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- PDB-3oee: Structure of four mutant forms of yeast F1 ATPase: alpha-F405S -

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基本情報

登録情報
データベース: PDB / ID: 3oee
タイトルStructure of four mutant forms of yeast F1 ATPase: alpha-F405S
要素(ATP synthase subunit ...) x 5
キーワードHYDROLASE / ATP SYNTHASE / ATP PHOSPHATASE / F1F0 ATPASE / ATP SYNTHESIS / ADP / PO4 / MITOCHONDRIA
機能・相同性
機能・相同性情報


Mitochondrial protein degradation / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space ...Mitochondrial protein degradation / proton motive force-driven ATP synthesis / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / ATP hydrolysis activity / mitochondrion / ATP binding / cytosol
類似検索 - 分子機能
ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 ...ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / Atp Synthase Epsilon Chain; Chain: I; / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / Pyruvate Kinase; Chain: A, domain 1 / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / Elongation Factor Tu (Ef-tu); domain 3 / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / ATP synthase subunit beta, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.74 Å
データ登録者Arsenieva, D. / Symersky, J. / Wang, Y. / Pagadala, V. / Mueller, D.M.
引用ジャーナル: To be Published
タイトル: Structure of four mutant forms of yeast F1 ATPase: alpha-F405S
著者: Arsenieva, D. / Symersky, J. / Wang, Y. / Pagadala, V. / Mueller, D.M.
履歴
登録2010年8月12日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年9月15日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22023年9月6日Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq_dif / struct_site
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_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_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_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.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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit alpha
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase subunit beta
P: ATP synthase subunit gamma
Q: ATP synthase subunit delta
R: ATP synthase subunit epsilon
S: ATP synthase subunit alpha
T: ATP synthase subunit alpha
U: ATP synthase subunit alpha
V: ATP synthase subunit beta
W: ATP synthase subunit beta
X: ATP synthase subunit beta
Y: ATP synthase subunit gamma
Z: ATP synthase subunit delta
1: ATP synthase subunit epsilon
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,126,28659
ポリマ－1,118,13827
非ポリマー8,14732
水1,51384
1
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit delta
I: ATP synthase subunit epsilon
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)375,46020
ポリマ－372,7139
非ポリマー2,74711
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: ATP synthase subunit alpha
K: ATP synthase subunit alpha
L: ATP synthase subunit alpha
M: ATP synthase subunit beta
N: ATP synthase subunit beta
O: ATP synthase subunit beta
P: ATP synthase subunit gamma
Q: ATP synthase subunit delta
R: ATP synthase subunit epsilon
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)375,46020
ポリマ－372,7139
非ポリマー2,74711
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
3
S: ATP synthase subunit alpha
T: ATP synthase subunit alpha
U: ATP synthase subunit alpha
V: ATP synthase subunit beta
W: ATP synthase subunit beta
X: ATP synthase subunit beta
Y: ATP synthase subunit gamma
Z: ATP synthase subunit delta
1: ATP synthase subunit epsilon
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)375,36519
ポリマ－372,7139
非ポリマー2,65310
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)110.430, 288.580, 187.170
Angle α, β, γ (deg.)90.00, 101.37, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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ATP synthase subunit ... , 5種, 27分子 ABCJKLSTUDEFMNOVWXGPYHQZIR1

#1: タンパク質
ATP synthase subunit alpha


分子量: 54947.309 Da / 分子数: 9 / 断片: UNP RESIDUES 36-545 / 変異: F405S / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ATP1, YBL099W, YBL0827 / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P07251, H+-transporting two-sector ATPase
#2: タンパク質
ATP synthase subunit beta


分子量: 52009.965 Da / 分子数: 9 / 断片: UNP RESIDUES 34-511 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ATP2, YJR121W, J2041 / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P00830, H+-transporting two-sector ATPase
#3: タンパク質 ATP synthase subunit gamma / F-ATPase gamma subunit


分子量: 30657.160 Da / 分子数: 3 / 断片: UNP RESIDUES 34-311 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ATP3, ATP3a, ATP3b, YBR039W, YBR0408 / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P38077, H+-transporting two-sector ATPase
#4: タンパク質 ATP synthase subunit delta / F-ATPase delta subunit


