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- PDB-6rke: Molybdenum storage protein - P212121, ADP, molybdate -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6rke
タイトルMolybdenum storage protein - P212121, ADP, molybdate
要素(Molybdenum storage protein subunit ...) x 2
キーワードMETAL BINDING PROTEIN / molybdenum storage protein / polyoxomolybdate clusters / ATP / amino acid kinase
機能・相同性
機能・相同性情報


nutrient reservoir activity / molybdenum ion binding / cytoplasm
類似検索 - 分子機能
Molybdenum storage protein subunit alpha/beta / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Chem-8M0 / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / MO(10)-O(35) Cluster / MO(8)-O(26) Cluster / Chem-M10 / MOLYBDATE ION / PHOSPHATE ION / Molybdenum storage protein subunit beta / Molybdenum storage protein subunit alpha
類似検索 - 構成要素
生物種Azotobacter vinelandii (窒素固定)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.7 Å
データ登録者Ermler, U. / Bruenle, S.
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2019
タイトル: Molybdate pumping into the molybdenum storage protein via an ATP-powered piercing mechanism.
著者: Steffen Brünle / Martin L Eisinger / Juliane Poppe / Deryck J Mills / Julian D Langer / Janet Vonck / Ulrich Ermler /
要旨: The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest ...The molybdenum storage protein (MoSto) deposits large amounts of molybdenum as polyoxomolybdate clusters in a heterohexameric (αβ) cage-like protein complex under ATP consumption. Here, we suggest a unique mechanism for the ATP-powered molybdate pumping process based on X-ray crystallography, cryoelectron microscopy, hydrogen-deuterium exchange mass spectrometry, and mutational studies of MoSto from . First, we show that molybdate, ATP, and Mg consecutively bind into the open ATP-binding groove of the β-subunit, which thereafter becomes tightly locked by fixing the previously disordered N-terminal arm of the α-subunit over the β-ATP. Next, we propose a nucleophilic attack of molybdate onto the γ-phosphate of β-ATP, analogous to the similar reaction of the structurally related UMP kinase. The formed instable phosphoric-molybdic anhydride becomes immediately hydrolyzed and, according to the current data, the released and accelerated molybdate is pressed through the cage wall, presumably by turning aside the Metβ149 side chain. A structural comparison between MoSto and UMP kinase provides valuable insight into how an enzyme is converted into a molecular machine during evolution. The postulated direct conversion of chemical energy into kinetic energy via an activating molybdate kinase and an exothermic pyrophosphatase reaction to overcome a proteinous barrier represents a novelty in ATP-fueled biochemistry, because normally, ATP hydrolysis initiates large-scale conformational changes to drive a distant process.
履歴
登録2019年4月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02019年12月18日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Advisory / Data collection ...Advisory / 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
B: Molybdenum storage protein subunit beta
A: Molybdenum storage protein subunit alpha
D: Molybdenum storage protein subunit beta
C: Molybdenum storage protein subunit alpha
F: Molybdenum storage protein subunit beta
E: Molybdenum storage protein subunit alpha
H: Molybdenum storage protein subunit beta
G: Molybdenum storage protein subunit alpha
J: Molybdenum storage protein subunit beta
I: Molybdenum storage protein subunit alpha
L: Molybdenum storage protein subunit beta
K: Molybdenum storage protein subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)373,43266
ポリマ－344,95912
非ポリマー28,47354
水23,2571291
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: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area88000 Å2
ΔGint-672 kcal/mol
Surface area90000 Å2
手法PISA
単位格子
Length a, b, c (Å)128.060, 148.860, 183.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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Molybdenum storage protein subunit ... , 2種, 12分子 BDFHJLACEGIK

#1: タンパク質
Molybdenum storage protein subunit beta / MoSto subunit beta


分子量: 28247.582 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (窒素固定)
株: DJ / ATCC BAA-1303 / 遺伝子: mosB, Avin_43210 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P84253
#2: タンパク質
Molybdenum storage protein subunit alpha / Mo storage protein subunit alpha / MoSto subunit alpha


