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- PDB-5hsa: Alcohol Oxidase AOX1 from Pichia Pastoris -

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基本情報

登録情報
データベース: PDB / ID: 5hsa
タイトルAlcohol Oxidase AOX1 from Pichia Pastoris
要素Alcohol oxidase 1
キーワードOXIDOREDUCTASE / alcohol oxidase / GMC oxidoreductase modified FAD (a-FAD)
機能・相同性
機能・相同性情報


methane catabolic process / alcohol oxidase activity / alcohol oxidase / methanol metabolic process / peroxisomal matrix / flavin adenine dinucleotide binding
類似検索 - 分子機能
GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
ARABINO-FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / PHOSPHATE ION / Alcohol oxidase 1
類似検索 - 構成要素
生物種Komagataella pastoris CBS 7435 (菌類)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Neumann, P. / Ficner, R. / Feussner, I. / Koch, C.
資金援助 ドイツ, 2件
組織認可番号国
German Research FoundationIRTG 1422 ドイツ
Goettingen UniversityOpen Access Publication Funds ドイツ
引用ジャーナル: Plos One / 年: 2016
タイトル: Crystal Structure of Alcohol Oxidase from Pichia pastoris.
著者: Koch, C. / Neumann, P. / Valerius, O. / Feussner, I. / Ficner, R.
履歴
登録2016年1月25日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年3月9日Provider: repository / タイプ: Initial release
改定 1.12024年1月10日Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Alcohol oxidase 1
B: Alcohol oxidase 1
C: Alcohol oxidase 1
D: Alcohol oxidase 1
E: Alcohol oxidase 1
F: Alcohol oxidase 1
G: Alcohol oxidase 1
H: Alcohol oxidase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)602,84547
ポリマ－591,9388
非ポリマー10,90739
水37,5252083
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)117.100, 165.190, 164.310
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A and (resseq 2:328 or resseq 330:605 or resseq...
21chain B and (resseq 2:328 or resseq 330:605 or resseq...
31chain C and (resseq 2:328 or resseq 330:605 or resseq...
41chain D and (resseq 2:328 or resseq 330:605 or resseq...
51chain E and (resseq 2:328 or resseq 330:605 or resseq...
61chain F and (resseq 2:328 or resseq 330:605 or resseq...
71chain G and (resseq 2:328 or resseq 330:605 or resseq...
81chain H and (resseq 2:328 or resseq 330:605 or resseq...
12chain A and (resseq 1:663 ) and not (name CA...
22chain B and (resseq 1:663 ) and not (name CA...
32chain C and (resseq 1:663 ) and not (name CA...
42chain D and (resseq 1:663 ) and not (name CA...
52chain E and (resseq 1:663 ) and not (name CA...
62chain F and (resseq 1:663 ) and not (name CA...
72chain G and (resseq 1:663 ) and not (name CA...
82chain H and (resseq 1:663 ) and not (name CA...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 2:328 or resseq 330:605 or resseq...A2 - 328
121chain A and (resseq 2:328 or resseq 330:605 or resseq...A330 - 605
131chain A and (resseq 2:328 or resseq 330:605 or resseq...A607 - 662
211chain B and (resseq 2:328 or resseq 330:605 or resseq...B2 - 328
221chain B and (resseq 2:328 or resseq 330:605 or resseq...B330 - 605
231chain B and (resseq 2:328 or resseq 330:605 or resseq...B607 - 662
311chain C and (resseq 2:328 or resseq 330:605 or resseq...C2 - 328
321chain C and (resseq 2:328 or resseq 330:605 or resseq...C330 - 605
331chain C and (resseq 2:328 or resseq 330:605 or resseq...C607 - 662
411chain D and (resseq 2:328 or resseq 330:605 or resseq...D2 - 328
421chain D and (resseq 2:328 or resseq 330:605 or resseq...D330 - 605
431chain D and (resseq 2:328 or resseq 330:605 or resseq...D607 - 662
511chain E and (resseq 2:328 or resseq 330:605 or resseq...E2 - 328
521chain E and (resseq 2:328 or resseq 330:605 or resseq...E330 - 605
531chain E and (resseq 2:328 or resseq 330:605 or resseq...E607 - 662
611chain F and (resseq 2:328 or resseq 330:605 or resseq...F2 - 328
621chain F and (resseq 2:328 or resseq 330:605 or resseq...F330 - 605
631chain F and (resseq 2:328 or resseq 330:605 or resseq...F607 - 662
711chain G and (resseq 2:328 or resseq 330:605 or resseq...G2 - 328
721chain G and (resseq 2:328 or resseq 330:605 or resseq...G330 - 605
731chain G and (resseq 2:328 or resseq 330:605 or resseq...G607 - 662
811chain H and (resseq 2:328 or resseq 330:605 or resseq...H2 - 328
821chain H and (resseq 2:328 or resseq 330:605 or resseq...H330 - 605
831chain H and (resseq 2:328 or resseq 330:605 or resseq...H607 - 662
112chain A and (resseq 1:663 ) and not (name CA...A1 - 663
212chain B and (resseq 1:663 ) and not (name CA...B1 - 663
312chain C and (resseq 1:663 ) and not (name CA...C1 - 663
412chain D and (resseq 1:663 ) and not (name CA...D1 - 663
512chain E and (resseq 1:663 ) and not (name CA...E1 - 663
612chain F and (resseq 1:663 ) and not (name CA...F1 - 663
712chain G and (resseq 1:663 ) and not (name CA...G1 - 663
812chain H and (resseq 1:663 ) and not (name CA...H1 - 663

