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- PDB-6xwl: Cystathionine beta-synthase from Toxoplasma gondii -

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基本情報

登録情報
データベース: PDB / ID: 6xwl
タイトルCystathionine beta-synthase from Toxoplasma gondii
要素Cystathionine beta-synthase
キーワードCYTOSOLIC PROTEIN / Transulfuration / hydrogen sulfide / homocysteine / CBS
機能・相同性
機能・相同性情報


cystathionine beta-synthase / cystathionine beta-synthase activity / cysteine biosynthetic process via cystathionine / cysteine biosynthetic process from serine / cytoplasm
類似検索 - 分子機能
Cystathionine beta-synthase / CBS-domain / CBS-domain / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme ...Cystathionine beta-synthase / CBS-domain / CBS-domain / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-synthase
類似検索 - 構成要素
生物種Toxoplasma gondii ME49 (トキソプラズマ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.201 Å
データ登録者Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Quintana, I. / Martinez-Chantar, M. / Astegno, A. / Martinez-Cruz, L.A.
資金援助 スペイン, 4件
組織認可番号国
Ministry of Economy and Competitiveness (MINECO)BFU2013-47531-R スペイン
Ministry of Economy and Competitiveness (MINECO)BES-2014-068464 スペイン
Ministry of Economy and Competitiveness (MINECO)BFU2016-77408-R スペイン
Ministry of Economy and Competitiveness (MINECO)BES-2017-080435 スペイン
引用ジャーナル: Comput Struct Biotechnol J / 年: 2021
タイトル: Structural insight into the unique conformation of cystathionine beta-synthase from Toxoplasma gondii .
著者: Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Nunez-Franco, R. / Gil-Pitarch, C. / Quintana, I. / Jimenez-Oses, G. / Dominici, P. / Martinez-Chantar, M.L. / ...著者: Fernandez-Rodriguez, C. / Oyenarte, I. / Conter, C. / Gonzalez-Recio, I. / Nunez-Franco, R. / Gil-Pitarch, C. / Quintana, I. / Jimenez-Oses, G. / Dominici, P. / Martinez-Chantar, M.L. / Astegno, A. / Martinez-Cruz, L.A.
履歴
登録2020年1月23日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年2月3日Provider: repository / タイプ: Initial release
改定 1.12021年8月4日Group: Database references / カテゴリ: citation / citation_author
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
改定 1.22024年1月24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 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: Cystathionine beta-synthase
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
E: Cystathionine beta-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)337,23212
ポリマ－335,7506
非ポリマー1,4836
水00
1
F: Cystathionine beta-synthase
A: Cystathionine beta-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)112,4114
ポリマ－111,9172
非ポリマー4942
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-50 kcal/mol
Surface area36330 Å2
手法PISA
2
B: Cystathionine beta-synthase
D: Cystathionine beta-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)112,4114
ポリマ－111,9172
非ポリマー4942
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-45 kcal/mol
Surface area36940 Å2
手法PISA
3
C: Cystathionine beta-synthase
E: Cystathionine beta-synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)112,4114
ポリマ－111,9172
非ポリマー4942
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-48 kcal/mol
Surface area37110 Å2
手法PISA
単位格子
Length a, b, c (Å)83.237, 83.237, 420.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 6 through 337 or (resid 338...
21(chain B and (resid 6 through 337 or (resid 338...
31(chain C and (resid 6 through 337 or (resid 338...
41(chain D and (resid 6 through 362 or resid 365...
51(chain E and (resid 6 through 337 or (resid 338...
61(chain F and (resid 6 through 362 or resid 365...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 6 through 337 or (resid 338...A6 - 337
121(chain A and (resid 6 through 337 or (resid 338...A338
131(chain A and (resid 6 through 337 or (resid 338...A6 - 1551
141(chain A and (resid 6 through 337 or (resid 338...A6 - 1551
151(chain A and (resid 6 through 337 or (resid 338...A6 - 1551
161(chain A and (resid 6 through 337 or (resid 338...A6 - 1551
211(chain B and (resid 6 through 337 or (resid 338...B6 - 337
221(chain B and (resid 6 through 337 or (resid 338...B338
231(chain B and (resid 6 through 337 or (resid 338...B6 - 513
311(chain C and (resid 6 through 337 or (resid 338...C6 - 337
321(chain C and (resid 6 through 337 or (resid 338...C338
331(chain C and (resid 6 through 337 or (resid 338...C6 - 513
341(chain C and (resid 6 through 337 or (resid 338...C6 - 513
351(chain C and (resid 6 through 337 or (resid 338...C6 - 513
361(chain C and (resid 6 through 337 or (resid 338...C6 - 513
411(chain D and (resid 6 through 362 or resid 365...D6 - 362
421(chain D and (resid 6 through 362 or resid 365...D365 - 373
431(chain D and (resid 6 through 362 or resid 365...D374
441(chain D and (resid 6 through 362 or resid 365...D6 - 513
451(chain D and (resid 6 through 362 or resid 365...D6 - 513
461(chain D and (resid 6 through 362 or resid 365...D6 - 513
471(chain D and (resid 6 through 362 or resid 365...D6 - 513
511(chain E and (resid 6 through 337 or (resid 338...E6 - 337
521(chain E and (resid 6 through 337 or (resid 338...E338
531(chain E and (resid 6 through 337 or (resid 338...E6 - 513
541(chain E and (resid 6 through 337 or (resid 338...E6 - 513
551(chain E and (resid 6 through 337 or (resid 338...E6 - 513
561(chain E and (resid 6 through 337 or (resid 338...E6 - 513
611(chain F and (resid 6 through 362 or resid 365...F6 - 362
621(chain F and (resid 6 through 362 or resid 365...F365 - 373
631(chain F and (resid 6 through 362 or resid 365...F374
641(chain F and (resid 6 through 362 or resid 365...F6 - 513
651(chain F and (resid 6 through 362 or resid 365...F6 - 513
661(chain F and (resid 6 through 362 or resid 365...F6 - 513
671(chain F and (resid 6 through 362 or resid 365...F6 - 513

