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- PDB-2wgm: Complete ion-coordination structure in the rotor ring of Na-depen... -

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基本情報

登録情報
データベース: PDB / ID: 2wgm
タイトルComplete ion-coordination structure in the rotor ring of Na-dependent F-ATP synthase
要素ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
キーワードMEMBRANE PROTEIN / F1FO-ATP SYNTHASE ROTOR / SODIUM-MOTIVE FORCE / CELL INNER MEMBRANE CF(0) / TRANSPORT / LIPID-BINDING / ION COORDINATION AND SELECTIVITY / HYDROGEN ION TRANSPORT / TRANSMEMBRANE / C-RING STRUCTURE / SODIUM TRANSPORT / CELL MEMBRANE / ATP SYNTHESIS
機能・相同性
機能・相同性情報


sodium ion transport / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
類似検索 - 分子機能
F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
NONAN-1-OL / ATP synthase subunit c, sodium ion specific
類似検索 - 構成要素
生物種ILYOBACTER TARTARICUS (バクテリア)
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Meier, T. / Pogoryelov, D. / Diederichs, K.
引用ジャーナル: J.Mol.Biol. / 年: 2009
タイトル: Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-ATP Synthases.
著者: Meier, T. / Krah, A. / Bond, P.J. / Pogoryelov, D. / Diederichs, K. / Faraldo-Gomez, J.D.
履歴
登録2009年4月21日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02009年6月9日Provider: repository / タイプ: Initial release
改定 1.12013年5月29日Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
改定 1.22023年12月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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 / _struct_conn.ptnr2_label_seq_id / _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

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集合体

登録構造単位
A: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
B: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
C: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
D: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
E: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
F: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
G: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
H: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
I: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
J: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
K: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
L: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
M: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
N: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
O: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
P: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
Q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
R: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
S: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
T: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
U: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
V: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
a: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
b: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
c: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
d: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
e: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
f: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
g: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
h: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
i: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
j: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
k: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
l: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
m: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
n: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
o: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
p: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
r: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
s: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
t: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
u: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
v: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)394,528132
ポリマ－387,16944
非ポリマー7,35988
水7,440413
1
a: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
b: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
c: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
d: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
e: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
f: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
g: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
h: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
i: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
j: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
k: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,63233
ポリマ－96,79211
非ポリマー1,84022
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area47390 Å2
ΔGint-479 kcal/mol
Surface area25010 Å2
手法PISA
2
l: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
m: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
n: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
o: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
p: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
r: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
s: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
t: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
u: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
v: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,63233
ポリマ－96,79211
非ポリマー1,84022
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area47490 Å2
ΔGint-475.9 kcal/mol
Surface area24960 Å2
手法PISA
3
A: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
B: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
C: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
D: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
E: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
F: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
G: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
H: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
I: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
J: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
K: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,63233
ポリマ－96,79211
非ポリマー1,84022
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area47540 Å2
ΔGint-476.7 kcal/mol
Surface area24890 Å2
手法PISA
4
L: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
M: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
N: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
O: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
P: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
Q: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
R: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
S: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
T: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
U: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
V: ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,63233
ポリマ－96,79211
非ポリマー1,84022
水19811
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area47530 Å2
ΔGint-473.9 kcal/mol
Surface area24970 Å2
手法PISA
単位格子
Length a, b, c (Å)146.690, 139.280, 151.910
Angle α, β, γ (deg.)90.00, 118.40, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301
311
321
331
341
351
361
371
381
391
401
411
421
431
441

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
211CHAIN B AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
311CHAIN C AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
411CHAIN D AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
511CHAIN E AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
611CHAIN F AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
711CHAIN G AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
811CHAIN H AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
911CHAIN I AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1011CHAIN J AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1111CHAIN K AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1211CHAIN L AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1311CHAIN M AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1411CHAIN N AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1511CHAIN O AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1611CHAIN P AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1711CHAIN Q AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1811CHAIN R AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
1911CHAIN S AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2011CHAIN T AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2111CHAIN U AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2211CHAIN V AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2311CHAIN a AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2411CHAIN b AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2511CHAIN c AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2611CHAIN d AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2711CHAIN e AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2811CHAIN f AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
2911CHAIN g AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3011CHAIN h AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3111CHAIN i AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3211CHAIN j AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3311CHAIN k AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3411CHAIN l AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3511CHAIN m AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3611CHAIN n AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3711CHAIN o AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3811CHAIN p AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
3911CHAIN q AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4011CHAIN r AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4111CHAIN s AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4211CHAIN t AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4311CHAIN u AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)
4411CHAIN v AND (RESSEQ 1:44 OR RESSEQ 47:47 OR RESSEQ 49:88 ) AND (NOT ELEMENT H)

