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- PDB-8hpj: Crystal structure of the bacterial oxalate transporter OxlT in a ... -

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基本情報

登録情報
データベース: PDB / ID: 8hpj
タイトルCrystal structure of the bacterial oxalate transporter OxlT in a ligand-free outward-facing form
要素
  • Fv fragment Heavy chain
  • Fv fragment Light chain
  • Oxalate:formate antiporter
キーワードTRANSPORT PROTEIN/IMMUNE SYSTEM / Transporter / TRANSPORT PROTEIN / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


oxalate transmembrane transporter activity / antiporter activity / monoatomic ion transport / plasma membrane
類似検索 - 分子機能
Oxalate/formate antiporter family transporter / Oxalate/formate antiporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Immunoglobulin-like ...Oxalate/formate antiporter family transporter / Oxalate/formate antiporter / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Oxalate:formate antiporter
類似検索 - 構成要素
生物種Oxalobacter formigenes (バクテリア)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.3 Å
データ登録者Shimamura, T. / Hirai, T. / Yamashita, A.
資金援助 日本, 1件
組織認可番号国
Japan Society for the Promotion of Science (JSPS)JP20H03195 日本
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota.
著者: Jaunet-Lahary, T. / Shimamura, T. / Hayashi, M. / Nomura, N. / Hirasawa, K. / Shimizu, T. / Yamashita, M. / Tsutsumi, N. / Suehiro, Y. / Kojima, K. / Sudo, Y. / Tamura, T. / Iwanari, H. / ...著者: Jaunet-Lahary, T. / Shimamura, T. / Hayashi, M. / Nomura, N. / Hirasawa, K. / Shimizu, T. / Yamashita, M. / Tsutsumi, N. / Suehiro, Y. / Kojima, K. / Sudo, Y. / Tamura, T. / Iwanari, H. / Hamakubo, T. / Iwata, S. / Okazaki, K.I. / Hirai, T. / Yamashita, A.
履歴
登録2022年12月12日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年2月15日Provider: repository / タイプ: Initial release
改定 1.12023年4月12日Group: Database references / Refinement description
カテゴリ: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_comp_id
改定 1.22024年11月6日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Oxalate:formate antiporter
B: Fv fragment Heavy chain
C: Fv fragment Light chain
D: Oxalate:formate antiporter
E: Fv fragment Heavy chain
F: Fv fragment Light chain


分子量 (理論値)分子数
合計 (水以外)147,6916
ポリマ－147,6916
非ポリマー00
水00
1
A: Oxalate:formate antiporter
B: Fv fragment Heavy chain
C: Fv fragment Light chain


分子量 (理論値)分子数
合計 (水以外)73,8463
ポリマ－73,8463
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Oxalate:formate antiporter
E: Fv fragment Heavy chain
F: Fv fragment Light chain


分子量 (理論値)分子数
合計 (水以外)73,8463
ポリマ－73,8463
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)76.870, 181.670, 81.170
Angle α, β, γ (deg.)90.000, 111.365, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 14 through 192 or resid 194...
d_2ens_1(chain "D" and (resid 14 through 192 or resid 194...
d_1ens_2(chain "B" and (resid 1 through 88 or resid 90 through 121))
d_2ens_2(chain "E" and (resid 1 through 88 or resid 90 through 121))
d_1ens_3(chain "C" and (resid 1 through 9 or resid 11 through 55 or resid 57 through 109))
d_2ens_3(chain "F" and (resid 1 through 9 or resid 11 through 55 or resid 57 through 109))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYGLYGLYAA11 - 18211 - 182
d_12ens_1LEULEUILEILEAA184 - 186184 - 186
d_13ens_1ILEILEASNASNAA188 - 268188 - 268
d_14ens_1GLYGLYILEILEAA270 - 384270 - 384
d_15ens_1SERSERALAALAAA386 - 393386 - 393
d_21ens_1LEULEUMETMETDD12 - 18112 - 181
d_22ens_1ILEILEILEILEDD183 - 185183 - 185
d_23ens_1ALAALAGLYGLYDD189 - 269189 - 269
d_24ens_1CYSCYSTHRTHRDD271 - 385271 - 385
d_25ens_1PHEPHETHRTHRDD387 - 394387 - 394
d_11ens_2LEULEUSERSERBB1 - 881 - 88
d_12ens_2ASPASPSERSERBB90 - 12190 - 121
d_21ens_2LEULEUSERSEREE1 - 881 - 88
d_22ens_2ASPASPSERSEREE90 - 12190 - 121
d_11ens_3GLUGLUSERSERCC1 - 91 - 9
d_12ens_3LYSLYSTYRTYRCC11 - 5511 - 55
d_13ens_3TYRTYRLYSLYSCC57 - 10957 - 109
d_21ens_3GLUGLUSERSERFF1 - 91 - 9
d_22ens_3LYSLYSTYRTYRFF11 - 5511 - 55
d_23ens_3TYRTYRLYSLYSFF57 - 10957 - 109