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要素

#1: タンパク質
Cystathionine beta-synthase


分子量: 55958.273 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Toxoplasma gondii ME49 (トキソプラズマ)
遺伝子: TGME49_259180
発現宿主: Toxoplasma gondii ME49 (トキソプラズマ)
参照: UniProt: A0A125YSJ9, cystathionine beta-synthase
#2: 化合物
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / ピリドキサ-ル5′-りん酸


分子量: 247.142 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C8H10NO6P / タイプ: SUBJECT OF INVESTIGATION
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: 2.51 Å3/Da / Density meas: 18 Mg/m3 / 溶媒含有率: 50.95 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.7 / 詳細: 8% PEG 3350 0.1M MES pH=5.7 / PH範囲: 5.5-6.1

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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: Diamond / ビームライン: I03 / 波長: 0.98 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2019年2月10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: 0.98 Å / 相対比: 1
反射解像度: 2.855→420.309 Å / Num. obs: 44707 / % possible obs: 89.7 % / 冗長度: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.038 / Rrim(I) all: 0.121 / Net I/σ(I): 12.4 / Num. measured all: 457518
反射 シェル

Num. unique obs: 2211 / Diffraction-ID: 1 / 冗長度: 9.7 %

解像度 (Å)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.855-3.241.299213740.6630.4361.3711.766.2
9.234-420.3090.044215050.9980.0150.04739.299.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PDB_EXTRACT3.25データ抽出
XDSデータ削減
autoPROC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: 1JBQ

