[日本語] English
万見
- PDB-7jj8: Crystal structure of the Zn(II)-bound ZnuA-like domain of Strepto... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7jj8
タイトルCrystal structure of the Zn(II)-bound ZnuA-like domain of Streptococcus pneumoniae AdcA
要素Zinc-binding lipoprotein AdcA
キーワードMETAL BINDING PROTEIN / AdcA / ZnuA / SBP / ATP-binding cassette transporter / Zn acquisition
機能・相同性
機能・相同性情報


zinc ion transport / establishment of competence for transformation / cell adhesion / zinc ion binding / plasma membrane
類似検索 - 分子機能
ZinT domain / ZinT (YodA) periplasmic lipocalin-like zinc-recruitment / Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Calycin / Prokaryotic membrane lipoprotein lipid attachment site profile.
類似検索 - ドメイン・相同性
Zinc-binding lipoprotein AdcA
類似検索 - 構成要素
生物種Streptococcus pneumoniae (肺炎レンサ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.03 Å
データ登録者Luo, Z. / More, J.R. / Kobe, B. / McDevitt, C.A.
資金援助 オーストラリア, 4件
組織認可番号国
National Health and Medical Research Council (NHMRC, Australia)1071659 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)1080784 オーストラリア
National Health and Medical Research Council (NHMRC, Australia)1122582 オーストラリア
Australian Research Council (ARC)DP170102102 オーストラリア
引用ジャーナル: Mbio / 年: 2021
タイトル: A Trap-Door Mechanism for Zinc Acquisition by Streptococcus pneumoniae AdcA.
著者: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / ...著者: Luo, Z. / Morey, J.R. / Deplazes, E. / Motygullina, A. / Tan, A. / Ganio, K. / Neville, S.L. / Eleftheriadis, N. / Isselstein, M. / Pederick, V.G. / Paton, J.C. / Cordes, T. / Harmer, J.R. / Kobe, B. / McDevitt, C.A.
履歴
登録2020年7月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年12月23日Provider: repository / タイプ: Initial release
改定 1.12021年3月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
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

-
集合体

登録構造単位
B: Zinc-binding lipoprotein AdcA
A: Zinc-binding lipoprotein AdcA
C: Zinc-binding lipoprotein AdcA
D: Zinc-binding lipoprotein AdcA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)133,0748
ポリマ－132,8124
非ポリマー2624
水8,323462
1
B: Zinc-binding lipoprotein AdcA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,2682
ポリマ－33,2031
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
2
A: Zinc-binding lipoprotein AdcA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,2682
ポリマ－33,2031
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
3
C: Zinc-binding lipoprotein AdcA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,2682
ポリマ－33,2031
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
D: Zinc-binding lipoprotein AdcA
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)33,2682
ポリマ－33,2031
非ポリマー651
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
Length a, b, c (Å)60.372, 67.956, 79.622
Angle α, β, γ (deg.)92.275, 104.697, 115.959
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYSERSER(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB27 - 681 - 42
12ALAALAGLNGLN(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB71 - 7645 - 50
13ALAALAPROPRO(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB78 - 9352 - 67
14LEULEULEULEU(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB95 - 9969 - 73
15LYSLYSGLYGLY(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB102 - 11876 - 92
16PHEPHELYSLYS(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB137 - 167111 - 141
17THRTHRGLNGLN(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB169 - 194143 - 168
18GLNGLNASPASP(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB197 - 227171 - 201
19PROPROLYSLYS(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB230 - 243204 - 217
110ASNASNSERSER(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB245 - 265219 - 239
111GLUGLUTHRTHR(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB267 - 282241 - 256
112ASPASPTHRTHR(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB285 - 286259 - 260
113ALAALAASPASP(chain A and (resseq 27:69 or resseq 71:76 or resseq...AB288 - 308262 - 282
21GLYGLYSERSER(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA27 - 681 - 42
22ALAALAGLNGLN(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA71 - 7645 - 50
23ALAALAPROPRO(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA78 - 9352 - 67
24LEULEULEULEU(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA95 - 9969 - 73
25LYSLYSGLYGLY(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA102 - 11876 - 92
26PHEPHELYSLYS(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA137 - 167111 - 141
27THRTHRGLNGLN(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA169 - 194143 - 168
28GLNGLNASPASP(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA197 - 227171 - 201
29PROPROLYSLYS(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA230 - 243204 - 217
210ASNASNSERSER(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA245 - 265219 - 239
211GLUGLUTHRTHR(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA267 - 282241 - 256
212ASPASPTHRTHR(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA285 - 286259 - 260
213ALAALAASPASP(chain B and (resseq 27:69 or resseq 71:76 or resseq...BA288 - 308262 - 282
31GLYGLYSERSER(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC27 - 681 - 42
32ALAALAGLNGLN(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC71 - 7645 - 50
33ALAALAPROPRO(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC78 - 9352 - 67
34LEULEULEULEU(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC95 - 9969 - 73
35LYSLYSGLYGLY(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC102 - 11876 - 92
36PHEPHELYSLYS(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC137 - 167111 - 141
37THRTHRGLNGLN(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC169 - 194143 - 168
38GLNGLNASPASP(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC197 - 227171 - 201
39PROPROLYSLYS(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC230 - 243204 - 217
310ASNASNSERSER(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC245 - 265219 - 239
311GLUGLUTHRTHR(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC267 - 282241 - 256
312ASPASPTHRTHR(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC285 - 286259 - 260
313ALAALAASPASP(chain C and (resseq 27:69 or resseq 71:76 or resseq...CC288 - 308262 - 282
41GLYGLYSERSER(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD27 - 681 - 42
42ALAALAGLNGLN(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD71 - 7645 - 50
43ALAALAPROPRO(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD78 - 9352 - 67
44LEULEULEULEU(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD95 - 9969 - 73
45LYSLYSGLYGLY(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD102 - 11876 - 92
46PHEPHELYSLYS(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD137 - 167111 - 141
47THRTHRGLNGLN(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD169 - 194143 - 168
48GLNGLNASPASP(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD197 - 227171 - 201
49PROPROLYSLYS(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD230 - 243204 - 217
410ASNASNSERSER(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD245 - 265219 - 239
411GLUGLUTHRTHR(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD267 - 282241 - 256
412ASPASPTHRTHR(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD285 - 286259 - 260
413ALAALAASPASP(chain D and (resseq 27:69 or resseq 71:76 or resseq...DD288 - 308262 - 282