NCSアンサンブル:
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixベクター
1given(0.716063907311, 0.0284701065203, 0.697453893588), (0.0297394932005, -0.999504954922, 0.0102668217891), (0.697400919981, 0.0133902248001, -0.716556109938)-4.37598690758, -25.8545451842, 11.0595319793
2given(0.716165270614, 0.0188428113173, 0.6976763244), (0.0162884792491, -0.999814457434, 0.0102828084794), (0.697740632765, 0.00399989601527, -0.716339312213)-3.94399358761, -25.6580377625, 10.8682863872
3given(0.718864407474, 0.0251295169816, 0.694695955828), (0.0210834758851, -0.99967480586, 0.0143446705378), (0.694830519416, 0.00433473234558, -0.719160454547)-3.93483775429, -25.7576552856, 11.2348251102

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要素

#1: タンパク質 Oxalate:formate antiporter / OFA / Oxalate:formate antiport protein / Oxalate:formate exchange protein


分子量: 45787.285 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Oxalobacter formigenes (バクテリア)
遺伝子: oxlT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q51330
#2: 抗体 Fv fragment Heavy chain


分子量: 15110.998 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Brevibacillus choshinensis (バクテリア)
#3: 抗体 Fv fragment Light chain


分子量: 12947.251 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Brevibacillus choshinensis (バクテリア)
Has protein modificationY

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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: 66.94 %
結晶化温度: 293 K / 手法: 脂質キュービック相法 / pH: 9
詳細: 100 mM Glycine, pH 9.0, 26-36% (v/v) PEG 400, 50-150 mM MnCl2

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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: SPring-8 / ビームライン: BL32XU / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2015年12月9日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 3.1→47.26 Å / Num. obs: 26204 / % possible obs: 88.4 % / 冗長度: 24.8 % / Biso Wilson estimate: 52.81 Å2 / CC1/2: 0.98 / Net I/σ(I): 5
反射 シェル解像度: 3.1→3.4 Å / Num. unique obs: 1310 / CC1/2: 0.69

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解析

ソフトウェア
名称バージョン分類
Coot0.9.6モデル構築
PHENIX1.19.2_4158精密化
XDSデータ削減
XSCALE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
開始モデル: 8HPK, 5B3N