分子量: 29245.582 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (窒素固定)
株: DJ / ATCC BAA-1303 / 遺伝子: mosA, Avin_43200 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P84308

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非ポリマー , 10種, 1345分子

#3: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
#4: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Mg
#5: 化合物
ChemComp-8M0 / bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI) / Octamolybdate [Mo(VI)8O28]8-


分子量: 1215.503 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Mo8O28
#6: 化合物
ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


分子量: 159.938 Da / 分子数: 6 / 由来タイプ: 合成 / 式: MoO4 / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 6 / 由来タイプ: 合成 / 式: PO4
#8: 化合物 ChemComp-LJB / MO(8)-O(26) Cluster


分子量: 1198.623 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H15Mo8O26
#9: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / コメント: ATP, エネルギー貯蔵分子*YM
#10: 化合物 ChemComp-M10 / (mu3-oxo)-tris(mu2-oxo)-nonakisoxo-trimolybdenum (VI) / Trimolybdate [Mo(VI)3O13]8-


分子量: 495.812 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mo3O13
#11: 化合物 ChemComp-LHW / MO(10)-O(35) Cluster


分子量: 1535.506 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H16Mo10O35
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1291 / 由来タイプ: 天然 / 式: 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: 2.54 Å3/Da / 溶媒含有率: 51.62 %
結晶化温度: 293 K / 手法: 蒸気拡散法
詳細: 2 mM landthanide, 0.1 M buffer system 4, ph 6.5, 30% precipitant mix 7

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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: SLS / ビームライン: X10SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年11月14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: 1.7→50 Å / Num. obs: 378712 / % possible obs: 99.2 % / 冗長度: 5.1 % / Net I/σ(I): 13.2
反射 シェル解像度: 1.7→1.8 Å / Num. unique obs: 59518

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.14_3260: ???)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: 4ndo