-
要素

#1: タンパク質
Zinc-binding lipoprotein AdcA


分子量: 33202.992 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (肺炎レンサ球菌)
株: ATCC BAA-255 / R6 / 遺伝子: adcA, spr1975 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q8CWN2
#2: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 462 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 2.11 Å3/Da / 溶媒含有率: 41.61 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M imidazole-MES, pH 6.5

-
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: Australian Synchrotron / ビームライン: MX1 / 波長: 0.954 Å
検出器タイプ: ADSC QUANTUM 210r / 検出器: CCD / 日付: 2015年5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: 0.954 Å / 相対比: 1
反射解像度: 2.03→19.36 Å / Num. obs: 68710 / % possible obs: 98.2 % / 冗長度: 3.9 % / Biso Wilson estimate: 28.9744951541 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.6
反射 シェル解像度: 2.03→2.1 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 6809 / CC1/2: 0.66

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
XDSデータスケーリング
PHASER位相決定
PHENIXモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 2OSV

2osv


解像度: 2.03→19.36 Å / SU ML: 0.233246804048 / 交差検証法: FREE R-VALUE / σ(F): 1.89478673062 / 位相誤差: 22.5871299159
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.212820796565 1999 2.90987961629 %
Rwork0.169005718258 66698 -
obs0.170294108042 68697 98.1582030692 %
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
原子変位パラメータBiso mean: 36.10957472 Å2
精密化ステップサイクル: LAST / 解像度: 2.03→19.36 Å
タンパク質核酸リガンド溶媒全体
原子数8352 0 4 462 8818
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.007405612004638504
X-RAY DIFFRACTIONf_angle_d0.9787315466211520
X-RAY DIFFRACTIONf_chiral_restr0.05672723030751320
X-RAY DIFFRACTIONf_plane_restr0.006510314078421476
X-RAY DIFFRACTIONf_dihedral_angle_d16.56781508315200
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.10.3017213507491420.2542472875344709X-RAY DIFFRACTION97.00059988
2.0808-2.13690.3224890658521430.2308819395034771X-RAY DIFFRACTION97.5774424146
2.1369-2.19970.2557554448921410.2117649565614704X-RAY DIFFRACTION97.2696245734
2.1997-2.27060.291710375771410.2119476488924766X-RAY DIFFRACTION97.5546719682
2.2706-2.35170.24421716281420.2006910888074718X-RAY DIFFRACTION97.9049153908
2.3517-2.44560.2332194163521410.1881530383114737X-RAY DIFFRACTION97.8339350181
2.4456-2.55670.2266741007871430.1778673048844755X-RAY DIFFRACTION98.2744783307
2.5567-2.69120.2177543684671430.1753129008694752X-RAY DIFFRACTION98.1552035292
2.6912-2.85930.2377891829231440.1875209108924821X-RAY DIFFRACTION98.5314546537
2.8593-3.07920.2267558954121430.1774554740484782X-RAY DIFFRACTION98.6183420104
3.0792-3.38760.2112445187091440.1639871987354789X-RAY DIFFRACTION98.7785342411
3.3876-3.87440.1908129263681440.1506875374944770X-RAY DIFFRACTION98.8135934044
3.8744-4.86850.1710759883041440.1296986871214824X-RAY DIFFRACTION98.8656716418
4.8685-19.35830.175922869151440.1539621814814800X-RAY DIFFRACTION99.0583049489
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)
11.84248237495-0.6268715927020.4409726632490.848287768621-0.3949966225830.7555892131370.01099522500740.0632546422239-0.0775904682570.00296862958667-0.0532589079162-0.0947465303299-0.05197758999610.1343413256330.0004038310182240.1719159524740.002173874624910.02005408107530.1693584579750.007821726100350.189639339949-23.310494121890.856036469165.3532577361