NCSアンサンブル:
ID
1
2

NCS oper:
IDCodeMatrixベクター
1given(0.989307, -0.100252, 0.105932), (0.10652, 0.000516, -0.99431), (0.099627, 0.994962, 0.011189)-25.767401, 153.914993, 243.416
2given(0.989475, 0.104045, 0.10057), (-0.101057, -0.000594, 0.99488), (0.103572, -0.994572, 0.009927)-15.4348, -244.904007, 153.302002
3given(0.978506, 0.00439, 0.206171), (0.004683, -0.999989, -0.000936), (0.206165, 0.001881, -0.978516)-41.109402, -90.633499, 396.71701
4given(-0.997777, 0.061253, -0.026255), (0.063253, 0.746383, -0.662504), (-0.020984, -0.662692, -0.748598)69.325104, 121.485001, 326.651001
5given(-0.995889, -0.08266, -0.037055), (-0.082798, 0.664688, 0.742519), (-0.036746, 0.742535, -0.668799)64.935898, -163.873993, 374.665985
6given(-0.982685, 0.075923, -0.169014), (0.076192, -0.665912, -0.74213), (-0.168893, -0.742157, 0.648597)98.605301, 73.276001, 43.1026
7given(-0.980639, -0.069663, -0.183014), (-0.070423, -0.746602, 0.661533), (-0.182723, 0.661613, 0.727241)94.807503, -211.740997, 91.1716
8given(0.989304, -0.100332, 0.105884), (0.106481, 0.000593, -0.994315), (0.099698, 0.994954, 0.01127)-25.7631, 153.919998, 243.399002
9given(0.989456, 0.104065, 0.100736), (-0.101211, -0.000721, 0.994865), (0.103603, -0.99457, 0.009819)-15.4717, -244.901993, 153.324997
10given(0.978494, 0.004316, 0.206228), (0.004631, -0.999989, -0.001043), (0.206221, 0.001976, -0.978503)-41.128101, -90.6091, 396.718994
11given(-0.997768, 0.061377, -0.026292), (0.063368, 0.746292, -0.662595), (-0.021047, -0.662783, -0.748516)69.3349, 121.498001, 326.631989
12given(-0.99588, -0.082737, -0.03711), (-0.082893, 0.66474, 0.742462), (-0.036761, 0.742479, -0.668859)64.944801, -163.852997, 374.678009
13given(-0.982672, 0.075873, -0.169114), (0.076287, -0.665967, -0.742071), (-0.168927, -0.742113, 0.648638)98.621201, 73.257797, 43.097301
14given(-0.980626, -0.069767, -0.183045), (-0.070412, -0.746437, 0.66172), (-0.182798, 0.661788, 0.727063)94.803802, -211.766006, 91.226303