8hpk

5b3n


解像度: 3.3→47.26 Å / SU ML: 0.4801 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.4568
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2859 1265 4.97 %
Rwork0.2596 24163 -
obs0.261 25428 81.6 %
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: 53.88 Å2
精密化ステップサイクル: LAST / 解像度: 3.3→47.26 Å
タンパク質核酸リガンド溶媒全体
原子数9517 0 0 0 9517
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00259766
X-RAY DIFFRACTIONf_angle_d0.593813269
X-RAY DIFFRACTIONf_chiral_restr0.04041480
X-RAY DIFFRACTIONf_plane_restr0.00611664
X-RAY DIFFRACTIONf_dihedral_angle_d17.50721343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.636956348262
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.720388762614
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.929423242916
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.430.3684290.3903789X-RAY DIFFRACTION23.69
3.43-3.590.361080.30931807X-RAY DIFFRACTION55.72
3.59-3.780.31921430.30652864X-RAY DIFFRACTION87.82
3.78-4.010.30811670.28673222X-RAY DIFFRACTION97.39
4.01-4.320.31821630.28093259X-RAY DIFFRACTION98.9
4.32-4.760.31481270.28652325X-RAY DIFFRACTION70.85
4.76-5.450.25371710.22543285X-RAY DIFFRACTION99.94
5.45-6.860.27421770.23373301X-RAY DIFFRACTION99.94
6.86-47.260.22521800.20923311X-RAY DIFFRACTION99.54
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)
11.8890458785-0.2608242502660.2940534305433.507342319890.1091699238341.57884710193-0.1510642333750.02517014471260.1815456645420.4280917506820.01463865222060.130335389668-0.145324934618-0.3287901489840.07002250708560.244595472211-0.1355894492580.03189499346620.2238993037050.01431935355430.3189875442039.70997445169-56.786146134213.3761827714
24.40403444083-1.65176358132.797548242091.87631882368-1.404073621212.43927856212-0.0212018479631-0.534222397109-0.61083042789-0.04967362139160.5565534445060.6131653554910.476123152463-0.523020471005-0.5556917770790.296783819437-0.0539138941320.02321759222920.4917042640510.07184859004730.4027779228288.41789724097-67.777428037615.1506415491
30.6237686444230.335970139212-0.4414488972820.548793767659-0.7112294207451.14846399719-0.037226084467-0.1398762657090.05203637792320.124984732262-0.0565259656151-0.0455458113695-0.094010952814-0.0621017264910.03383300855240.3115486970870.0311614272602-0.1018820630190.0750887556685-0.09646421695220.26688598852630.271098616-57.100408313910.2646918486
49.41558987333.82569761733-3.123960541623.43015380333-1.734095263683.377664917490.276440958514-0.791021574412-1.006843493480.00519494744816-0.106638870395-0.02207778103760.6046449969810.04464845614060.02641344686630.543759023365-0.00550916871289-0.06570009489940.2495039800270.08067064530630.63063077473829.1636151791-79.478761897124.1757134859
54.42888636794-0.84396238508-1.411734153310.514788876094-1.198927410056.506287244270.452376336403-0.9227338170090.7443817502080.817878756642-0.127407931065-0.067102792412-1.357596520640.669179046309-0.6688912708990.719635086084-0.0461050925841-0.03379765606840.428974498927-0.1406223502390.59200749980139.1468627023-12.42318072564.9516702726
64.353630507420.472967394265-1.732722607193.19329019252.887047281173.70188870886-0.1584366480240.05986109984950.533897255017-0.1204438641970.1518940498030.01166250153540.2080171454510.240340904294-0.1536502021670.4667476281860.0374867885972-0.1726556867680.200966607359-0.1171283356390.37165995146734.5396098678-22.42203644720.525458156679