NCS oper: (Code: given
Matrix: (0.994071, 0.037842, 0.101931), (0.022885, 0.843657, -0.536395), (-0.106293, 0.535547, 0.837789)
ベクター: -2.8298, 13.8727, -8.73288)

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要素

#1: タンパク質 ...
ATP SYNTHASE SUBUNIT C, SODIUM ION SPECIFIC / C11 RING / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / F- ...C11 RING / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / F-ATPASE SUBUNIT C


分子量: 8799.304 Da / 分子数: 44 / 由来タイプ: 天然 / 詳細: GERMAN COLLECTION OF MICROORGANISMS (DSM) / 由来: (天然) ILYOBACTER TARTARICUS (バクテリア) / 株: 2382 / 参照: UniProt: Q8KRV3
#2: 化合物...
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 44 / 由来タイプ: 合成 / 式: Na
#3: 化合物...
ChemComp-F09 / NONAN-1-OL / 1-ノナノ-ル


分子量: 144.254 Da / 分子数: 44 / 由来タイプ: 合成 / 式: C9H20O
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 413 / 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: 3.5 Å3/Da / 溶媒含有率: 66.1 % / 解説: NONE
結晶化pH: 4.5 / 詳細: pH 4.5

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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: ESRF / ビームライン: ID29 / 波長: 0.9756
検出器タイプ: ADSC CCD / 検出器: CCD / 日付: 2004年2月8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: 0.9756 Å / 相対比: 1
反射解像度: 2.35→40 Å / Num. obs: 220545 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 11 % / Biso Wilson estimate: 39.81 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.8
反射 シェル解像度: 2.35→2.45 Å / 冗長度: 7.5 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.8 / % possible all: 91

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解析

ソフトウェア
名称バージョン分類
PHENIX(PHENIX.REFINE)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: PDB ENTRY 1YCE