1jbq


解像度: 3.201→46.136 Å / SU ML: 0.33 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 33.75 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.277 2137 4.99 %
Rwork0.253 40697 -
obs0.2544 42834 79.88 %
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 max: 183.82 Å2 / Biso mean: 89.6753 Å2 / Biso min: 48.57 Å2
精密化ステップサイクル: final / 解像度: 3.201→46.136 Å
タンパク質核酸リガンド溶媒全体
原子数21306 0 90 0 21396
Biso mean--100.25 --
残基数----2841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A7110X-RAY DIFFRACTION5.413TORSIONAL
12B7110X-RAY DIFFRACTION5.413TORSIONAL
13C7110X-RAY DIFFRACTION5.413TORSIONAL
14D7110X-RAY DIFFRACTION5.413TORSIONAL
15E7110X-RAY DIFFRACTION5.413TORSIONAL
16F7110X-RAY DIFFRACTION5.413TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.24-3.27490.4331380.393478023
3.2749-3.35680.3243480.337495328
3.3568-3.44750.327460.3261104330
3.4475-3.5490.3343940.3189168151
3.549-3.66350.35351050.322238169
3.6635-3.79430.31982000.3032340798
3.7943-3.94620.32712000.29213296100
3.9462-4.12570.33761640.27813395100
4.1257-4.3430.28621900.25863401100
4.343-4.61490.28591710.24853435100
4.6149-4.97080.27612080.2473327100
4.9708-5.47030.29951730.25183387100
5.4703-6.26020.3671300.27253480100
6.2602-7.88090.24351770.24163383100
7.8809-46.130.1921930.1897334899
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)
12.46861.06240.85652.02191.07335.379-0.1954-0.4940.24840.1801-0.04930.16010.02260.06210.19480.21390.0446-0.17480.3701-0.13950.480837.8645-1.612913.4554
22.83150.87691.72130.9090.43023.90860.3815-1.28010.25030.3212-0.56170.39821.1538-0.99060.07350.42210.0369-0.03960.7527-0.18060.507324.982-10.57116.2618
30.52110.51390.68370.7662-0.19893.99520.45830.2758-0.39560.65920.03750.06542.73450.1649-0.3221.2513-0.0359-0.12050.51280.05211.089927.5467-36.1056-2.3847
45.67952.68852.71331.87963.21767.51530.6910.4575-1.3399-0.76640.0796-0.57861.20110.392-0.81191.44510.2229-0.00430.90990.07721.247331.5684-39.0156-29.5909
51.7552-1.05592.30990.8597-1.11573.38410.36970.0946-0.27170.1769-0.2328-0.42380.44090.94460.41971.83260.2927-0.08890.3037-0.01840.742231.1585-37.1545-10.3862
63.16022.3151-3.2952.0209-1.35597.45890.0004-0.9472-1.2069-0.1652-0.1174-0.20371.42150.89820.14951.81570.1098-0.27730.757-0.04571.02623.599-43.6628-9.4896
73.33930.5082.40032.05260.9633.615-0.2255-0.1430.2254-0.4536-0.20820.19080.0666-0.16570.1920.3579-0.0391-0.21370.2198-0.11230.352623.6454-10.7979-9.5816
83.94112.23930.95112.1659-0.04954.967-0.59250.34290.4681-0.21060.49420.2352-0.07830.13680.00630.5722-0.0739-0.22240.2717-0.03080.417324.6011-8.2321-22.3995
92.52920.78511.56832.4642-0.16923.0204-0.54761.13590.3571-0.77350.2989-0.0394-0.3431.2770.07150.5834-0.1956-0.20380.547-0.00850.460737.9824-2.8896-18.5551
101.91341.28040.83350.91610.3720.65270.3391.1319-1.07970.15350.2096-0.18281.22381.9096-0.22760.80590.45070.00131.349-0.25350.820859.1592-17.66950.1308
111.47621.7592-0.54144.9731.01985.7625-0.07750.2879-0.50671.35460.0231-1.19841.05230.6509-0.00431.37810.5185-0.08861.11010.07330.745259.4333-22.809127.5875
124.3674-2.65760.85342.87750.99881.97280.20820.1367-1.002-0.80230.0750.01090.88951.2728-0.20650.90460.5139-0.03351.2207-0.09670.837462.7791-19.49077.0238
131.9174-0.02461.07582.73111.21442.3799-0.3245-0.04411.0399-0.0208-0.20790.4357-0.5481-0.30290.39970.2416-0.0058-0.20040.28010.02560.78718.2611-36.746254.2453