4ndo


解像度: 1.7→49.492 Å / SU ML: 0.21 / 交差検証法: FREE R-VALUE / σ(F): 0.57 / 位相誤差: 21.98
Rfactor反射数%反射
Rfree0.2137 36605 5.06 %
Rwork0.1937 --
obs0.1947 723359 97.19 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 1.7→49.492 Å
タンパク質核酸リガンド溶媒全体
原子数24089 0 1024 1291 26404
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00625994
X-RAY DIFFRACTIONf_angle_d2.5236577
X-RAY DIFFRACTIONf_dihedral_angle_d8.81420910
X-RAY DIFFRACTIONf_chiral_restr0.0464044
X-RAY DIFFRACTIONf_plane_restr0.0054466
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.337113090.321622968X-RAY DIFFRACTION98
1.7193-1.73950.32313210.299623355X-RAY DIFFRACTION99
1.7395-1.76070.29112250.282923405X-RAY DIFFRACTION99
1.7607-1.7830.300712050.265923337X-RAY DIFFRACTION99
1.783-1.80650.28511960.257523432X-RAY DIFFRACTION99
1.8065-1.83120.275512270.248323390X-RAY DIFFRACTION99
1.8312-1.85740.266212550.2423161X-RAY DIFFRACTION99
1.8574-1.88510.283812180.249523167X-RAY DIFFRACTION98
1.8851-1.91460.273811840.252523036X-RAY DIFFRACTION98
1.9146-1.9460.267911840.242123079X-RAY DIFFRACTION97
1.946-1.97950.256712190.228623306X-RAY DIFFRACTION99
1.9795-2.01550.256613090.224523227X-RAY DIFFRACTION99
2.0155-2.05430.242512910.212623205X-RAY DIFFRACTION99
2.0543-2.09620.235611680.209923318X-RAY DIFFRACTION99
2.0962-2.14180.230511880.200723282X-RAY DIFFRACTION99
2.1418-2.19160.223112710.19623265X-RAY DIFFRACTION99
2.1916-2.24640.233612510.203823095X-RAY DIFFRACTION98
2.2464-2.30720.245311950.199623185X-RAY DIFFRACTION98
2.3072-2.37510.219712110.18723020X-RAY DIFFRACTION97
2.3751-2.45170.196112390.180522555X-RAY DIFFRACTION96
2.4517-2.53940.219611960.185722689X-RAY DIFFRACTION96
2.5394-2.6410.195112990.180522792X-RAY DIFFRACTION97
2.641-2.76120.213412080.186822730X-RAY DIFFRACTION97
2.7612-2.90680.210412630.188322447X-RAY DIFFRACTION95
2.9068-3.08890.220212170.188422142X-RAY DIFFRACTION94
3.0889-3.32730.216912670.195521892X-RAY DIFFRACTION93
3.3273-3.66210.190810580.182421766X-RAY DIFFRACTION92
3.6621-4.19170.172511540.159722151X-RAY DIFFRACTION94
4.1917-5.28020.142811410.139521922X-RAY DIFFRACTION93
5.2802-49.51260.184411360.186422435X-RAY DIFFRACTION95
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)
12.6046-0.5395-4.01679.5241-1.47769.8607-0.2012-0.3268-0.21320.40020.1252-0.7160.26490.7863-0.0110.1367-0.025-0.08410.2515-0.00960.217775.7846-24.8874-35.9963
21.1627-1.04771.27761.6532-1.6522.3860.03930.20680.0284-0.1871-0.0871-0.16430.10620.240.05550.1713-0.04080.0380.14-0.01860.190465.3611-12.7189-72.0745
33.3731-1.0574-2.74950.63150.74212.5331-0.0467-0.0477-0.0624-0.0529-0.0096-0.05420.00770.06530.06560.1613-0.0236-0.00020.12910.00460.170952.0023-14.2183-66.6575
49.8007-8.45759.03522.034-7.13798.5073-0.1267-0.6426-0.1270.592-0.2497-0.29830.34280.09650.17370.4147-0.0167-0.05950.26950.01980.351466.2596-25.6262-70.3865
50.76110.1432-0.07761.2014-0.75621.3671-0.01340.063-0.0326-0.0821-0.0107-0.10710.01490.09120.02820.1227-0.01860.00180.1213-0.00270.152461.0825-11.1275-61.0447