1yce


解像度: 2.35→39.678 Å / SU ML: 0 / σ(F): 1.99 / 位相誤差: 29.09 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2451 10959 5 %
Rwork0.2203 --
obs0.2215 219965 98.63 %
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 / Bsol: 54.877 Å2 / ksol: 0.386 e/Å3
原子変位パラメータBiso mean: 60.4 Å2
Baniso -1Baniso -2Baniso -3
1--22.873 Å20 Å20.9992 Å2
2--16.2039 Å20 Å2
3---6.6691 Å2
精密化ステップサイクル: LAST / 解像度: 2.35→39.678 Å
タンパク質核酸リガンド溶媒全体
原子数27104 0 484 413 28001
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01257464
X-RAY DIFFRACTIONf_angle_d0.704104456
X-RAY DIFFRACTIONf_dihedral_angle_d13.36713860
X-RAY DIFFRACTIONf_chiral_restr0.0534664
X-RAY DIFFRACTIONf_plane_restr0.0028624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A582X-RAY DIFFRACTIONPOSITIONAL
12B582X-RAY DIFFRACTIONPOSITIONAL0.06
13C582X-RAY DIFFRACTIONPOSITIONAL0.032
14D582X-RAY DIFFRACTIONPOSITIONAL0.036
15E582X-RAY DIFFRACTIONPOSITIONAL0.034
16F582X-RAY DIFFRACTIONPOSITIONAL0.035
17G582X-RAY DIFFRACTIONPOSITIONAL0.035
18H582X-RAY DIFFRACTIONPOSITIONAL0.036
19I582X-RAY DIFFRACTIONPOSITIONAL0.034
110J582X-RAY DIFFRACTIONPOSITIONAL0.036
111K582X-RAY DIFFRACTIONPOSITIONAL0.043
112L582X-RAY DIFFRACTIONPOSITIONAL0.03
113M582X-RAY DIFFRACTIONPOSITIONAL0.034
114N582X-RAY DIFFRACTIONPOSITIONAL0.031
115O582X-RAY DIFFRACTIONPOSITIONAL0.029
116P582X-RAY DIFFRACTIONPOSITIONAL0.031
117Q582X-RAY DIFFRACTIONPOSITIONAL0.03
118R582X-RAY DIFFRACTIONPOSITIONAL0.032
119S582X-RAY DIFFRACTIONPOSITIONAL0.034
120T582X-RAY DIFFRACTIONPOSITIONAL0.036
121U582X-RAY DIFFRACTIONPOSITIONAL0.037
122V582X-RAY DIFFRACTIONPOSITIONAL0.034
123A582X-RAY DIFFRACTIONPOSITIONAL0.027
124B582X-RAY DIFFRACTIONPOSITIONAL0.034
125C582X-RAY DIFFRACTIONPOSITIONAL0.033
126D582X-RAY DIFFRACTIONPOSITIONAL0.032
127E582X-RAY DIFFRACTIONPOSITIONAL0.03
128F582X-RAY DIFFRACTIONPOSITIONAL0.03
129G582X-RAY DIFFRACTIONPOSITIONAL0.032
130H582X-RAY DIFFRACTIONPOSITIONAL0.034
131I582X-RAY DIFFRACTIONPOSITIONAL0.034
132J582X-RAY DIFFRACTIONPOSITIONAL0.038
133K582X-RAY DIFFRACTIONPOSITIONAL0.037
134L582X-RAY DIFFRACTIONPOSITIONAL0.028
135M582X-RAY DIFFRACTIONPOSITIONAL0.035
136N582X-RAY DIFFRACTIONPOSITIONAL0.035
137O582X-RAY DIFFRACTIONPOSITIONAL0.033
138P582X-RAY DIFFRACTIONPOSITIONAL0.036
139Q582X-RAY DIFFRACTIONPOSITIONAL0.039
140R582X-RAY DIFFRACTIONPOSITIONAL0.035
141S582X-RAY DIFFRACTIONPOSITIONAL0.033
142T582X-RAY DIFFRACTIONPOSITIONAL0.037
143U582X-RAY DIFFRACTIONPOSITIONAL0.036
144V582X-RAY DIFFRACTIONPOSITIONAL0.033
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.37670.38273070.34036073X-RAY DIFFRACTION86
2.3767-2.40470.34613260.32226424X-RAY DIFFRACTION91
2.4047-2.4340.3663270.32186582X-RAY DIFFRACTION94
2.434-2.46480.34413620.30046838X-RAY DIFFRACTION97
2.4648-2.49720.31783730.28497027X-RAY DIFFRACTION100
2.4972-2.53140.31963290.26197077X-RAY DIFFRACTION100
2.5314-2.56760.28523420.24967018X-RAY DIFFRACTION100
2.5676-2.60590.27983750.23617016X-RAY DIFFRACTION100
2.6059-2.64660.26633660.23087045X-RAY DIFFRACTION100
2.6466-2.690.25113830.22556974X-RAY DIFFRACTION100