74.58842809581-0.744305474856-0.7358225082567.573188754290.3204554552534.22076928708-0.2377460288850.211263265880.74939431793-0.1873331912120.142303724342-0.385868745119-0.681834233270.540709516115-0.08734674623230.641821247774-0.0235752378690.05602950118080.305944490859-0.07711584405680.8028160694942.6720046223-19.1173265238-2.17517277207
81.79614905921-0.679762129833-0.9986098485456.51945891783-0.365283478642.20830818584-0.168196081653-0.08434706557480.3764553972820.2732679844560.134353369010.595086857343-0.482385821306-0.03449446658890.015141713380.6440191339620.0966611093538-0.1578783957740.274854545022-0.2075929171190.77142726394931.2020520987-19.63974648543.31090611613
91.905054803742.25769037221.037261582684.097321154630.2136195141231.29028421866-0.0286787107262-0.02289586776530.91498641396-0.677145934022-0.3493935249710.466201329878-0.694440491402-0.4780731231320.299327664711.306038023710.195616919433-0.1321701555940.491634429878-0.1093184499650.50594877253921.5825886575-22.2396118252-14.579377183
101.949925512574.19375291843-0.3013183858689.15601709571-0.7840226141750.181622892682-0.8373656878650.06960030297030.429918719705-0.3289093079620.5132434706010.793029262629-0.983068403443-0.7774538076450.2960317543611.203083222660.372072246584-0.3220509131771.11797917957-0.221856809270.7909961559724.94307022311-11.4411544674-4.97640491441
110.894466617746-1.34564065758-1.506990774742.038676865962.329337225982.81797092870.407610464614-0.0402997871396-0.3967838541550.06923761271650.0821176126966-0.2977304147560.7221721350770.00990629888609-0.2950737088520.8894190495010.209588230368-0.4970792907481.01219333351-0.2533460078380.85043016653211.2112998507-21.5414001547-8.92146503479
126.49572507845-5.981060889696.333379627376.22150862045-5.818611845877.747103320581.475946129330.119570111433-1.29904290422-1.727379248140.1742944137021.349975285931.367647762030.180231846649-1.495752278080.7269985831820.0984922333283-0.3024479364210.776333936101-0.2011243625710.98156480584320.3729219255-32.392050891-9.77366544244
132.10834967469-1.11091650866-2.032567632123.092331415922.221291613595.367013699260.221326234952-0.193173265563-0.384069409723-0.8475857190230.1599539273820.329087433175-0.914401421277-0.294183918486-0.1154722030240.4407845145470.147754198754-0.1616970036420.633818850895-0.1991960827050.55247468154719.133528178-19.9190009536-0.96173880995
142.64820026154-0.4851973555170.7080703067970.595028226290.5856841092241.19961626291-0.418114974589-0.4303139721951.701853955440.2298976992280.178458603252-0.528719492061-0.4764366378160.04933591474740.2628798267870.4254354877490.145659297324-0.290895149560.576701755353-0.3404967277141.0512842492220.3039550694-13.98985720333.46996488169
155.62785580993-5.40923511153.64375969165.20753620438-3.590743514023.308010159580.353095364799-1.214908237880.6519157378381.853029534390.0721181479678-1.640043465960.808588528773-0.750299210526-0.430992577020.966720409093-0.050340248798-0.2504569926940.606235286069-0.02953744369240.85727025667413.4947997082-24.94148965876.73139484262
162.5558388871-3.03583384344-3.860015481244.387810739034.604520150095.83005266134-0.560346417364-0.0619616628371-0.283155940674-0.87175474759-0.7513734743581.88482878097-0.689019167051-1.96351999111.552623289820.5401367759490.132788176586-0.09629562694040.743031834449-0.2591636180010.75864069664310.2742064026-25.8546111426-0.873736350594
178.28487038145-5.42310464652-5.120933127764.610020982315.501603144857.521712469250.423778789050.339018163623-1.49090286788-0.8875557594570.06698844373912.155626718760.0462160017717-0.6829828676170.256627282630.8995750631080.200011185111-0.1051768783790.4251361364080.06202728698091.106247540311.4728024102-25.5180627407-6.2476149523