分子量: 14565.385 Da / 分子数: 3 / 断片: UNP RESIDUES 23-160 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ATP16, YDL004W, YD8119.03, D2935 / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: Q12165, H+-transporting two-sector ATPase
#5: タンパク質 ATP synthase subunit epsilon / ATPase subunit epsilon


分子量: 6618.359 Da / 分子数: 3 / 断片: UNP RESIDUES 2-62 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: ATP15, YPL271W, P0345 / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P21306, H+-transporting two-sector ATPase

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非ポリマー , 4種, 116分子

#6: 化合物
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


分子量: 506.196 Da / 分子数: 15 / 由来タイプ: 合成 / 式: C10H17N6O12P3
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM
#7: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 15 / 由来タイプ: 合成 / 式: Mg
#8: 化合物 ChemComp-PO4 / PHOSPHATE ION


分子量: 94.971 Da / 分子数: 2 / 由来タイプ: 合成 / 式: PO4
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 84 / 由来タイプ: 天然 / 式: H2O

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詳細

構成要素の詳細CHAIN A, J, S: ALPHA SUBUNIT(E) CHAIN B, K, T: ALPHA SUBUNIT (TP) CHAIN C, L, U: ALPHA SUBUNIT (DP) ...CHAIN A, J, S: ALPHA SUBUNIT(E) CHAIN B, K, T: ALPHA SUBUNIT (TP) CHAIN C, L, U: ALPHA SUBUNIT (DP) CHAIN D, M, V: BETA SUBUNIT (DP) CHAIN E, N, W: BETA SUBUNIT (E) CHAIN F, O, X: BETA SUBUNIT (TP) CHAIN G, P, Y: GAMMA SUBUNIT CHAIN H, Q, Z: DELTA SUBUNIT CHAIN I, R, 1: EPSILON SUBUNIT

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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: 2.61 Å3/Da / 溶媒含有率: 52.96 %
結晶化温度: 277 K / pH: 7.3
詳細: 5.5% PEG 6000, 10% GLYCEROL, 4% METHANOL, 0.05M SODIUM ACETATE, 0.5MM NICKEL SULPHATE, 0.5MM AMP/PNP, 0.025 MM ADP, 2MM MAGNESIUM CHLORIDE, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: APS / ビームライン: 23-ID-D / 波長: 0.97931
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2007年6月22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: 0.97931 Å / 相対比: 1
反射解像度: 2.74→40 Å / Num. obs: 289154 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 2.5 % / Biso Wilson estimate: 73 Å2 / Rsym value: 0.069 / Net I/σ(I): 11.3
反射 シェル解像度: 2.74→2.84 Å / Rsym value: 0.718 / % possible all: 97.5

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解析

ソフトウェア
名称バージョン分類
Blu-Iceデータ収集
MOLREP位相決定
REFMAC5.5.0102精密化
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 2HLD

