281824.129037141380.0726666383154-0.0651995794441-0.4042703165090.1792671028180.215113760775-0.249936267833-0.175738807473-0.0102515284289-0.2367458681320.2755800536970.02158737797120.03510063418110.394880483829-0.01275543419790.275105444221-2.8788575329943.232155106283.9010396517
404.443083796782.47844799071-1.281438939491.96448283458-1.051321121460.807083419252-0.0892612384121-0.357813467886-0.1418933962910.309550980673-0.04311924150870.01695697591260.126106463870.07524412953650.1392169623060.424427703049-0.01903087855970.04792054852420.3592606893240.04292980056650.284019643932-14.425135276433.773514586690.1449630313
410.5617886789590.359821047074-0.01766841952011.29396334414-0.005692427181410.4197545169060.100109495034-0.1258031261930.05639056210770.259613777394-0.1141036949010.1813888097010.0355775956734-0.02131392207970.01701499146070.3097340357630.01751265671220.08692812243970.324931969936-0.001780183066940.2716774359-24.139206511734.799915305682.7993715556
420.588035195136-0.06027710806450.3042323675731.10268535276-0.4161716599660.3593816491120.124806874043-0.1015873413630.1753109811510.166498507659-0.1235793508290.304043679527-0.156880292002-0.170906784591-0.01309567741140.2799691595330.05981836700940.09700292217080.40913406741-0.01828650904790.421693121984-34.811950566343.4720416274.564064838
430.6111753697390.232425485858-0.05356439168572.83297413208-0.198133334170.7539774022280.01302850220650.0500124297170.119096704326-0.130756113375-0.09860394707790.0326010586515-0.16249999716-0.2937045059130.09021920971420.2600929073780.06463888998570.04099729429770.3774436279580.01067750487860.398061664682-31.888039716747.994311201865.1391762788
443.450924683941.136469426350.8344199417051.80258711350.2455008680771.53209105703-0.0621202569444-0.2673538585360.5397475252430.0177710032945-0.1273530257110.396706427228-0.202617182008-0.2500661535710.1719172772730.3183291348670.0633152551860.0594235407720.238654287171-0.03793235823180.389039620579-21.330723431867.174731974373.6088456434
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503.51989710986-1.22348506159-1.039130375464.748924288362.466089314163.7860007407-0.09319760710880.499135836385-0.474329769737-0.608778763057-0.2348280582090.122891518924-0.0224331962633-0.4095636388280.3195967124850.3733579382390.02000651282640.01684443685310.455681660525-0.04399129824130.381487976812-10.450443127439.482550186621.6464481592
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 352 )
7X-RAY DIFFRACTION7chain 'A' and (resid 353 through 403 )
8X-RAY DIFFRACTION8chain 'A' and (resid 404 through 484 )
9X-RAY DIFFRACTION9chain 'A' and (resid 485 through 526 )
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 36 )
11X-RAY DIFFRACTION11chain 'B' and (resid 37 through 312 )
12X-RAY DIFFRACTION12chain 'B' and (resid 313 through 344 )
13X-RAY DIFFRACTION13chain 'B' and (resid 345 through 395 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 10 )
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 40 )
17X-RAY DIFFRACTION17chain 'C' and (resid 41 through 53 )
18X-RAY DIFFRACTION18chain 'C' and (resid 54 through 72 )
19X-RAY DIFFRACTION19chain 'C' and (resid 73 through 87 )
20X-RAY DIFFRACTION20chain 'C' and (resid 88 through 125 )
21X-RAY DIFFRACTION21chain 'C' and (resid 126 through 144 )
22X-RAY DIFFRACTION22chain 'C' and (resid 145 through 152 )
23X-RAY DIFFRACTION23chain 'C' and (resid 153 through 169 )
24X-RAY DIFFRACTION24chain 'D' and (resid 2 through 36 )
25X-RAY DIFFRACTION25chain 'D' and (resid 37 through 82 )
26X-RAY DIFFRACTION26chain 'D' and (resid 83 through 133 )
27X-RAY DIFFRACTION27chain 'E' and (resid 12 through 45 )
28X-RAY DIFFRACTION28chain 'E' and (resid 46 through 96 )
29X-RAY DIFFRACTION29chain 'E' and (resid 97 through 260 )
30X-RAY DIFFRACTION30chain 'E' and (resid 261 through 331 )
31X-RAY DIFFRACTION31chain 'E' and (resid 332 through 382 )
32X-RAY DIFFRACTION32chain 'E' and (resid 383 through 441 )
33X-RAY DIFFRACTION33chain 'E' and (resid 442 through 526 )
34X-RAY DIFFRACTION34chain 'F' and (resid 4 through 36 )
35X-RAY DIFFRACTION35chain 'F' and (resid 37 through 66 )
36X-RAY DIFFRACTION36chain 'F' and (resid 67 through 312 )
37X-RAY DIFFRACTION37chain 'F' and (resid 313 through 344 )
38X-RAY DIFFRACTION38chain 'F' and (resid 345 through 395 )
39X-RAY DIFFRACTION39chain 'G' and (resid 2 through 10 )
40X-RAY DIFFRACTION40chain 'G' and (resid 11 through 25 )
41X-RAY DIFFRACTION41chain 'G' and (resid 26 through 87 )
42X-RAY DIFFRACTION42chain 'G' and (resid 88 through 125 )
43X-RAY DIFFRACTION43chain 'G' and (resid 126 through 152 )
44X-RAY DIFFRACTION44chain 'G' and (resid 153 through 169 )
45X-RAY DIFFRACTION45chain 'H' and (resid 2 through 10 )
46X-RAY DIFFRACTION46chain 'H' and (resid 11 through 36 )
47X-RAY DIFFRACTION47chain 'H' and (resid 37 through 45 )
48X-RAY DIFFRACTION48chain 'H' and (resid 46 through 63 )
49X-RAY DIFFRACTION49chain 'H' and (resid 64 through 82 )
50X-RAY DIFFRACTION50chain 'H' and (resid 83 through 95 )
51X-RAY DIFFRACTION51chain 'H' and (resid 96 through 125 )
52X-RAY DIFFRACTION52chain 'H' and (resid 126 through 138 )

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

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