188.40843556304-1.89523274988-1.976497134920.6874962168570.9561283611151.461909089140.171838743361-0.3271622112491.442241158510.6991820561990.0129080296308-0.948457821097-0.22750958663-0.0175656009462-0.3818981317951.227431795010.0556855805107-0.3482738624130.391346632801-0.055322425620.95737051138713.3392126975-14.9574426046-0.458615408475
194.96337338826-4.01028712934-3.766552981474.90305082072.283121713423.252117879140.6966310352490.3525721400750.0213489439832-1.04833218377-0.374793189033-0.7455269629090.241378814445-0.71931201918-0.2057944352440.7174253849570.0927528713142-0.1094322363070.505736647709-0.2640121330140.57941143009525.6728908954-25.3558743822-7.14353105031
202.55989602342.064471696061.415382631971.772455590181.147883231510.7831732171360.3635967946290.608116849951-0.849953694273-1.29412034671-0.198609581372-0.247540017805-0.209024270164-0.4471895720140.07603730977271.403912609990.183117824394-0.3439045101920.655665666352-0.007499550797251.006439530688.60395724056-6.18490822407-6.54509290583
213.32939065894-1.72585146725-0.2268994215873.26492051340.9811314291932.181538954320.0899656896398-0.249987735005-0.333065623712-0.249462197719-0.05984483370140.879426325560.0502526084919-0.284968133761-0.1546141591580.1390998764680.0418407019186-0.1035031662960.4313452222770.2218931648130.3508205087647.5843050567829.894054130611.2731390751
223.5373287164-1.997187102861.906553390716.37216677136-1.692863362944.491901077580.26672585817-0.1809650763710.208841663917-0.410750905610.007412669278070.278598905647-0.00135368893719-0.60657076292-0.06809773463020.1090490491020.05021613264740.03098530248190.3285352913350.04326319389260.40082949684619.374054801632.91650200743.8426122728
231.916764789511.02523862576-0.4256173365041.74576990893-0.2222538464060.918021258003-0.003223005366120.0686436295315-0.117111673671-0.1943820628230.3390257356170.08564783815220.00298730195884-0.437843145663-0.2399907245290.2808022107450.111624732525-0.1736489463270.4607326007280.04038874348860.4324265299198.028373843530.71093839987.15320489842
240.7187138853320.649542282977-0.737919129461.08772371351-0.2131002839991.463778849280.1341208283280.1150033431660.1150931214160.04871323290450.07781021923010.283271075101-0.259348038785-0.1015835072420.07534743038750.3160229464410.0686839984362-0.1140890958660.163421878317-0.1415720093130.42197105905819.70295137936.5328955419.7331923546
250.859633175204-0.2155906657540.07215028666090.245379901793-0.4555533826661.07887609789-0.05034661422090.05035963263160.1806330586120.0393262040264-0.111016291823-0.200359096375-0.0794367762420.0598212430305-0.08838241158930.1393124514890.1577525595070.01140218191760.188511898063-0.2035538859680.49183048409925.967953911536.293406262722.8396726352
264.88476584122.02819667614-4.351745681964.7894819599-5.248360973696.87113939373-0.9330800594160.0129868825263-0.5947959814680.3723313654270.183098034646-0.793351993650.68248203367-0.2132592911480.6166437550340.6896506860510.194527037104-0.1532369273170.372409924902-0.2007436855840.96155372159427.0349711152-12.514220626934.5814503927
270.123184627878-0.339986582681-0.2826539259955.188499611562.974652151081.781665118370.3916799915740.177157755511-0.423656307326-0.220902098470.16466744838-0.5349674773210.5622347069660.5550011851750.07984784936040.4884031280430.1351946031020.02171074666560.295267658683-0.1752386056440.55325572604529.09259515262.3380204200925.8545034976