68.13711.42544.33220.45291.53575.3579-0.22960.16460.5403-0.06050.0513-0.0909-0.45910.01340.19250.2253-0.03260.01570.1146-0.00820.233465.5717.395-59.1762
70.8938-0.20560.32351.3485-0.27180.6931-0.01180.05540.1484-0.0948-0.0021-0.2616-0.0770.17730.0220.191-0.04570.02020.1702-0.00550.232968.4385-3.4202-62.5087
84.0822-1.2493-0.55573.6744.99327.2018-0.02380.13110.2968-0.14470.051-0.0288-0.48030.1976-0.04410.1773-0.0191-0.00960.08960.04520.165247.25320.3059-62.6802
90.93560.2975-0.46250.5736-0.09510.4650.0047-0.00560.0076-0.0131-0.0052-0.0171-0.0023-0.00970.00140.15020.0046-0.01470.15050.00090.14353.0805-29.9642-42.5422
103.4517-1.34512.6441.4349-1.37163.9692-0.0967-0.17950.21240.21690.0044-0.169-0.28340.13740.08880.1457-0.0209-0.0030.1413-0.01940.119357.1004-18.0973-31.4752
115.58961.5241-0.9923.63410.84335.2871-0.0092-0.24590.40390.09540.05450.3161-0.3776-0.2427-0.03660.15110.0094-0.01180.1687-0.01820.093647.7516-21.4412-27.1655
129.0502-3.0502-1.80258.63510.52997.14490.28520.57720.8663-0.2019-0.604-0.0312-1.60090.36120.30110.5061-0.024-0.08150.32960.04520.342438.3484-3.677-82.2062
130.8236-0.6502-0.27621.80980.30650.45950.08160.13030.0192-0.2586-0.0649-0.1223-0.01060.0676-0.01490.23160.00840.01040.2218-0.0120.116450.5757-33.1453-87.832
144.65890.9046-1.36850.5192-0.12010.64580.0439-0.01920.0714-0.04790.0226-0.03470.03680.0237-0.07720.23620.0110.01630.17-0.00640.150246.9631-45.7778-79.0736
151.75622.25211.72535.1322-2.47632.07230.0143-0.30940.52450.30870.11120.259-0.9812-0.1957-0.07860.37830.03730.01190.2586-0.0510.322462.665-33.4171-80.4032
166.3763-0.3953-3.22870.67440.01261.6986-0.06150.1144-0.1276-0.05230.05430.05950.0613-0.04210.00060.2096-0.0013-0.00230.139-0.01150.132740.663-36.4453-81.7413
171.5011-0.6672-0.11622.29940.11181.28510.0470.279-0.0717-0.3825-0.050.03130.0917-0.038-0.00910.26150.00980.0260.2286-0.01990.117144.6311-39.8199-98.5587
185.3363-4.47891.97378.5405-2.2835.39180.01210.32130.0039-0.4744-0.05830.01380.1531-0.07230.04780.2862-0.0646-0.00310.2076-0.03530.210935.545-53.3277-87.1746
190.71640.2502-0.37630.3959-0.29870.9762-0.02120.0234-0.0827-0.05760.0045-0.01780.065-0.03430.02360.14610.0058-0.00230.137-0.00350.157633.9715-23.4861-66.0079
201.6329-0.6487-0.12653.80710.59192.1735-0.01330.19950.0598-0.33480.01330.2573-0.0851-0.22710.00590.11380.0083-0.02590.17480.01270.125620.0108-20.794-74.3548
212.02995.7649-5.48846.0135-3.27276.211-0.31181.4934-1.5887-1.0648-0.1442-0.58260.4401-0.49090.41220.60280.0171-0.03480.4568-0.13020.52251.1173-68.3852-80.395
221.24980.59690.46840.57690.43830.80990.03650.1619-0.1643-0.05890.0373-0.1880.11050.1582-0.08080.20570.06760.02830.18750.00270.249871.0699-49.9005-64.5415
231.90010.721-1.73270.9755-0.9482.558-0.02770.0921-0.098-0.06150.0077-0.13730.04820.01550.02950.12930.0213-0.00290.1271-0.00620.16867.3055-41.0907-51.9312