2.69-2.73640.26743500.22417057X-RAY DIFFRACTION100
2.7364-2.78610.24283730.21797022X-RAY DIFFRACTION100
2.7861-2.83970.26643730.21676992X-RAY DIFFRACTION100
2.8397-2.89760.25243530.20317023X-RAY DIFFRACTION100
2.8976-2.96060.25193490.20857039X-RAY DIFFRACTION100
2.9606-3.02950.21943910.21157004X-RAY DIFFRACTION99
3.0295-3.10520.24943660.2097052X-RAY DIFFRACTION100
3.1052-3.18910.24433810.21477016X-RAY DIFFRACTION100
3.1891-3.28290.24744060.22626979X-RAY DIFFRACTION100
3.2829-3.38880.27573770.2227069X-RAY DIFFRACTION100
3.3888-3.50990.23693520.22797022X-RAY DIFFRACTION100
3.5099-3.65030.243440.20757108X-RAY DIFFRACTION100
3.6503-3.81630.22524070.20437042X-RAY DIFFRACTION100
3.8163-4.01730.24163840.20547030X-RAY DIFFRACTION100
4.0173-4.26880.22043370.19777091X-RAY DIFFRACTION100
4.2688-4.59790.20493860.19227065X-RAY DIFFRACTION100
4.5979-5.05980.21894100.19647059X-RAY DIFFRACTION100
5.0598-5.790.23573640.21577073X-RAY DIFFRACTION100
5.79-7.28740.19133920.18227131X-RAY DIFFRACTION100
7.2874-39.68340.20873740.21427058X-RAY DIFFRACTION98
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)
1-0.4142-0.3669-0.26980.79140.12130.4566-0.0487-0.14640.24970.01550.0626-0.03140.00560.0569-0.03340.2440.0074-0.01460.27050.03760.21497.471211.749732.6749
23.2209-0.42260.04470.806-0.20860.5962-0.2354-0.93140.4372-0.01660.07670.035-0.12670.1020.10160.3193-0.0047-0.03580.4022-0.08420.28145.779220.778136.8354
31.0499-0.5536-0.0601-0.0203-0.42180.6049-0.2785-0.08220.83030.02940.1610.0417-0.1120.00560.09390.3333-0.0125-0.00210.2351-0.21140.56023.89730.538335.4143
42.27050.1360.7335-0.5971-0.22420.7607-0.0429-0.13651.7298-0.0960.00460.2528-0.1620.03330.04920.3399-0.04490.00530.2209-0.15930.98712.422637.981128.8252
50.3618-0.59230.01070.51660.350.8497-0.22120.01081.1989-0.13360.0861-0.0418-0.09580.06760.08710.3599-0.0332-0.00270.14310.09980.87231.776340.728919.1934
60.71370.172-0.07071.07690.35651.2644-0.09430.56431.1385-0.09450.08430.0283-0.08060.1345-0.00440.3523-0.0062-0.00260.28080.29010.80752.178737.92569.5756
70.0576-0.692-0.60220.86470.1290.8679-0.00560.56620.2379-0.0966-0.016-0.16830.0431-0.01160.03020.3563-0.04390.00540.50490.26910.46343.560730.4482.9732
82.0906-0.1982-0.43620.7254-0.30831.0076-0.27460.91730.6129-0.12440.1626-0.0244-0.00190.23180.10040.3213-0.03490.01530.57620.13480.34365.397720.6951.5451
90.689-0.37330.4520.64960.01870.6553-0.25950.48370.0214-0.0460.0907-0.0586-0.01540.15670.10370.3271-0.02590.03650.4431-0.01920.28937.161511.74065.6764
101.8669-1.27640.14420.28910.13261.2123-0.12430.2185-0.2665-0.05160.107-0.15770.0620.2056-0.01990.32480.02580.03490.2862-0.05660.38498.27986.465314.1721
111.1803-0.7126-0.180.27610.44110.5877-0.1726-0.1531-0.31320.04840.07530.08040.04380.06090.08490.31320.02020.00430.23940.09840.37098.3946.424724.209
120.6683-0.1699-0.87620.6013-0.50841.01120.0014-0.28450.1433-0.00530.0338-0.04030.02360.0114-0.02990.28970.0140.00620.1754-0.13450.4052-69.908422.510531.9134
131.24010.05350.20470.9112-0.04391.0350.0363-0.62280.31620.0216-0.0437-0.03440.0355-0.0704-0.00870.2482-0.0073-0.01380.2826-0.0710.2132-68.238314.119537.2551