282.25982849020.468125316384-0.4734373961924.0771259903-0.9620005398522.855905882230.06265405037840.0994120322366-0.4701650454460.154441496359-0.04848076723830.3689317627470.579393441727-0.2170237168170.2531323684960.7263904158430.04101147460470.005053082023360.162525309016-0.1794868198690.64629348977617.5733325846-3.5685462010938.6947704623
293.266949251571.55955030332-1.476581947021.82121663608-0.9751825450273.02668145638-0.553326565910.318833321398-1.20993215859-0.801014529418-0.0401262840511-0.1499253446350.6795789549180.1286352494090.787567875991.189960047920.1100438287670.007327205847890.310051531108-0.1377009493440.8873360247431.7467910029-2.1292766126735.9906951055
305.902530983212.4290370839-1.850936992131.236373249640.5303444544427.633242559040.22195378934-1.0864228567-0.6546433006580.994251501586-0.569598726326-0.4579925434021.468923442240.7504476319470.1968063061891.01845554395-0.0137200247509-0.3135563556590.4186176036650.0702422189490.59062008990528.1613585551-7.2585228760140.1252227345
310.0205408875988-0.299943537615-0.1368402444846.791233750913.881584271192.38254783747-0.100761353159-0.209029856443-0.5198378740511.52008102702-0.4713618102421.562622814930.682356822646-0.6115891809220.5439585090390.885654144712-0.04619683268960.311905314110.373099572564-0.02997699025911.1276306529816.5339298458-13.067678699947.613872664
321.081983120580.943908404067-0.3044621815643.68905794645-2.32693336021.56778509261-0.0088776704423-0.0699974803274-0.7087035345040.513171720513-0.04339578534960.1714073835930.2664384860580.01131195488880.1522433738281.058340773590.176305802359-0.0220869525810.289106903753-0.04141765199140.84058958307220.3509077006-9.4614297708232.1391490866
331.31084935938-0.0166944237358-0.5459648282720.05632269274750.4343261695163.4929866791-0.301493477419-0.071006767847-0.38729835556-0.558805219382-0.0341343122780.4620823368850.972760130332-0.620071722080.4387953806680.798257882587-0.0472272063197-0.1055046197220.42754206908-0.2056913376341.0027537074519.8434872184-5.1305373503330.1984162264
345.05093781159-4.28229446411-3.421340385039.075910911490.3024366300644.31660610039-0.477665817025-0.9824423155210.101489901909-0.01588254006070.05147330881-0.1557624224420.237450887404-1.295026163370.4496126442440.712709536418-0.00598196418994-0.1420795278850.95519018755-0.03571529936210.6179246667940.474769327041-2.72552045836.1520305006
351.461653964212.456367861871.512075408924.203120586022.446781597161.66878453279-0.3342874327330.179093165449-0.2222652660280.525332977662-0.5981383610330.6838924302840.252455251082-0.823080617330.4411534677520.760276593083-0.0361462921387-0.09816488438110.589559375644-0.4234281694461.18792777695-1.85937666895-4.5355454792624.3274785993
361.05612335128-1.00365710362-0.2150578883410.9599404559160.1197916117291.1860042993-0.3802824634530.0935864797178-0.6321602396890.1312912881560.225390582794-0.3149386882080.7640002364360.215246670248-0.3900406796580.7368041899360.085829441071-0.05860677534120.317805804708-0.2405968510130.76441507321410.663485601-8.7703147521423.5813597317
373.011034661331.161996097710.02098793368313.997497056072.870935682012.309011970650.008209361718770.01141748962960.177111204534-0.753972388491-0.19396368253-0.5093315427050.1141974074450.002440801286180.1158052327260.8091797088120.305203079675-0.02118955394690.484124713843-0.2107632641470.8478974105159.58100795209-0.45613678880415.5166869072
381.415481225291.788957520590.3954643503676.892097699961.224692283275.77757213236-0.4226456721241.060168007680.82717524534-0.0608079336509-0.1003033627631.14795638535-0.550197860243-0.4777654615961.080895978210.7162455507340.00727597584856-0.5000920711960.722975808941-0.1570726373051.25202674254-0.01657331491140.26666491677121.6612774578
