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- PDB-2jd7: Crystal Structure of the Fe-soaked Ferritin from the Hyperthermop... -

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基本情報

登録情報
データベース: PDB / ID: 2jd7
タイトルCrystal Structure of the Fe-soaked Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus furiosus
要素FERRITIN HOMOLOG
キーワードMETAL TRANSPORT / IRON / PORES / FERRITIN / ARCHAEON / ENTRY CHANNELS / THERMOSTABILITY / HYPERTHERMOPHILE / FERROXIDASE CENTER METAL TRANSPORT
機能・相同性
機能・相同性情報


ferroxidase activity / intracellular sequestering of iron ion / ferric iron binding / ferrous iron binding / iron ion transport / cytosol
類似検索 - 分子機能
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
: / Ferritin homolog
類似検索 - 構成要素
生物種PYROCOCCUS FURIOSUS (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Tatur, J. / Hagen, W.R. / Matias, P.M.
引用
ジャーナル: J.Biol.Inorg.Chem. / 年: 2007
タイトル: Crystal Structure of the Ferritin from the Hyperthermophilic Archaeal Anaerobe Pyrococcus Furiosus
著者: Tatur, J. / Hagen, W.R. / Matias, P.M.
#1: ジャーナル: Acta Crystallogr.,Sect.F / 年: 2005
タイトル: Crystallization and Preliminary X-Ray Characterization of a Ferritin from the Hyperthermophilic Archaeon and Anaerobe Pyrococcus Furiosus
著者: Matias, P.M. / Tatur, J. / Carrondo, M.A. / Hagen, W.R.
履歴
登録2007年1月5日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02007年2月27日Provider: repository / タイプ: Initial release
改定 1.12011年5月8日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32023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_ncs_dom_lim / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

ダウンロードとリンク

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集合体

登録構造単位
0: FERRITIN HOMOLOG
1: FERRITIN HOMOLOG
2: FERRITIN HOMOLOG
3: FERRITIN HOMOLOG
4: FERRITIN HOMOLOG
5: FERRITIN HOMOLOG
6: FERRITIN HOMOLOG
7: FERRITIN HOMOLOG
8: FERRITIN HOMOLOG
9: FERRITIN HOMOLOG
A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
G: FERRITIN HOMOLOG
H: FERRITIN HOMOLOG
I: FERRITIN HOMOLOG
J: FERRITIN HOMOLOG
K: FERRITIN HOMOLOG
L: FERRITIN HOMOLOG
M: FERRITIN HOMOLOG
N: FERRITIN HOMOLOG
O: FERRITIN HOMOLOG
P: FERRITIN HOMOLOG
Q: FERRITIN HOMOLOG
R: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
Y: FERRITIN HOMOLOG
Z: FERRITIN HOMOLOG
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)740,521170
ポリマ－731,99236
非ポリマー8,529134
水6,630368
1
0: FERRITIN HOMOLOG
1: FERRITIN HOMOLOG
2: FERRITIN HOMOLOG
3: FERRITIN HOMOLOG
4: FERRITIN HOMOLOG
5: FERRITIN HOMOLOG
6: FERRITIN HOMOLOG
7: FERRITIN HOMOLOG
8: FERRITIN HOMOLOG
9: FERRITIN HOMOLOG
G: FERRITIN HOMOLOG
H: FERRITIN HOMOLOG
I: FERRITIN HOMOLOG
J: FERRITIN HOMOLOG
K: FERRITIN HOMOLOG
L: FERRITIN HOMOLOG
M: FERRITIN HOMOLOG
N: FERRITIN HOMOLOG
O: FERRITIN HOMOLOG
P: FERRITIN HOMOLOG
Q: FERRITIN HOMOLOG
R: FERRITIN HOMOLOG
Y: FERRITIN HOMOLOG
Z: FERRITIN HOMOLOG
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)493,457111
ポリマ－487,99524
非ポリマー5,46287
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PQS
2
A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
ヘテロ分子