140.75530.1304-0.04460.64950.05630.8685-0.161-0.1565-0.1385-0.01910.0907-0.00840.0701-0.19740.05930.2828-0.0214-0.01250.23210.07010.211-66.36494.268537.122
15-0.00520.7113-0.3166-0.0241-0.06090.9553-0.21570.0482-0.3035-0.06260.12180.01660.1202-0.04140.07070.3224-0.02540.01320.11920.11150.4534-64.8881-3.986231.5549
16-1.26150.6869-0.0460.579-0.20181.0412-0.0720.2736-0.1332-0.10690.082-0.0563-0.0419-0.0692-0.01680.333-0.0170.00680.1591-0.01620.4834-64.2384-7.946622.3794
17-0.30990.01290.25140.4617-0.22771.3496-0.07560.1611-0.2738-0.19680.0620.08150.0677-0.0339-0.00540.3561-0.0440.01120.2184-0.10770.4255-64.645-6.475412.4837
180.5404-0.72640.12390.7064-0.0620.3395-0.0750.7937-0.2225-0.11360.0785-0.0107-0.0034-0.1602-0.03870.3348-0.08460.00270.5233-0.10480.2155-65.96450.04694.9472
190.5175-0.4634-0.23890.5824-0.01460.5408-0.16060.94780.0718-0.11020.17110.0354-0.0568-0.1411-0.02170.3578-0.0452-0.00150.57580.03930.2224-67.83839.53372.2576
201.48550.0949-0.22740.8737-0.16631.0074-0.23180.72050.5572-0.02430.20260.0181-0.0471-0.21830.00470.3064-0.00340.00020.51740.15130.3314-69.581318.98165.1414
210.6437-1.1037-0.49480.3838-0.11891.11420.00660.23890.7072-0.0409-0.00930.1705-0.059-0.0497-0.04120.32210.0316-0.02040.26660.15150.5778-70.730625.331412.8576
222.108-0.1948-0.21460.3684-0.23041.3429-0.197-0.09781.19920.04520.1046-0.1228-0.1154-0.10580.0580.3270.0373-0.01030.1158-0.03280.6042-70.829126.665722.8215
230.8613-0.59210.68621.15490.50530.7171-0.0339-0.8412-0.37330.09280.06220.0718-0.03-0.0279-0.01060.27920.0372-0.02290.3580.21420.292233.800678.67460.1167
241.7804-0.53120.17510.7613-0.2340.24980.0445-1.03910.01520.072-0.07360.0081-0.02870.04670.00940.3444-0.0352-0.02180.54710.08070.275532.104587.602664.473
252.8666-0.24491.2540.3394-0.20681.0237-0.0869-0.87460.19850.0494-0.00470.0428-0.11820.01260.05570.3362-0.0352-0.00510.428-0.07040.30330.204297.404363.2502
26-0.1790.3157-0.50990.8902-0.1380.9899-0.155-0.18050.6278-0.07580.06390.0454-0.12070.05130.04780.3505-0.0355-0.00760.2398-0.0980.460528.7267104.968756.8009
270.71970.5223-0.15890.21870.04150.5996-0.0173-0.11790.8124-0.0656-0.01060.2201-0.11060.00870.04050.3986-0.0661-0.03830.20090.01060.535628.0925107.936247.2214
280.30360.4401-0.47860.78490.23670.3503-0.04670.20330.1885-0.10870.0690.00650.0094-0.0389-0.01020.344-0.0375-0.02590.22280.13580.420928.4973105.312237.559
29-0.8441-0.195-1.28971.2852-0.23780.3033-0.09910.5062-0.1095-0.03160.0721-0.0194-0.0054-0.0593-0.00090.3155-0.0677-0.00670.40860.09540.250929.875397.974830.8369
301.6077-0.4319-0.32110.83610.08830.8157-0.17450.6787-0.0264-0.03460.12990.12270.04520.06190.03660.3122-0.0397-0.00590.3364-0.01750.221231.735188.253129.1773
310.9082-0.26580.3480.21940.23150.8055-0.15720.1801-0.684-0.06310.0756-0.02320.08650.10180.04990.3749-0.01860.01160.322-0.11920.492833.505979.215433.0961
320.5699-0.18340.0873-0.00730.0960.5815-0.26310.0771-0.6020.08010.13810.0170.08650.03140.08790.34910.00860.01990.1939-0.00750.66934.6373.747741.5114