246.1935-3.24980.12775.43954.2624.98190.36291.1552-0.4471-0.3425-0.22790.61180.1438-0.49780.28930.33130.0204-0.0440.36210.00510.314869.6443-37.5789-71.4682
251.64120.8472-1.53890.212-0.62931.96650.0240.0680.02310.0272-0.0080.01630.0059-0.0348-0.02360.19560.0376-0.00940.16750.0070.212463.2847-51.3662-55.4765
260.99960.10880.1161.54130.19041.37210.04070.0705-0.1592-0.073-0.0541-0.2840.22230.25890.01850.19810.07590.02290.21160.01050.284879.7409-56.8332-56.1452
274.04721.79760.24337.40880.38014.6112-0.067-0.0731-0.20020.0850.0553-0.45170.06230.22690.03860.10830.0396-0.03580.15220.02180.142772.6047-49.1636-39.5267
280.55770.1106-0.22940.1602-0.03970.85250.01120.0092-0.089-0.04480.0083-0.02570.1216-0.0303-0.01560.20640.0064-0.00630.14240.00880.18639.5662-55.9021-60.1792
291.346-0.4856-0.73650.49760.3610.877-0.014-0.01560.103-0.00910.0418-0.03810.02030.055-0.0330.20170.0012-0.0110.14940.01310.16641.3693-46.8188-60.7225
301.815-0.6332-0.85470.40870.54241.48270.0389-0.0183-0.0469-0.0523-0.0113-0.05110.08990.1134-0.02870.18940.0125-0.01140.14280.01060.203748.1342-55.9595-57.8214
316.74181.92943.19326.00951.95315.17820.28320.3094-0.742-0.4558-0.0695-0.11661.01230.2724-0.17550.4140.02470.02120.1609-0.01860.326741.8034-76.598-60.6322
324.09630.13810.54750.6389-0.13852.055-0.03580.0967-0.3076-0.009-0.0124-0.06850.33580.04790.03950.2079-0.00040.0010.07310.01690.211842.1197-65.9288-53.8502
339.236-0.03244.6676.6935-0.57643.150.2678-0.9366-0.57530.0650.0039-0.17040.4115-0.3969-0.27760.2035-0.01640.01810.20410.04840.156641.1-69.6962-45.9961
342.7999-0.2378-3.00221.29231.27239.3897-0.02520.2117-0.1092-0.0523-0.07910.54650.2078-0.66550.13220.1611-0.0175-0.03830.27490.08740.3727-22.7286-41.2478-47.1036
351.65150.5622-1.05971.023-0.62251.76490.0178-0.10050.09810.19390.02730.2352-0.0345-0.2074-0.05480.18220.01430.07330.2061-0.02190.2571-7.64-22.0756-19.7892
367.80667.55882.04337.46381.35686.1299-0.2923-0.0523-0.8719-0.307-0.0747-0.0831.35920.61160.36240.51850.06640.07110.32180.00630.3938-14.1351-38.2404-16.9912
371.7262-0.0795-0.42910.99480.38931.60150.0242-0.03270.24180.01070.0160.3341-0.2375-0.338-0.03820.2170.0480.04970.25220.02890.3759-18.2188-18.0358-29.7915
383.04271.37811.84693.9001-2.76156.23130.0816-0.14270.262-0.065-0.08530.2858-0.5556-0.3446-0.01450.29580.05160.0660.2317-0.02580.4252-4.0999-7.5134-27.9319
391.38510.5416-0.51250.5741-0.16640.6454-0.01540.00780.0346-0.06070.050.12040.0063-0.0839-0.02980.1546-0.0045-0.02520.16980.04680.1841.5214-39.4142-50.581
401.7459-0.385-0.11580.90220.21630.3644-0.0643-0.07960.03360.09880.07370.06610.0322-0.0308-0.01090.1377-0.0173-0.00950.13280.03960.12754.6771-41.5023-42.1013
417.1414-2.2467-2.91831.48360.62951.4692-0.0136-0.26240.21040.10570.1080.14770.0244-0.0073-0.03430.1468-0.03210.00580.14880.02790.1926-5.3941-35.0677-42.7201
420.54460.2965-0.09131.70530.11551.4036-0.040.07220.0499-0.10080.10180.24420.0906-0.2781-0.04120.1227-0.0209-0.01920.18540.07270.2085-3.7954-33.577-56.7917