A: FERRITIN HOMOLOG
B: FERRITIN HOMOLOG
C: FERRITIN HOMOLOG
D: FERRITIN HOMOLOG
E: FERRITIN HOMOLOG
F: FERRITIN HOMOLOG
S: FERRITIN HOMOLOG
T: FERRITIN HOMOLOG
U: FERRITIN HOMOLOG
V: FERRITIN HOMOLOG
W: FERRITIN HOMOLOG
X: FERRITIN HOMOLOG
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)494,129118
ポリマ－487,99524
非ポリマー6,13494
水43224
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
手法PQS
単位格子
Length a, b, c (Å)254.301, 342.878, 266.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X
251Y
261Z
2710
2811
2912
3013
3114
3215
3316
3417
3518
3619

NCSドメイン領域:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLUAK1717
21GLUGLUGLUGLUBL1717
31GLUGLUGLUGLUCM1717
41GLUGLUGLUGLUDN1717
51GLUGLUGLUGLUEO1717
61GLUGLUGLUGLUFP1717
71GLUGLUGLUGLUGQ1717
81GLUGLUGLUGLUHR1717
91GLUGLUGLUGLUIS1717
101GLUGLUGLUGLUJT1717
111GLUGLUGLUGLUKU1717
121GLUGLUGLUGLULV1717
131GLUGLUGLUGLUMW1717
141GLUGLUGLUGLUNX1717
151GLUGLUGLUGLUOY1717
161GLUGLUGLUGLUPZ1717
171GLUGLUGLUGLUQAA1717
181GLUGLUGLUGLURBA1717
194GLUGLUGLUGLUSCA1717
204GLUGLUGLUGLUTDA1717
214GLUGLUGLUGLUUEA1717
224GLUGLUGLUGLUVFA1717
234GLUGLUGLUGLUWGA1717
244GLUGLUGLUGLUXHA1717
254GLUGLUGLUGLUYIA1717
264GLUGLUGLUGLUZJA1717
274GLUGLUGLUGLU0A1717
284GLUGLUGLUGLU1B1717
294GLUGLUGLUGLU2C1717
304GLUGLUGLUGLU3D1717
314GLUGLUGLUGLU4E1717
324GLUGLUGLUGLU5F1717
334GLUGLUGLUGLU6G1717
344GLUGLUGLUGLU7H1717
354GLUGLUGLUGLU8I1717
364GLUGLUGLUGLU9J1717
12GLUGLUHISHISAK49 - 5349 - 53
22GLUGLUHISHISBL49 - 5349 - 53
32GLUGLUHISHISCM49 - 5349 - 53
42GLUGLUHISHISDN49 - 5349 - 53
52GLUGLUHISHISEO49 - 5349 - 53
62GLUGLUHISHISFP49 - 5349 - 53
72GLUGLUHISHISGQ49 - 5349 - 53
82GLUGLUHISHISHR49 - 5349 - 53
92GLUGLUHISHISIS49 - 5349 - 53
102GLUGLUHISHISJT49 - 5349 - 53
112GLUGLUHISHISKU49 - 5349 - 53
122GLUGLUHISHISLV49 - 5349 - 53
132GLUGLUHISHISMW49 - 5349 - 53
142GLUGLUHISHISNX49 - 5349 - 53
152GLUGLUHISHISOY49 - 5349 - 53
162GLUGLUHISHISPZ49 - 5349 - 53
172GLUGLUHISHISQAA49 - 5349 - 53
182GLUGLUHISHISRBA49 - 5349 - 53
195GLUGLUHISHISSCA49 - 5349 - 53
205GLUGLUHISHISTDA49 - 5349 - 53
215GLUGLUHISHISUEA49 - 5349 - 53
225GLUGLUHISHISVFA49 - 5349 - 53
235GLUGLUHISHISWGA49 - 5349 - 53
245GLUGLUHISHISXHA49 - 5349 - 53
255GLUGLUHISHISYIA49 - 5349 - 53
265GLUGLUHISHISZJA49 - 5349 - 53
275GLUGLUHISHIS0A49 - 5349 - 53
285GLUGLUHISHIS1B49 - 5349 - 53
295GLUGLUHISHIS2C49 - 5349 - 53
305GLUGLUHISHIS3D49 - 5349 - 53
315GLUGLUHISHIS4E49 - 5349 - 53
325GLUGLUHISHIS5F49 - 5349 - 53
335GLUGLUHISHIS6G49 - 5349 - 53
345GLUGLUHISHIS7H49 - 5349 - 53
355GLUGLUHISHIS8I49 - 5349 - 53
365GLUGLUHISHIS9J49 - 5349 - 53
13GLUGLUGLUGLUAK126 - 130126 - 130
23GLUGLUGLUGLUBL126 - 130126 - 130
33GLUGLUGLUGLUCM126 - 130126 - 130
43GLUGLUGLUGLUDN126 - 130126 - 130
53GLUGLUGLUGLUEO126 - 130126 - 130
63GLUGLUGLUGLUFP126 - 130126 - 130
73GLUGLUGLUGLUGQ126 - 130126 - 130
83GLUGLUGLUGLUHR126 - 130126 - 130