142.38611.20650.61453.94331.09732.8228-0.0541-0.5770.73540.6311-0.13250.44510.0135-0.33650.1340.35260.1196-0.01610.5421-0.14720.63715.6854-41.339566.279
155.00991.26420.04015.18160.61434.2966-0.0066-0.0425-0.1680.6555-0.2039-0.61690.71180.2270.19680.37840.00660.04140.41160.02420.489117.9923-58.05758.4105
164.19782.106-2.15411.3186-0.10994.3071-0.36510.4793-0.08030.1730.7809-0.49471.8664-0.3773-0.44441.30230.0433-0.30391.4258-0.52361.448138.7908-78.927133.4844
172.6621-2.19141.60751.9113-1.25871.01820.03760.0619-0.60630.08630.3123-0.09880.29790.8804-0.46580.42010.3212-0.20912.4206-0.69951.127936.9358-70.645817.5437
181.45150.63861.83611.14840.27482.61110.04090.8638-0.52990.39080.4213-0.73680.12661.65790.56650.82030.5693-0.42891.7546-0.42271.356834.9186-69.464837.1901
197.1918-2.18471.54710.6779-0.72673.28160.34721.7052-2.9032-0.3946-1.0381-0.0361.14950.8470.54511.09650.4904-0.08421.5953-0.42041.949933.1782-79.431738.3385
201.71050.2741-0.89493.45551.272.61-0.38010.0753-0.9725-0.1412-0.14550.46650.344-0.16020.41030.35590.03630.210.2690.06490.766818.2764-11.325683.7811
213.0764-0.4514-0.56512.40920.51413.23-0.03040.7397-0.6826-0.6752-0.19680.4084-0.0956-0.28250.20550.3213-0.09680.00930.4836-0.19290.624815.696-6.710671.7076
222.74191.54431.45112.42972.63015.4476-0.1976-0.73230.0033-0.73820.1841-0.2734-1.49950.0381-0.02740.55620.02890.15030.70740.02560.643625.230517.185490.36
230.36560.8592-0.1135.0096-3.32723.21720.6178-1.74021.4059-0.42750.26521.22170.13481.4186-0.5420.676-0.02110.03232.0769-0.93641.303538.652419.7251116.8977
241.5712-1.66380.05281.792-0.23460.7351-0.2737-1.14731.4246-0.050.6268-1.0561-0.84591.07660.09570.7768-0.7010.18511.6897-0.55111.220833.764225.6552100.3749
252.46571.12972.06953.61580.04022.9957-0.1622-0.02570.93750.305-0.64190.5573-0.6415-0.16520.69790.3493-0.0279-0.12220.5721-0.0750.80057.6724-43.234538.0933
262.2331.65251.3743.3236-0.14442.2774-0.30831.6027-0.0587-0.3720.53960.03090.73460.9304-0.10340.36070.0541-0.03930.838-0.31810.547916.8108-63.512836.2978
272.08750.27051.20911.41880.31392.2551-0.27411.36540.7592-0.62720.17520.4146-0.0890.65380.05320.1983-0.0958-0.34691.42130.24160.81411.4981-50.720424.6689
280.88790.16680.93873.41922.36284.0714-0.35641.68170.5888-1.05320.0075-0.07-1.01130.77120.68760.1951-0.3139-0.27391.31950.43340.715518.0924-40.479227.2861
293.39714.53761.16927.39531.32810.4363-0.57941.64780.06890.18080.9345-1.8126-0.58710.6532-0.12040.5798-0.1721-0.23071.12340.39291.020735.7505-37.955538.2483
300.1893-0.5939-0.20833.9644-0.94041.1839-0.36350.86871.19060.39490.112-1.5824-0.63581.23610.2030.4165-0.202-0.29391.80870.26411.701455.6101-34.803858.9154
313.2321.3758-0.38040.59680.20546.491-1.3487-0.36980.46070.58080.3394-0.83640.15570.96070.86110.94530.5413-0.3640.9443-0.17681.233548.2757-40.00773.7725
327.30433.0747-1.79283.3801-0.71340.4417-0.25182.290.0254-0.75191.35230.36070.2083-1.7294-0.69480.3242-0.08290.031.10230.36190.896745.713-39.646754.9144
332.69030.12440.72522.13761.23743.6409-0.4403-0.49280.5642-0.93960.25980.1872-0.35070.63610.4230.461-0.1286-0.18391.50490.43341.211450.4809-31.094153.9249
343.1605-0.0172-1.7362.80220.79614.1934-0.2725-1.0677-0.0166-0.3151-0.12690.4329-0.80280.3315-0.07680.0183-0.00330.12280.6968-0.06910.523512.45558.17101.99
352.2594-1.1818-0.50931.33240.79952.4449-0.515-1.7071-0.49180.77040.30460.62260.88030.58970.2379-0.09560.19280.41541.47840.42550.770814.5153-5.2961112.9175