434.10440.4530.75124.58116.27898.98340.08010.3880.3584-0.2109-0.05220.2347-0.1598-0.4239-0.06340.2061-0.0152-0.06160.30290.19450.3088-10.7014-28.9978-65.9344
441.3696-0.0745-0.60092.18171.72022.3084-0.04140.17210.2083-0.11760.09580.2505-0.1369-0.1458-0.05020.1833-0.0191-0.03880.2120.09930.2173-1.6908-30.1902-57.765
456.6033-2.0065-3.78333.54852.58218.99390.0306-0.14511.3252-0.65390.3441-0.089-1.0465-0.1011-0.39690.2668-0.0158-0.07680.26890.06090.46161.0979-23.2133-61.5888
465.8586-0.05932.91416.2138-0.36259.5149-0.1291-0.34031.05480.2240.09780.0719-1.3435-0.33520.060.5171-0.02440.11760.2527-0.09360.41599.1347-9.7583-7.1304
470.5335-0.0168-0.0821.7733-0.63430.73180.084-0.14770.0110.222-0.0370.1762-0.0702-0.1232-0.06110.2745-0.04360.05650.3164-0.00260.19020.7209-47.72160.3144
486.21080.6875-1.4610.4899-0.35610.86070.1109-0.03850.14350.1065-0.02890.0609-0.0739-0.0527-0.09720.1703-0.01920.02450.18170.01320.110711.3911-49.8155-9.0419
492.0328-8.07061.16586.62522.61089.96440.26270.36340.4313-0.634-0.08690.098-1.1123-0.2568-0.02470.3867-0.04340.01990.33130.03870.3327-7.3168-43.1771-8.955
505.73461.4571-2.52461.1169-0.66421.17810.026-0.01690.0553-0.0485-0.0371-0.0499-0.03110.033-0.01350.2345-0.02550.00950.22790.0190.149314.2553-38.7002-6.7502
510.131-0.3610.61272.591-1.81572.84920.0654-0.2139-0.00690.08390.03560.0962-0.1043-0.0228-0.12670.279-0.05230.07940.317-0.00220.19759.4763-45.12797.7452
521.588-1.087-2.3258.55953.84244.42410.0023-0.1980.06940.38040.0569-0.5776-0.16840.5399-0.07150.2543-0.0719-0.02370.42250.00040.17118.9465-43.150313.4118
531.07630.6392-0.5623.3143-1.42822.10730.102-0.30340.08540.3348-0.03290.1382-0.2338-0.0489-0.06380.2395-0.02790.0360.2965-0.00310.14726.8635-40.21728.9652
542.12671.62892.87856.15513.44812.39740.1696-0.3231-0.05180.5809-0.1535-0.09930.09830.1120.00910.2997-0.01380.01330.30250.04150.206824.1264-53.0608-0.2164
552.1017-0.211-0.90990.8455-0.02060.91580.0396-0.10450.09690.1425-0.01330.0139-0.0825-0.0118-0.03460.1641-0.02940.00570.1546-0.02140.144219.1692-21.972-24.2307
560.7174-0.2045-0.71540.4720.27523.1238-0.0028-0.1366-0.04910.15170.02310.12970.1424-0.04310.00010.1816-0.01970.02630.19360.00520.192914.049-28.3592-22.7454
571.7649-0.32710.38743.4957-0.77832.2108-0.0127-0.40180.3330.464-0.0541-0.1464-0.2682-0.06390.05320.202-0.03080.00030.2383-0.05650.208527.4456-16.9904-15.2245
586.36621.9798-1.30546.8907-0.69627.9611-0.1432-0.4846-0.2820.6879-0.3185-0.93430.86290.74570.38070.33480.0225-0.02240.27780.00580.258736.6294-20.9202-15.7624
599.14510.1884-3.65326.98343.39957.7136-0.1448-0.8196-0.26360.91010.1768-0.35850.47480.6326-0.1250.29680.0018-0.05840.27360.10410.257915.7769-73.5228-11.4611
600.36560.0497-0.11140.3761-0.29020.62590.0027-0.03490.03990.04960.03030.1266-0.0061-0.086-0.02720.1772-0.04390.01640.22350.02920.2318-12.6813-55.8735-31.7776
612.1141-1.29172.26969.6479-2.7892.06390.015-0.76980.31580.5393-0.0019-0.5531-0.58850.5932-0.01460.2803-0.0405-0.02710.3375-0.01560.2824-12.6761-49.7263-17.2545