93GLUGLUGLUGLUIS126 - 130126 - 130
103GLUGLUGLUGLUJT126 - 130126 - 130
113GLUGLUGLUGLUKU126 - 130126 - 130
123GLUGLUGLUGLULV126 - 130126 - 130
133GLUGLUGLUGLUMW126 - 130126 - 130
143GLUGLUGLUGLUNX126 - 130126 - 130
153GLUGLUGLUGLUOY126 - 130126 - 130
163GLUGLUGLUGLUPZ126 - 130126 - 130
173GLUGLUGLUGLUQAA126 - 130126 - 130
183GLUGLUGLUGLURBA126 - 130126 - 130
196GLUGLUGLUGLUSCA126 - 130126 - 130
206GLUGLUGLUGLUTDA126 - 130126 - 130
216GLUGLUGLUGLUUEA126 - 130126 - 130
226GLUGLUGLUGLUVFA126 - 130126 - 130
236GLUGLUGLUGLUWGA126 - 130126 - 130
246GLUGLUGLUGLUXHA126 - 130126 - 130
256GLUGLUGLUGLUYIA126 - 130126 - 130
266GLUGLUGLUGLUZJA126 - 130126 - 130
276GLUGLUGLUGLU0A126 - 130126 - 130
286GLUGLUGLUGLU1B126 - 130126 - 130
296GLUGLUGLUGLU2C126 - 130126 - 130
306GLUGLUGLUGLU3D126 - 130126 - 130
316GLUGLUGLUGLU4E126 - 130126 - 130
326GLUGLUGLUGLU5F126 - 130126 - 130
336GLUGLUGLUGLU6G126 - 130126 - 130
346GLUGLUGLUGLU7H126 - 130126 - 130
356GLUGLUGLUGLU8I126 - 130126 - 130
366GLUGLUGLUGLU9J126 - 130126 - 130
17GLUGLUGLUGLUAK9494
27GLUGLUGLUGLUBL9494
37GLUGLUGLUGLUCM9494
47GLUGLUGLUGLUDN9494
57GLUGLUGLUGLUEO9494
67GLUGLUGLUGLUFP9494
77GLUGLUGLUGLUGQ9494
87GLUGLUGLUGLUHR9494
97GLUGLUGLUGLUIS9494
107GLUGLUGLUGLUJT9494
117GLUGLUGLUGLUKU9494
127GLUGLUGLUGLULV9494
137GLUGLUGLUGLUMW9494
147GLUGLUGLUGLUNX9494
157GLUGLUGLUGLUOY9494
167GLUGLUGLUGLUPZ9494
177GLUGLUGLUGLUQAA9494
187GLUGLUGLUGLURBA9494
198GLUGLUGLUGLUSCA9494
208GLUGLUGLUGLUTDA9494
218GLUGLUGLUGLUUEA9494
228GLUGLUGLUGLUVFA9494
238GLUGLUGLUGLUWGA9494
248GLUGLUGLUGLUXHA9494
258GLUGLUGLUGLUYIA9494
268GLUGLUGLUGLUZJA9494
278GLUGLUGLUGLU0A9494
288GLUGLUGLUGLU1B9494
298GLUGLUGLUGLU2C9494
308GLUGLUGLUGLU3D9494
318GLUGLUGLUGLU4E9494
328GLUGLUGLUGLU5F9494
338GLUGLUGLUGLU6G9494
348GLUGLUGLUGLU7H9494
358GLUGLUGLUGLU8I9494
368GLUGLUGLUGLU9J9494
19FEFEFEFEATB - VB201 - 203
29FEFEFEFEBXB - ZB201 - 203
39FEFEFEFECCC - EC201 - 203
49FEFEFEFEDIC - KC201 - 203
59FEFEFEFEELC - NC201 - 203
69FEFEFEFEFOC - QC201 - 203
79FEFEFEFEGRC - TC201 - 203
89FEFEFEFEHWC - YC201 - 203
99FEFEFEFEIAD - CD201 - 203
109FEFEFEFEJFD - HD201 - 203
119FEFEFEFEKJD - LD201 - 203
129FEFEFEFELMD - OD201 - 203
139FEFEFEFEMPD - RD201 - 203
149FEFEFEFENSD - UD201 - 203
159FEFEFEFEOVD - XD201 - 203
169FEFEFEFEPZD - BE201 - 203
179FEFEFEFEQCE - EE201 - 203
189FEFEFEFERFE - HE201 - 203
1910FEFEFEFESJE - LE201 - 203
2010FEFEFEFETNE - PE201 - 203
2110FEFEFEFEURE - TE201 - 203
2210FEFEFEFEVUE - WE201 - 203
2310FEFEFEFEWZE - BF201 - 203
2410FEFEFEFEXDF - FF201 - 203
2510FEFEFEFEYGF - IF201 - 203
2610FEFEFEFEZLF - NF201 - 203
2710FEFEFEFE0KA - MA201 - 203
2810FEFEFEFE1NA - PA201 - 203
2910FEFEFEFE2RA - TA201 - 203
3010FEFEFEFE3VA - XA201 - 203
3110FEFEFEFE4AB - CB201 - 203
3210FEFEFEFE5DB - FB201 - 203
3310FEFEFEFE6GB - IB201 - 203
3410FEFEFEFE7JB - LB201 - 203
3510FEFEFEFE8MB - OB201 - 203
3610FEFEFEFE9QB - SB201 - 203