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Alcohol oxidase 1 / AOX 1 / Methanol oxidase 1 / MOX 1


分子量: 73992.195 Da / 分子数: 8 / 断片: Residues 3-610 / 由来タイプ: 組換発現
由来: (組換発現) Komagataella pastoris CBS 7435 (菌類)
遺伝子: AOX1, PP7435_Chr4-0130 / 発現宿主: Komagataella pastoris CBS 7435 (菌類) / 参照: UniProt: F2QY27, alcohol oxidase

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非ポリマー , 8種, 2122分子

#2: 化合物
ChemComp-FAS / ARABINO-FLAVIN-ADENINE DINUCLEOTIDE


分子量: 785.550 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C27H33N9O15P2
#3: 化合物
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / ヘキサエチレングリコ-ル


分子量: 282.331 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C12H26O7 / コメント: 沈殿剤*YM
#4: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C6H14O4
#5: 化合物 ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 2 / 由来タイプ: 合成 / 式: PO4
#6: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Ca
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2083 / 由来タイプ: 天然 / 式: H2O

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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: 2.67 Å3/Da / 溶媒含有率: 53.96 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: protein (15 mg/ml in 20 mM Na-HEPES, pH 7.5) was mixed with equal amount of reservoir solution containing 100 mM HEPES, pH 7.5, 200 mM CaCl2 and 33.3 % (w/v) PEG 400.
PH範囲: 7-8

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: BESSY / ビームライン: 14.1 / 波長: 0.91842 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年11月22日 / 詳細: mirrors
放射モノクロメーター: GRAPHITE, / 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: 0.91842 Å / 相対比: 1
反射解像度: 2.35→50 Å / Num. all: 254643 / Num. obs: 254643 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 3.2 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.128 / Rsym value: 0.128 / Χ2: 1.013 / Net I/av σ(I): 9.77 / Net I/σ(I): 9.77 / Num. measured all: 815776
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)最高解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.452.750.7821.678073530203293140.5110.96597.1
2.45-2.550.6092.388309525624255130.6730.7399.6
2.55-2.810.3993.5816393050448502180.8310.47899.5
2.81-3.530.1428.5624352074914743620.9790.1799.3
3.53-3.890.06616.276219519330191050.9930.07998.8
3.89-4.250.05418.914250913316131160.9950.06598.5
4.25-4.610.0482130271951293480.9960.05898.3
4.61-140.04123.6910617233287325530.9970.04997.8
14-170.02432.7216975675450.9990.02896.1
17-500.02632.0616526955690.9990.03281.9
5034

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
最高解像度最低解像度
Rotation2.41 Å24.93 Å
Translation2.41 Å24.93 Å

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解析

ソフトウェア
名称バージョン分類
XSCALEVERSION Oct 15, 2015 BUILT=20151231データスケーリング
PHASER2.5.0位相決定
PHENIX1.9.162精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3q9t