2hld


解像度: 2.74→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU ML: 0.323 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.359 / 立体化学のターゲット値: ENGH & HUBER
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
Rfactor反射数%反射Selection details
Rfree0.259 5965 2 %RANDOM
Rwork0.212 ---
obs0.213 289050 98.63 %-
all-289050 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MSAK
原子変位パラメータBiso mean: 89.9 Å2
Refine analyzeLuzzati coordinate error free: 0.359 Å
精密化ステップサイクル: LAST / 解像度: 2.74→20 Å
タンパク質核酸リガンド溶媒全体
原子数72101 0 490 84 72675
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.26
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.74→2.81 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.331 465 -
Rwork0.307 21128 -
obs--99.37 %
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)
13.65981.5833-0.15288.5206-1.08793.2364-0.156-0.34990.42761.10280.1527-0.1564-0.07390.21180.00340.41330.1047-0.1170.5112-0.18490.253321.98150.632883.1447
22.2443-0.3776-0.33071.26750.26261.4938-0.13940.0053-0.04890.2460.04120.2839-0.0171-0.09090.09820.0890.01750.03170.2146-0.09810.4915-5.50852.91969.1662
33.05770.70890.87244.64560.08953.2292-0.20660.62240.0778-0.45520.24160.45080.1094-0.5581-0.0350.1277-0.0283-0.02990.7223-0.11950.7436-30.7598.435852.407
45.22460.3796-1.92524.41951.58822.0553-0.1197-0.268-0.2190.22480.1023-0.19240.21150.30770.01750.20520.1414-0.06540.40190.01390.400935.7119-30.496859.26
51.4017-0.2353-0.3072.57750.31312.2925-0.10980.1814-0.1244-0.7326-0.00840.16580.1580.00440.11820.3764-0.01380.03120.2827-0.01910.242421.4287-31.189531.8572
62.5412-0.2879-0.37222.7886-0.35642.45410.14380.62320.1075-1.0485-0.19920.3998-0.2189-0.30210.05541.23570.0194-0.32470.807-0.16220.50944.0405-31.15276.6925
73.23381.6718-0.20816.14530.86524.3108-0.17990.05050.24880.02330.2332-0.6803-0.06070.4939-0.05340.0224-0.06190.01770.6059-0.12050.859852.42327.02955.0245
81.2257-0.4098-0.02411.97590.10331.28170.05370.11090.3623-0.56620.0902-0.2617-0.45410.1784-0.14390.4713-0.14690.19480.39890.00990.652134.470723.326535.9857
93.5453-0.58040.4643.36-0.39334.2461-0.00830.2970.2487-0.8519-0.01420.499-0.7509-1.08070.02261.32320.1070.06660.8590.13230.67714.993235.691915.4017
106.73170.6488-4.61615.89781.0185.4251-0.0578-0.4520.18390.74660.1387-0.9562-0.59650.7366-0.08090.4456-0.0913-0.26760.5439-0.22420.751538.333616.957972.1561
111.65170.14050.40292.186-0.17571.2826-0.0084-0.05460.467-0.08560.0929-0.05-0.52490.0162-0.08450.2725-0.04330.0230.3071-0.0580.63114.283528.809959.8346
123.52280.22980.38632.754-0.77893.6683-0.03930.56990.5424-1.03440.09850.403-0.482-0.3264-0.05920.70480.0935-0.16140.49710.14340.7354-8.615331.632239.109
134.26840.81870.17077.19792.71143.4539-0.266-0.6884-0.50450.98260.3915-0.14290.21310.1769-0.12550.36590.1573-0.00910.37870.05060.202918.9842-22.218376.4282
142.09270.4203-0.61292.31510.39821.7324-0.1330.1726-0.1888-0.0159-0.06480.71690.1412-0.25950.19780.16550.00770.04890.265-0.07420.5239-2.5166-27.108756.31
152.2080.8349-1.01372.28260.16714.68560.00830.7423-0.0241-0.66130.02491.1038-0.2991-1.2548-0.03320.6182-0.062-0.35511.0926-0.20131.1606-24.0081-27.8334.6162