621.29850.7376-0.23071.398-0.36860.6253-0.06740.098-0.0004-0.09340.06560.06830.0130.01350.00470.188-0.03380.00350.20610.02670.1929-9.3873-68.7727-33.8419
633.8909-1.90441.10933.0213-0.91681.7914-0.0116-0.2623-0.22920.2730.05310.27730.1258-0.2451-0.05070.2009-0.06070.02170.17540.00310.1927-15.246-71.0618-26.3922
646.125-5.0577-0.09124.41220.27296.75370.0126-0.0001-0.2175-0.04950.0290.23820.2815-0.12120.03510.2106-0.1112-0.01490.23830.02060.2166-10.7659-64.1238-48.0966
651.09740.1934-0.9250.5475-0.66262.68170.0268-0.0893-0.0260.0206-0.039-0.01140.12080.06460.01940.1506-0.00150.00260.12820.01270.155422.211-57.9523-27.275
661.87741.6782-1.00342.157-1.62261.79620.0477-0.02720.10760.00930.00050.10350.0202-0.1044-0.040.16820.01610.0110.1527-0.0110.147517.3265-49.8513-27.5215
676.17414.7831-3.07964.9967-3.30372.6724-0.04850.02510.0576-0.03980.08370.14030.0851-0.1788-0.09230.1405-0.0209-0.00070.1707-0.00410.08811.1907-60.2013-26.2594
683.2226-0.37221.13921.10870.63972.4743-0.0213-0.2553-0.17520.1665-0.0159-0.00640.3695-0.00840.01680.1932-0.02210.02180.16170.04070.167522.9636-67.95-29.116
698.6927-0.46726.07136.30570.06987.26490.4605-0.4586-1.01490.4244-0.09190.03560.9983-0.0566-0.39450.38820.00460.04010.23360.04550.318925.644-79.91-29.5042
704.01070.34241.23620.95550.03883.42370.0027-0.1372-0.2515-0.0305-0.03460.05220.3775-0.02950.0280.16210.01310.01340.08780.01270.162923.3389-68.5981-33.03
712.05480.6542-2.30047.20431.05455.594-0.18360.583-0.191-0.74980.10740.55240.5175-0.07980.01250.326-0.0212-0.03450.19870.05770.300725.2938-71.6953-40.8027
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'B' and (resid 29 through 68 )
3X-RAY DIFFRACTION3chain 'B' and (resid 69 through 121 )
4X-RAY DIFFRACTION4chain 'B' and (resid 122 through 137 )
5X-RAY DIFFRACTION5chain 'B' and (resid 138 through 199 )
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 219 )
7X-RAY DIFFRACTION7chain 'B' and (resid 220 through 270 )
8X-RAY DIFFRACTION8chain 'A' and (resid 5 through 30 )
9X-RAY DIFFRACTION9chain 'A' and (resid 31 through 169 )
10X-RAY DIFFRACTION10chain 'A' and (resid 170 through 243 )
11X-RAY DIFFRACTION11chain 'A' and (resid 244 through 276 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 14 )
13X-RAY DIFFRACTION13chain 'D' and (resid 15 through 68 )
14X-RAY DIFFRACTION14chain 'D' and (resid 69 through 121 )
15X-RAY DIFFRACTION15chain 'D' and (resid 122 through 142 )
16X-RAY DIFFRACTION16chain 'D' and (resid 143 through 179 )
17X-RAY DIFFRACTION17chain 'D' and (resid 180 through 270 )
18X-RAY DIFFRACTION18chain 'C' and (resid 6 through 30 )
19X-RAY DIFFRACTION19chain 'C' and (resid 31 through 169 )
20X-RAY DIFFRACTION20chain 'C' and (resid 170 through 276 )
21X-RAY DIFFRACTION21chain 'F' and (resid 2 through 14 )
22X-RAY DIFFRACTION22chain 'F' and (resid 15 through 68 )
23X-RAY DIFFRACTION23chain 'F' and (resid 69 through 121 )