3q9t


解像度: 2.35→40.877 Å / SU ML: 0.28 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 21.96 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2049 12276 4.82 %Thin shells
Rwork0.1774 242261 --
obs0.1787 254537 98.72 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 119.15 Å2 / Biso mean: 44.3283 Å2 / Biso min: 12.49 Å2
精密化ステップサイクル: final / 解像度: 2.35→40.877 Å
タンパク質核酸リガンド溶媒全体
原子数41592 0 716 2084 44392
Biso mean--47.28 38.78 -
残基数----5295
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00643518
X-RAY DIFFRACTIONf_angle_d0.92258962
X-RAY DIFFRACTIONf_chiral_restr0.0386124
X-RAY DIFFRACTIONf_plane_restr0.0047692
X-RAY DIFFRACTIONf_dihedral_angle_d15.27816120
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A3236X-RAY DIFFRACTIONPOSITIONAL0.018
12B3236X-RAY DIFFRACTIONPOSITIONAL0.018
13C3236X-RAY DIFFRACTIONPOSITIONAL0.018
14D3236X-RAY DIFFRACTIONPOSITIONAL0.017
15E3236X-RAY DIFFRACTIONPOSITIONAL0.02
16F3236X-RAY DIFFRACTIONPOSITIONAL0.019
17G3236X-RAY DIFFRACTIONPOSITIONAL0.018
18H3236X-RAY DIFFRACTIONPOSITIONAL0.018
21A1484X-RAY DIFFRACTIONPOSITIONAL0.049
22B1484X-RAY DIFFRACTIONPOSITIONAL0.049
23C1484X-RAY DIFFRACTIONPOSITIONAL0.026
24D1484X-RAY DIFFRACTIONPOSITIONAL0.019
25E1484X-RAY DIFFRACTIONPOSITIONAL0.026
26F1484X-RAY DIFFRACTIONPOSITIONAL0.03
27G1484X-RAY DIFFRACTIONPOSITIONAL0.021
28H1484X-RAY DIFFRACTIONPOSITIONAL0.021
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.32944130.3077841825497
2.3767-2.40470.33334170.29837928834597
2.4047-2.4340.32734170.29047911832897
2.434-2.46480.29224130.27157943835698
2.4648-2.49720.30694160.261581598575100
2.4972-2.53140.28914170.259981638580100
2.5314-2.56760.27624110.252880618472100
2.5676-2.60590.28054150.24148137855299
2.6059-2.64660.27714130.240781128525100
2.6466-2.690.29524120.241880828494100
2.69-2.73640.28044160.23868177859399
2.7364-2.78610.27144110.23488114852599
2.7861-2.83970.26254120.229381058517100
2.8397-2.89760.25644130.21368124853799
2.8976-2.96060.24464100.2238094850499
2.9606-3.02950.25284120.20768116852899
3.0295-3.10520.22944120.20548142855499
3.1052-3.18910.24024090.20468099850899
3.1891-3.2830.2384090.19578104851399
3.283-3.38890.21094090.18898119852899
3.3889-3.50990.19894080.17298094850299
3.5099-3.65040.18344070.16328098850599
3.6504-3.81640.16724050.14788092849799
3.8164-4.01740.15494050.13588101850699
4.0174-4.26890.14784020.12818049845199
4.2689-4.59810.13984040.1168076848098
4.5981-5.06010.13164020.11218086848898
5.0601-5.79050.16184010.13258072847398
5.7905-7.28870.15654000.13448072847298
7.2887-40.88280.15163850.13527990837595
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)
10.0336-0.03150.0020.0531-0.00420.0775-0.020.29290.2026-0.1338-0.02490.1161-0.0215-0.2625-0.05130.1552-0.0085-0.08330.51060.11980.2684-2.9767-21.0588173.4304
20.00050.00070.00020.00060.00010.0007-0.00260.00190.0065-0.0067-0.00670.0008-0.00090.0003-00.32850.0031-0.01490.35740.13680.431222.0303-4.3987173.0153
30.0006-0.00020.00010.0003-0.00010.0004-0.00420.00370.0029-0.0004-0.0050.00530.00170.000200.4274-0.0298-0.03030.48080.02060.382415.8162-34.6425155.682
40.00090.0001-0.00010.0006-0.00020.0002-0.00420.0045-0.0040.00010.0071-0.0015-0.0029-0.003200.314-0.0812-0.03490.4106-0.01660.4059-10.4495-33.5422200.6968
50.0650.0057-0.04280.0180.03330.08370.04610.05550.2281-0.0108-0.02510.0306-0.0407-0.08710.00760.1960.015-0.00920.18880.04690.376315.2825-9.6411194.7657
60.0017-0.00130.00180.00130.00040.0027-0.01360.01620.0317-0.02290.0153-0.00410.0182-0.02110.0010.20770.0293-0.02030.33760.17760.261512.4814-11.139165.1435