364.1125-3.03140.28952.3165-0.10110.1899-0.1925-1.6439-0.15530.17470.2135-1.19170.6170.5355-0.08140.52310.25670.06421.1360.51841.05935.6301-10.23199.8474
372.49281.7324-1.94932.1449-0.45012.3623-0.7427-0.5055-0.5148-0.24510.3934-0.26740.17930.65480.34240.67850.04590.16770.93390.10391.03954.2397-11.548672.386
382.0083-0.288-0.97221.45220.51156.5878-1.24320.5975-0.8227-1.54620.5355-0.4495-0.97870.72240.7051.0034-0.47110.24940.719-0.10730.939943.086-6.158364.6448
392.9541-1.8411-0.76441.74161.19071.0479-0.0762-0.4959-0.16490.18120.49260.22090.1955-0.109-0.31030.21760.14510.08981.4050.45210.947848.8647-13.459185.6185
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 6 through 254 )F6 - 254
2X-RAY DIFFRACTION2chain 'F' and (resid 255 through 319 )F255 - 319
3X-RAY DIFFRACTION3chain 'F' and (resid 320 through 375 )F320 - 375
4X-RAY DIFFRACTION4chain 'F' and (resid 376 through 428 )F376 - 428
5X-RAY DIFFRACTION5chain 'F' and (resid 429 through 461 )F429 - 461
6X-RAY DIFFRACTION6chain 'F' and (resid 462 through 513 )F462 - 513
7X-RAY DIFFRACTION7chain 'A' and (resid 6 through 139 )A6 - 139
8X-RAY DIFFRACTION8chain 'A' and (resid 140 through 253 )A140 - 253
9X-RAY DIFFRACTION9chain 'A' and (resid 254 through 319 )A254 - 319
10X-RAY DIFFRACTION10chain 'A' and (resid 320 through 375 )A320 - 375
11X-RAY DIFFRACTION11chain 'A' and (resid 376 through 431 )A376 - 431
12X-RAY DIFFRACTION12chain 'A' and (resid 432 through 513 )A432 - 513
13X-RAY DIFFRACTION13chain 'B' and (resid 6 through 139 )B6 - 139
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 285 )B140 - 285
15X-RAY DIFFRACTION15chain 'B' and (resid 286 through 349 )B286 - 349
16X-RAY DIFFRACTION16chain 'B' and (resid 350 through 375 )B350 - 375
17X-RAY DIFFRACTION17chain 'B' and (resid 376 through 428 )B376 - 428
18X-RAY DIFFRACTION18chain 'B' and (resid 429 through 461 )B429 - 461
19X-RAY DIFFRACTION19chain 'B' and (resid 462 through 513 )B462 - 513
20X-RAY DIFFRACTION20chain 'C' and (resid 6 through 139 )C6 - 139
21X-RAY DIFFRACTION21chain 'C' and (resid 140 through 285 )C140 - 285
22X-RAY DIFFRACTION22chain 'C' and (resid 286 through 386 )C286 - 386
23X-RAY DIFFRACTION23chain 'C' and (resid 387 through 428 )C387 - 428
24X-RAY DIFFRACTION24chain 'C' and (resid 429 through 513 )C429 - 513
25X-RAY DIFFRACTION25chain 'D' and (resid 6 through 69 )D6 - 69
26X-RAY DIFFRACTION26chain 'D' and (resid 70 through 139 )D70 - 139
27X-RAY DIFFRACTION27chain 'D' and (resid 140 through 245 )D140 - 245
28X-RAY DIFFRACTION28chain 'D' and (resid 246 through 319 )D246 - 319
29X-RAY DIFFRACTION29chain 'D' and (resid 320 through 349 )D320 - 349
30X-RAY DIFFRACTION30chain 'D' and (resid 350 through 375 )D350 - 375
31X-RAY DIFFRACTION31chain 'D' and (resid 376 through 428 )D376 - 428
32X-RAY DIFFRACTION32chain 'D' and (resid 429 through 461 )D429 - 461
33X-RAY DIFFRACTION33chain 'D' and (resid 462 through 513 )D462 - 513
34X-RAY DIFFRACTION34chain 'E' and (resid 6 through 163 )E6 - 163
35X-RAY DIFFRACTION35chain 'E' and (resid 164 through 319 )E164 - 319
36X-RAY DIFFRACTION36chain 'E' and (resid 320 through 349 )E320 - 349
37X-RAY DIFFRACTION37chain 'E' and (resid 350 through 404 )E350 - 404
38X-RAY DIFFRACTION38chain 'E' and (resid 405 through 437 )E405 - 437
39X-RAY DIFFRACTION39chain 'E' and (resid 438 through 513 )E438 - 513

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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