163.81831.5667-1.6935.6306-1.22264.0004-0.06270.19360.00640.0780.1557-0.91920.25550.8851-0.09290.08710.07960.0420.6112-0.06260.726552.4447-17.752147.5393
171.16940.00880.10371.29280.1550.98010.01150.38020.1992-0.79380.03-0.5511-0.02090.3367-0.04150.6328-0.04340.27440.50440.01650.513839.8063-7.324522.7978
182.8658-0.5519-0.40182.44281.11351.98830.04260.59130.176-0.78090.05390.19660.0396-0.1753-0.09651.0931-0.0167-0.03550.6980.18230.374716.03052.2715.5027
190.64910.99770.05016.3499-0.62112.804-0.0548-0.0937-0.1878-0.0572-0.1662-0.78280.42340.64080.2210.21060.02860.07540.6780.15440.746936.0085-101.712269.1906
201.256-0.0192-0.3321.6254-0.5662.67720.09330.2749-0.1794-0.613-0.1385-0.14810.26730.2060.04520.56740.0630.11880.3992-0.0250.370919.8529-99.146742.7807
212.04140.40.34383.3374-0.21763.26140.09350.65840.0958-0.6064-0.00520.52140.2287-0.5721-0.08831.163-0.0057-0.13440.8768-0.09210.66571.1218-98.905618.2888
221.6711-0.1662-0.88692.21740.21692.88310.1408-0.31540.16010.3678-0.22-0.2278-0.20860.31220.07910.5476-0.3128-0.07960.5102-0.04260.326716.9696-70.383788.5227
231.8039-0.2131-0.42772.3522-0.24671.28670.1287-0.02450.24110.2331-0.03220.3953-0.2981-0.1648-0.09660.4113-0.09480.14580.2682-0.06220.4374-11.8465-65.345576.6601
244.12351.07231.07321.841-0.80081.98940.05770.30670.2382-0.31890.12930.63680.0772-0.8704-0.18690.68530.14830.05360.93140.09991.1542-38.6337-61.173462.4518
252.9741-0.5694-1.05554.51770.78943.8487-0.0161-0.4775-0.3130.4912-0.0176-0.12110.13380.28540.03380.5289-0.1802-0.03790.55930.18130.319.717-108.9873101.1389
261.13661-0.44922.0374-0.38511.8731-0.06820.0241-0.3197-0.2266-0.04440.11350.1364-0.05250.11260.3681-0.0880.0350.2964-0.00220.444-12.1324-121.185983.2591
273.6373-0.48340.22893.2115-0.31974.03450.19460.7688-0.273-1.0893-0.18740.66450.4543-0.5161-0.00720.8404-0.2324-0.11640.793-0.13450.7655-35.0647-130.100664.8493
283.6386-0.784-2.38454.18121.76475.0331-0.0934-0.4062-0.58190.2901-0.0629-0.76340.50930.76810.15630.42370.001-0.0410.56410.23620.605224.7124-118.681384.4534
291.52760.5555-0.39662.1645-0.64931.6047-0.11790.2365-0.3986-0.57590.07750.240.64830.06710.04040.6771-0.01050.03470.40820.01460.61339.0424-126.029860.2924
301.53411.3539-1.4642.3062-1.34463.4905-0.04620.6234-0.1163-0.51080.15630.90160.3106-0.9833-0.11011.1518-0.3126-0.35991.1417-0.0241.2339-13.8663-123.149539.5715
313.9101-2.5465-1.37417.839-0.02533.7007-0.0875-0.2648-0.03040.3289-0.0063-0.925-0.40980.69130.09390.2915-0.2147-0.03970.50850.08140.477231.7445-77.781669.5832
321.3201-0.1611-0.53771.9745-0.88681.55420.1850.26490.1114-0.3858-0.1770.016-0.1026-0.0401-0.0080.40990.00880.09750.3658-0.04460.31510.6713-68.788450.2251
334.3388-0.25220.08860.9782-0.15353.54530.04041.0467-0.2903-0.7658-0.05370.53220.0674-0.73460.01330.88260.1298-0.12710.97510.05080.6861-12.3766-63.383230.9004
346.4370.8914-0.6247.7999-1.73594.3935-0.0105-0.89340.10161.2368-0.0363-0.0897-0.27030.15450.04680.6981-0.2566-0.04610.5348-0.07740.1494.9329-83.8566104.4129
351.5711-0.19710.23051.6571-0.23421.44770.1535-0.31590.0340.44890.01310.5525-0.1627-0.2884-0.16660.4729-0.15350.18940.3844-0.03560.5039-21.7594-90.230593.1033