395.882907049154.395680740974.101860224973.513689776282.705424265043.422374740590.464278616772-0.1629682132-0.1262099071120.483368465772-0.88293757992-0.3237988244810.422623070167-0.3288350037840.128629081830.646661869930.065880351244-0.1358995042390.536375249789-0.3217537280071.19455745134.47906796051-10.285283604420.5244173399
401.803348721730.242958036474-0.2272491969230.7725499585-0.415091833440.2285713647560.188017570966-0.270022478844-0.559127664569-0.165415109595-0.2227197936710.8414174835960.702465803843-0.9684636712450.1241242161430.463480615594-0.2479524150540.08674334237810.506742739882-0.001039161785860.7595537270138.598818219470.26144217825333.5893283166
410.2946498723991.007992411460.7952464576473.931949903042.992814372632.29987332112-0.56804828724-0.245954962167-0.5576064286020.680618090491-0.5981638254991.160764500832.05020160716-1.075175523021.359545332021.12580298971-0.1226031675110.4677273299650.652767040896-0.3101972568791.01635678047-2.97824139235-19.90528200521.8974910252
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 12 through 169 )DD12 - 1691 - 158
22chain 'D' and (resid 170 through 219 )DD170 - 219159 - 203
33chain 'D' and (resid 220 through 394 )DD220 - 394204 - 378
44chain 'D' and (resid 395 through 412 )DD395 - 412379 - 396
55chain 'E' and (resid 1 through 26 )EE1 - 261 - 26
66chain 'E' and (resid 27 through 60 )EE27 - 6027 - 60
77chain 'E' and (resid 61 through 91 )EE61 - 9161 - 91
88chain 'E' and (resid 92 through 121 )EE92 - 12192 - 121
99chain 'F' and (resid 1 through 11 )FF1 - 111 - 11
1010chain 'F' and (resid 12 through 20 )FF12 - 2012 - 20
1111chain 'F' and (resid 21 through 26 )FF21 - 2621 - 26
1212chain 'F' and (resid 27 through 34 )FF27 - 3427 - 34
1313chain 'F' and (resid 35 through 40 )FF35 - 4035 - 40
1414chain 'F' and (resid 41 through 50 )FF41 - 5041 - 50
1515chain 'F' and (resid 51 through 63 )FF51 - 6351 - 63
1616chain 'F' and (resid 64 through 69 )FF64 - 6964 - 69
1717chain 'F' and (resid 70 through 77 )FF70 - 7770 - 77
1818chain 'F' and (resid 78 through 92 )FF78 - 9278 - 92
1919chain 'F' and (resid 93 through 104 )FF93 - 10493 - 104
2020chain 'F' and (resid 105 through 110 )FF105 - 110105 - 110
2121chain 'A' and (resid 11 through 50 )AA11 - 501 - 40
2222chain 'A' and (resid 51 through 80 )AA51 - 8041 - 70
2323chain 'A' and (resid 81 through 189 )AA81 - 18971 - 179
2424chain 'A' and (resid 190 through 281 )AA190 - 281180 - 264
2525chain 'A' and (resid 282 through 410 )AA282 - 410265 - 393
2626chain 'B' and (resid 1 through 26 )BB1 - 261 - 26
2727chain 'B' and (resid 27 through 34 )BB27 - 3427 - 34
2828chain 'B' and (resid 35 through 67 )BB35 - 6735 - 67
2929chain 'B' and (resid 68 through 77 )BB68 - 7768 - 77
3030chain 'B' and (resid 78 through 84 )BB78 - 8478 - 84
3131chain 'B' and (resid 85 through 91 )BB85 - 9185 - 91
3232chain 'B' and (resid 92 through 98 )BB92 - 9892 - 98
3333chain 'B' and (resid 99 through 123 )BB99 - 12399 - 123
3434chain 'C' and (resid 1 through 11 )CC1 - 111 - 11
3535chain 'C' and (resid 12 through 34 )CC12 - 3412 - 34
3636chain 'C' and (resid 35 through 50 )CC35 - 5035 - 50
3737chain 'C' and (resid 51 through 63 )CC51 - 6351 - 63
3838chain 'C' and (resid 64 through 77 )CC64 - 7764 - 77
3939chain 'C' and (resid 78 through 92 )CC78 - 9278 - 92
4040chain 'C' and (resid 93 through 104 )CC93 - 10493 - 104
4141chain 'C' and (resid 105 through 110 )CC105 - 110105 - 110

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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

他の情報も見る