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要素

#1: タンパク質 ...
FERRITIN HOMOLOG / FERRITIN


分子量: 20333.123 Da / 分子数: 36 / 由来タイプ: 組換発現 / 由来: (組換発現) PYROCOCCUS FURIOSUS (古細菌) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: Q8U2T8
#2: 化合物...
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 108 / 由来タイプ: 合成 / 式: Fe
#3: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 26 / 由来タイプ: 合成 / 式: SO4
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 368 / 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: 4 Å3/Da / 溶媒含有率: 69 %
結晶化詳細: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 ...詳細: THE CRYSTALS USED FOR DATA COLLECTION WERE GROWN AGAINST 0.5 ML OF 2 M AMMONIUM SULPHATE RESERVOIR SOLUTION, WITH DROPS CONTAINING 2 MICRO-L OF 5 MG/ML PROTEIN SOLUTION IN 50 MM HEPES, PH 7 AND EQUAL AMOUNT OF THE RESERVOIR SOLUTION. IRON SOAKING OF FERRITIN CRYSTALS WAS PERFORMED BY TRANSFERRING THEM TO A 10-20 MICRO-L DROP OF A SOLUTION WITH COMPOSITION 20 MM FESO4, 2 MM NA2S2O4, 25 % GLYCEROL AND 2 M AMMONIUM SULFATE, FOR 15 MINUTES.