362.8405-0.355-0.00932.8153-0.06031.5320.19450.5150.053-0.59890.03010.9029-0.0905-0.5716-0.22460.494-0.057-0.10010.75120.04340.9754-41.7046-95.549470.2249
371.0338-1.8111.29533.2905-2.35661.7163-0.2301-0.40490.01960.66790.339-0.042-0.3886-0.1368-0.10891.9097-0.0179-0.10051.8194-0.28490.761233.9281-36.072183.6659
380.5387-0.0447-0.27231.08540.40771.0495-0.1041-0.24460.47720.22620.0659-0.2847-0.2484-0.24530.03821.40710.0735-0.47190.9593-0.27340.956150.7991-21.2947162.3731
390.99810.4162-0.81790.7944-0.09433.20250.15980.3360.4342-0.5284-0.0037-0.4609-0.6850.1317-0.15611.8333-0.1264-0.22821.17770.00961.887568.924-10.8594140.1023
401.8451.70491.37332.51940.58581.64440.3572-0.43550.15710.229-0.29550.81320.2625-0.0931-0.06161.5416-0.10330.25861.8601-0.00621.2108-1.214-35.7019162.2042
410.6658-0.8447-0.3442.15230.2390.83580.0581-0.08410.03020.1298-0.10270.6969-0.0845-0.51470.04460.9045-0.1619-0.01861.54-0.17360.84143.418-34.0071131.9199
423.13150.0944-0.21342.1779-0.38811.2708-0.21930.4663-0.1898-0.37920.01880.1102-0.1102-0.40460.20051.35310.0243-0.18051.4758-0.18910.78459.8582-29.6056102.587
431.9184-0.3165-1.76961.0747-0.05831.7689-0.3164-0.0619-0.35590.44620.27450.46430.1436-0.13640.04191.8057-0.18430.11331.7240.2760.986118.5507-71.7013167.9141
441.46750.10480.12481.7074-0.28170.8015-0.162-0.3788-0.36940.30260.3312-0.03590.5687-0.1405-0.16921.5348-0.1354-0.23120.84760.04510.622640.7526-73.489145.9449
452.94350.1813-1.29620.22220.15971.32390.05330.2033-0.2707-0.1223-0.0211-0.25230.19140.5978-0.03222.04260.0111-0.14641.2095-0.01751.105559.7544-72.3611121.8608
465.92930.2636-1.4450.06660.10852.66940.2517-0.5965-0.10750.3096-0.14530.01330.1048-0.4906-0.10642.0932-0.0044-0.03891.81140.12160.638736.4758-61.3475180.6393
472.1236-0.10261.11761.1797-0.70572.692-0.0422-0.4885-0.21270.37180.1033-0.35510.48920.2894-0.06111.40830.0689-0.36430.9631-0.11260.703959.3972-54.031162.6642
482.0457-0.267-0.83021.89290.5630.77650.03330.56240.3618-0.14680.2186-0.82790.32320.2669-0.25191.3107-0.0103-0.28381.2351-0.10261.324173.0332-45.4089136.1628
492.3929-2.63982.143.1175-2.65613.0878-0.5131-0.04190.21070.87260.4189-0.0524-0.0228-0.49760.09421.7601-0.04190.0941.533-0.17650.771517.1196-22.1636173.8719
500.4150.2933-0.37152.2115-0.09641.3852-0.0403-0.14290.33150.48910.0488-0.04580.0058-0.2572-0.00851.00310.0185-0.09321.1344-0.17380.784223.3476-9.9936147.4549
511.91130.8136-0.21833.6809-0.58193.5181-0.02620.39540.1627-0.43760.1436-0.61170.1415-0.0352-0.11730.8830.0476-0.03791.0133-0.07440.972632.5184-1.2079119.7055
520.0291-0.1151-0.21711.13342.07923.96730.0778-0.0441-0.09040.4602-0.11440.23590.5387-0.21690.03661.7232-0.36050.26421.81340.27941.3921-2.0845-59.539158.3324
532.1938-0.0038-1.22630.36990.071.004-0.1814-0.1458-0.46320.1885-0.09630.57310.2766-0.56310.27771.407-0.6239-0.0131.38990.12141.07511.427-64.4375131.8933
543.2307-0.36011.11324.04410.27124.36940.09570.14940.129-0.0426-0.0402-0.10030.08080.0188-0.05550.7888-0.2912-0.09150.6193-0.050.348331.5625-57.2504109.1674
5512.9192-1.62911.84861.8114-1.794213.5111-0.7272-0.0141.4424-0.71750.00910.1121-0.4496-0.80820.7180.7689-0.0389-0.09890.53010.08270.60243.219-0.632235.0515