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79X-RAY DIFFRACTION40chain 'F' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)F156 - 191
80X-RAY DIFFRACTION40chain 'F' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)F307 - 425
81X-RAY DIFFRACTION40chain 'F' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)F449 - 520
82X-RAY DIFFRACTION40chain 'F' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)F545 - 567
83X-RAY DIFFRACTION41chain 'F' and (resid 426:448 )F426 - 448
84X-RAY DIFFRACTION42chain 'F' and (resid 521:544 )F521 - 544
85X-RAY DIFFRACTION43chain 'G' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )G2 - 71
86X-RAY DIFFRACTION43chain 'G' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )G83 - 155
87X-RAY DIFFRACTION43chain 'G' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )G192 - 245
88X-RAY DIFFRACTION43chain 'G' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )G255 - 306
89X-RAY DIFFRACTION43chain 'G' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )G568 - 650
90X-RAY DIFFRACTION44chain 'G' and (resid 72:81 )G72 - 81
91X-RAY DIFFRACTION45chain 'G' and (resid 246:254 )G246 - 254
92X-RAY DIFFRACTION46chain 'G' and (resid 651:663 )G651 - 663
93X-RAY DIFFRACTION47chain 'G' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)G156 - 191
94X-RAY DIFFRACTION47chain 'G' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)G307 - 425
95X-RAY DIFFRACTION47chain 'G' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)G449 - 520
96X-RAY DIFFRACTION47chain 'G' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)G545 - 567
97X-RAY DIFFRACTION48chain 'G' and (resid 426:448 )G426 - 448
98X-RAY DIFFRACTION49chain 'G' and (resid 521:544 )G521 - 544
99X-RAY DIFFRACTION50chain 'H' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )H2 - 71
100X-RAY DIFFRACTION50chain 'H' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )H83 - 155
101X-RAY DIFFRACTION50chain 'H' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )H192 - 245
102X-RAY DIFFRACTION50chain 'H' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )H255 - 306
103X-RAY DIFFRACTION50chain 'H' and (resid 2:71 or resid 83:155 or resid 192:245 or resid 255:306 or resid 568:650 )H568 - 650
104X-RAY DIFFRACTION51chain 'H' and (resid 72:81 )H72 - 81
105X-RAY DIFFRACTION52chain 'H' and (resid 246:254 )H246 - 254
106X-RAY DIFFRACTION53chain 'H' and (resid 651:663 )H651 - 663
107X-RAY DIFFRACTION54chain 'H' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)H156 - 191
108X-RAY DIFFRACTION54chain 'H' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)H307 - 425
109X-RAY DIFFRACTION54chain 'H' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)H449 - 520
110X-RAY DIFFRACTION54chain 'H' and (resid 156:191 or resid 307:425 or resid 449:520 or resid 545:567)H545 - 567
111X-RAY DIFFRACTION55chain 'H' and (resid 426:448 )H426 - 448
112X-RAY DIFFRACTION56chain 'H' and (resid 521:544 )H521 - 544
113X-RAY DIFFRACTION57chain 'A' and resid 718:718A718
114X-RAY DIFFRACTION58chain 'B' and resid 718:718B718
115X-RAY DIFFRACTION59chain 'C' and resid 718:718C718
116X-RAY DIFFRACTION60chain 'D' and resid 718:718D718
117X-RAY DIFFRACTION61chain 'E' and resid 718:718E718
118X-RAY DIFFRACTION62chain 'F' and resid 718:718F718
119X-RAY DIFFRACTION63chain 'G' and resid 718:718G718
120X-RAY DIFFRACTION64chain 'H' and resid 718:718H718

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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