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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: BM14 / 波長: 1.4585
検出器タイプ: MARRSEARCH / 検出器: CCD / 日付: 2006年6月25日 / 詳細: COLLIMATING AND FOCUSSING MIRRO
放射モノクロメーター: CHANNEL-CUT SI(111) / 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: 1.4585 Å / 相対比: 1
反射解像度: 2.8→42 Å / Num. obs: 280407 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / 冗長度: 3.6 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.2
反射 シェル解像度: 2.8→2.95 Å / 冗長度: 2.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 94.1

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解析

ソフトウェア
名称バージョン分類
REFMAC5.3.0021精密化
MOSFLMデータ削減
SCALA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: REFINED 2JD6 COORDINATES

2jd6


解像度: 2.8→204.12 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.01 / SU ML: 0.219 / 交差検証法: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.311 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: ELECTRON DENSITY FOR C-TERMINAL RESIDU BEYOND 167 (667) WAS NOT VISIBLE.
Rfactor反射数%反射Selection details
Rfree0.25 14187 5.1 %RANDOM
Rwork0.199 ---
obs0.201 266173 99.1 %-
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 39.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2---1.4 Å20 Å2
3----0.11 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→204.12 Å
タンパク質核酸リガンド溶媒全体
原子数49788 0 238 368 50394
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02251170
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.97868946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46955982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27124.7362667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.208159363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.23915252
X-RAY DIFFRACTIONr_chiral_restr0.1010.26987
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0239300
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.225167
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.234930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21605
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.084330917
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3744.548006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.847623570
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.241920937
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / 数: 208 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDタイプRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.050.05
9Itight positional0.050.05
10Jtight positional0.050.05
11Ktight positional0.050.05
12Ltight positional0.050.05
13Mtight positional0.050.05
14Ntight positional0.050.05
15Otight positional0.050.05
16Ptight positional0.050.05
17Qtight positional0.050.05
18Rtight positional0.050.05
19Stight positional0.050.05
20Ttight positional0.050.05
21Utight positional0.050.05
22Vtight positional0.050.05
23Wtight positional0.050.05
24Xtight positional0.050.05
25Ytight positional0.050.05
26Ztight positional0.050.05
270tight positional0.050.05
281tight positional0.050.05
292tight positional0.050.05
303tight positional0.050.05
314tight positional0.050.05
325tight positional0.050.05
336tight positional0.050.05
347tight positional0.050.05
358tight positional0.050.05
369tight positional0.050.05
1Atight thermal0.190.5
2Btight thermal0.180
3Ctight thermal0.190
4Dtight thermal0.160
5Etight thermal0.210
6Ftight thermal0.170
7Gtight thermal0.190
8Htight thermal0.240
9Itight thermal0.150
10Jtight thermal0.130
11Ktight thermal0.170
12Ltight thermal0.120
13Mtight thermal0.180
14Ntight thermal0.160
15Otight thermal0.230
16Ptight thermal0.180
17Qtight thermal0.150
18Rtight thermal0.180
19Stight thermal0.190.5
20Ttight thermal0.180
21Utight thermal0.190
22Vtight thermal0.160
23Wtight thermal0.210
24Xtight thermal0.170
25Ytight thermal0.190
26Ztight thermal0.240
270tight thermal0.150
281tight thermal0.130
292tight thermal0.170
303tight thermal0.120
314tight thermal0.180
325tight thermal0.160
336tight thermal0.230
347tight thermal0.180
358tight thermal0.150
369tight thermal0.180
LS精密化 シェル解像度: 2.8→2.87 Å / Total num. of bins used: 20 /
Rfactor反射数
Rfree0.375 983
Rwork0.314 17823

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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

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