331.34970.4062-0.64210.4560.02191.2287-0.1585-0.3889-0.89480.00350.09820.07270.04910.1610.02990.3350.0381-0.00170.23480.11550.641634.724973.540751.5459
341.0595-0.6969-0.64070.6404-0.27990.54660.0119-0.5108-0.03780.0510.05050.0001-0.0098-0.0597-0.05650.29080.0077-0.0150.3413-0.00570.2696-43.615489.485259.5979
351.6667-0.6048-0.3091.21350.36020.5489-0.0038-0.997-0.50250.0617-0.0012-0.05930.1151-0.04680.01880.3083-0.0128-0.03710.48240.16940.2211-41.922280.992564.7598
360.0394-0.5846-0.01671.03780.21.4652-0.0937-0.8856-0.61590.10250.0606-0.00430.1852-0.0156-0.01510.33150.00860.0150.47160.30240.5596-40.039471.110364.4031
370.6220.1385-0.919-0.08810.12681.168-0.1668-0.2769-1.55690.01850.0434-0.13340.216-0.13260.08290.3506-0.0254-0.00750.33060.26830.9872-38.510162.985558.701
38-0.33430.21390.35180.8364-0.2041.2445-0.1687-0.2998-1.1062-0.13030.09840.19880.2182-0.18930.08520.3553-0.0601-0.00160.17290.08851.0223-37.911959.171449.4333
39-0.11140.39790.35160.7271-0.11211.3251-0.06890.3112-0.9838-0.00510.12950.06720.1394-0.107-0.10530.3042-0.0589-0.02470.2098-0.16361.0778-38.31960.864339.5343
400.4964-0.93320.880.91310.2030.98150.06080.1622-0.732-0.0345-0.09350.10550.06130.03290.02980.3265-0.04270.00480.2785-0.22560.6384-39.659267.521432.174
412.0543-0.0050.49020.61910.25691.0346-0.07490.6904-0.6302-0.02840.0171-0.09880.01-0.14190.03470.2827-0.0282-0.03810.4389-0.11120.3639-41.497677.044929.674
422.5740.6732-0.45441.14760.10960.8568-0.12750.7657-0.1077-0.04180.07880.05160.0193-0.13770.06560.2933-0.0183-0.02890.34890.04640.2854-43.253686.46732.759
432.3745-1.55270.04330.32090.13321.4372-0.14220.07010.28560.02110.06220.1163-0.0689-0.16940.06920.27810.0113-0.01430.18260.05690.283-44.373492.664340.6228
440.2908-0.6022-0.04430.5331-0.24781.4465-0.071-0.35780.17890.01830.0077-0.0146-0.0105-0.14520.03980.30570.0364-0.00880.201-0.01650.3709-44.461493.836550.5957
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L
13X-RAY DIFFRACTION13CHAIN M
14X-RAY DIFFRACTION14CHAIN N
15X-RAY DIFFRACTION15CHAIN O
16X-RAY DIFFRACTION16CHAIN P
17X-RAY DIFFRACTION17CHAIN Q
18X-RAY DIFFRACTION18CHAIN R
19X-RAY DIFFRACTION19CHAIN S
20X-RAY DIFFRACTION20CHAIN T
21X-RAY DIFFRACTION21CHAIN U
22X-RAY DIFFRACTION22CHAIN V
23X-RAY DIFFRACTION23CHAIN a
24X-RAY DIFFRACTION24CHAIN b
25X-RAY DIFFRACTION25CHAIN c
26X-RAY DIFFRACTION26CHAIN d
27X-RAY DIFFRACTION27CHAIN e
28X-RAY DIFFRACTION28CHAIN f
29X-RAY DIFFRACTION29CHAIN g
30X-RAY DIFFRACTION30CHAIN h
31X-RAY DIFFRACTION31CHAIN i
32X-RAY DIFFRACTION32CHAIN j
33X-RAY DIFFRACTION33CHAIN k
34X-RAY DIFFRACTION34CHAIN l
35X-RAY DIFFRACTION35CHAIN m
36X-RAY DIFFRACTION36CHAIN n
37X-RAY DIFFRACTION37CHAIN o
38X-RAY DIFFRACTION38CHAIN p
39X-RAY DIFFRACTION39CHAIN q
40X-RAY DIFFRACTION40CHAIN r
41X-RAY DIFFRACTION41CHAIN s
42X-RAY DIFFRACTION42CHAIN t
43X-RAY DIFFRACTION43CHAIN u
44X-RAY DIFFRACTION44CHAIN v

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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

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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

+
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