564.9433-0.96791.36662.4012-0.72392.28950.05170.36570.20870.0726-0.12530.24270.0454-0.17730.07360.9847-0.0896-0.06971.08440.13280.6493-31.629916.51472.7209
5715.73980.419610.38472.1793-0.100210.59950.31220.72510.193-0.6589-0.03010.71820.5213-0.4711-0.28210.672-0.1444-0.05780.6187-0.03440.6879-13.1605-93.203955.1367
582.4459-0.06321.25212.1965-0.04564.4057-0.03080.03990.2384-0.1228-0.07090.0019-0.2226-0.30770.10171.0172-0.0449-0.16751.3663-0.10260.8993-48.728-102.223622.2338
595.69022.5708-7.36362.7902-5.092614.2929-0.0395-0.6554-0.03340.1493-0.2744-0.3472-0.05891.0060.31391.1245-0.1178-0.13910.8746-0.09210.667139.6823-36.5877132.4628
603.14940.6899-1.30750.3462-0.60291.35960.14830.8804-0.1533-0.111-0.0412-0.23810.16840.0967-0.10711.1524-0.1618-0.01361.44490.04221.075962.383-32.636995.9727
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 97
2X-RAY DIFFRACTION2A98 - 382
3X-RAY DIFFRACTION3A383 - 509
4X-RAY DIFFRACTION4B25 - 97
5X-RAY DIFFRACTION5B98 - 382
6X-RAY DIFFRACTION6B383 - 509
7X-RAY DIFFRACTION7C26 - 97
8X-RAY DIFFRACTION8C98 - 382
9X-RAY DIFFRACTION9C383 - 509
10X-RAY DIFFRACTION10D6 - 82
11X-RAY DIFFRACTION11D83 - 357
12X-RAY DIFFRACTION12D358 - 475
13X-RAY DIFFRACTION13E8 - 82
14X-RAY DIFFRACTION14E83 - 357
15X-RAY DIFFRACTION15E358 - 475
16X-RAY DIFFRACTION16F7 - 82
17X-RAY DIFFRACTION17F83 - 357
18X-RAY DIFFRACTION18F358 - 475
19X-RAY DIFFRACTION19J26 - 97
20X-RAY DIFFRACTION20J98 - 382
21X-RAY DIFFRACTION21J383 - 509
22X-RAY DIFFRACTION22K21 - 97
23X-RAY DIFFRACTION23K98 - 382
24X-RAY DIFFRACTION24K383 - 509
25X-RAY DIFFRACTION25L26 - 97
26X-RAY DIFFRACTION26L98 - 382
27X-RAY DIFFRACTION27L383 - 509
28X-RAY DIFFRACTION28M6 - 82
29X-RAY DIFFRACTION29M83 - 357
30X-RAY DIFFRACTION30M358 - 475
31X-RAY DIFFRACTION31N6 - 82
32X-RAY DIFFRACTION32N83 - 357
33X-RAY DIFFRACTION33N358 - 475
34X-RAY DIFFRACTION34O7 - 82
35X-RAY DIFFRACTION35O83 - 357
36X-RAY DIFFRACTION36O358 - 474
37X-RAY DIFFRACTION37S27 - 97
38X-RAY DIFFRACTION38S98 - 382
39X-RAY DIFFRACTION39S383 - 509
40X-RAY DIFFRACTION40T26 - 97
41X-RAY DIFFRACTION41T98 - 382
42X-RAY DIFFRACTION42T383 - 509
43X-RAY DIFFRACTION43U26 - 97
44X-RAY DIFFRACTION44U98 - 382
45X-RAY DIFFRACTION45U383 - 509
46X-RAY DIFFRACTION46V6 - 82
47X-RAY DIFFRACTION47V83 - 357
48X-RAY DIFFRACTION48V358 - 475
49X-RAY DIFFRACTION49W8 - 82
50X-RAY DIFFRACTION50W83 - 357
51X-RAY DIFFRACTION51W358 - 474
52X-RAY DIFFRACTION52X7 - 82
53X-RAY DIFFRACTION53X83 - 357
54X-RAY DIFFRACTION54X358 - 475
55X-RAY DIFFRACTION55G1 - 25
56X-RAY DIFFRACTION55G234 - 276
57X-RAY DIFFRACTION56G26 - 233
58X-RAY DIFFRACTION56H11 - 136
59X-RAY DIFFRACTION56I8 - 61
60X-RAY DIFFRACTION57P1 - 25
61X-RAY DIFFRACTION57P234 - 276
62X-RAY DIFFRACTION58P26 - 233
63X-RAY DIFFRACTION58Q12 - 137
64X-RAY DIFFRACTION58R10 - 47
65X-RAY DIFFRACTION59Y1 - 25
66X-RAY DIFFRACTION59Y234 - 275
67X-RAY DIFFRACTION60Y26 - 233
68X-RAY DIFFRACTION60Z119 - 135
69X-RAY DIFFRACTION6019 - 45

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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