24X-RAY DIFFRACTION24chain 'F' and (resid 122 through 142 )
25X-RAY DIFFRACTION25chain 'F' and (resid 143 through 179 )
26X-RAY DIFFRACTION26chain 'F' and (resid 180 through 270 )
27X-RAY DIFFRACTION27chain 'E' and (resid 5 through 30 )
28X-RAY DIFFRACTION28chain 'E' and (resid 31 through 97 )
29X-RAY DIFFRACTION29chain 'E' and (resid 98 through 143 )
30X-RAY DIFFRACTION30chain 'E' and (resid 144 through 190 )
31X-RAY DIFFRACTION31chain 'E' and (resid 191 through 221 )
32X-RAY DIFFRACTION32chain 'E' and (resid 222 through 261 )
33X-RAY DIFFRACTION33chain 'E' and (resid 262 through 276 )
34X-RAY DIFFRACTION34chain 'H' and (resid 3 through 37 )
35X-RAY DIFFRACTION35chain 'H' and (resid 38 through 121 )
36X-RAY DIFFRACTION36chain 'H' and (resid 122 through 142 )
37X-RAY DIFFRACTION37chain 'H' and (resid 143 through 270 )
38X-RAY DIFFRACTION38chain 'G' and (resid 5 through 30 )
39X-RAY DIFFRACTION39chain 'G' and (resid 31 through 97 )
40X-RAY DIFFRACTION40chain 'G' and (resid 98 through 143 )
41X-RAY DIFFRACTION41chain 'G' and (resid 144 through 169 )
42X-RAY DIFFRACTION42chain 'G' and (resid 170 through 204 )
43X-RAY DIFFRACTION43chain 'G' and (resid 205 through 221 )
44X-RAY DIFFRACTION44chain 'G' and (resid 222 through 261 )
45X-RAY DIFFRACTION45chain 'G' and (resid 262 through 276 )
46X-RAY DIFFRACTION46chain 'J' and (resid 4 through 28 )
47X-RAY DIFFRACTION47chain 'J' and (resid 29 through 68 )
48X-RAY DIFFRACTION48chain 'J' and (resid 69 through 121 )
49X-RAY DIFFRACTION49chain 'J' and (resid 122 through 142 )
50X-RAY DIFFRACTION50chain 'J' and (resid 143 through 179 )
51X-RAY DIFFRACTION51chain 'J' and (resid 180 through 199 )
52X-RAY DIFFRACTION52chain 'J' and (resid 200 through 227 )
53X-RAY DIFFRACTION53chain 'J' and (resid 228 through 270 )
54X-RAY DIFFRACTION54chain 'I' and (resid 5 through 30 )
55X-RAY DIFFRACTION55chain 'I' and (resid 31 through 97 )
56X-RAY DIFFRACTION56chain 'I' and (resid 98 through 169 )
57X-RAY DIFFRACTION57chain 'I' and (resid 170 through 261 )
58X-RAY DIFFRACTION58chain 'I' and (resid 262 through 276 )
59X-RAY DIFFRACTION59chain 'L' and (resid 4 through 28 )
60X-RAY DIFFRACTION60chain 'L' and (resid 29 through 121 )
61X-RAY DIFFRACTION61chain 'L' and (resid 122 through 142 )
62X-RAY DIFFRACTION62chain 'L' and (resid 143 through 227 )
63X-RAY DIFFRACTION63chain 'L' and (resid 228 through 270 )
64X-RAY DIFFRACTION64chain 'K' and (resid 5 through 30 )
65X-RAY DIFFRACTION65chain 'K' and (resid 31 through 97 )
66X-RAY DIFFRACTION66chain 'K' and (resid 98 through 143 )
67X-RAY DIFFRACTION67chain 'K' and (resid 144 through 169 )
68X-RAY DIFFRACTION68chain 'K' and (resid 170 through 204 )
69X-RAY DIFFRACTION69chain 'K' and (resid 205 through 221 )
70X-RAY DIFFRACTION70chain 'K' and (resid 222 through 261 )
71X-RAY DIFFRACTION71chain 'K' and (resid 262 through 276 )

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlc1.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