21.436796603390.4109632102-0.201942943930.58087056068-0.1331316303530.6200812869870.0264562129404-0.0343048877044-0.103375669227-0.0153751513947-0.0004335644725470.06029362434630.0809655619638-0.04873033353435.44600338375E-50.1971802324270.005946668412860.001115283147750.1727084070120.003464623876160.183363865858-48.934776486687.874658639165.7888183887
30.114706028629-0.0290015719095-0.02719532856340.1624905897020.009841093552980.0293224690819-0.0123170363103-0.04643506964480.224633499353-0.01244245471110.0349104652697-0.0663611059598-0.389486246991-0.0155983711019-9.86988951664E-50.2855582390910.0790365755693-0.02293135890170.272504310025-0.03569070668730.350753737869-41.914309520863.600645562775.8514845829
40.1472010929470.007160494057760.007426111694990.124685198377-0.05476036380080.240752180566-0.00646518851133-0.7151787413020.2559525395280.06271311726080.138887048977-0.057954505546-0.08514949330020.13765603665-0.001117502262710.3382853922540.07058451175830.03937073942760.374111055882-0.0606552320070.329721724677-37.548990298859.596419334889.7465362264
50.2469290222130.0669286269234-0.08642587897450.1716765574930.09805231336040.356984430504-0.0118524173476-0.0171338002616-0.107316979577-0.07743034612-0.07434276200290.229996293033-0.0293558131883-0.149808909711-0.0002010420677410.2408502746150.0352049540183-0.0004163669971660.287971766992-0.04073282040860.376124955769-43.866528725251.323746492182.9009736014
60.103930817395-0.0573668465041-0.1203516481130.08470955179080.08131889793020.129050214746-0.144540891519-0.10216388489-0.09673861087160.0719591502211-0.04515719422720.0142518798749-0.0215290097043-0.004236424427661.43142930283E-50.2312050802490.009864008078890.04050823616510.1983680688810.004078471709040.267527383959-28.254592391746.623400624477.368388028
70.2416652945960.0035145289894-0.04723639299830.3270604718710.3261461776270.754454936260.1598040281070.360369753894-0.078991239126-0.34655515357-0.1844642240880.201318348241-0.189429563107-0.197309367656-0.004545299565770.2904729100950.057048180247-0.08527056635620.315140234401-0.03966825057240.261353088107-38.342948708657.02801173364.8287123517
80.5673344844390.0609567657265-0.1256462944960.1793280791320.05298283623060.0377590980781-0.00360926615134-0.107930641269-0.132174614228-0.0273105405863-0.0005279557956020.01127263671140.03639537791730.116200688037-8.4611583309E-50.1843358646930.009984372212550.01459895784780.1892975743590.002130417084490.164500862494-15.434268970252.069657723776.5498675436
90.402072888726-0.1052891908840.193368262110.05198040427950.05049165293940.3771372826720.0600228931452-0.3140141219260.201952490221-0.1037688672190.0556670299525-0.0255779313150.01901763870410.119284601136.25508857718E-50.2134206020320.004100279854030.01690326153640.290955190038-0.07932839114410.291153469506-5.9902275571157.337648261883.4476916959
100.0300904156096-0.0103497495495-0.02910489174420.443096341740.3626305911720.312339788516-0.060675464962-0.101095633570.223224312487-0.06279330163320.099502214704-0.0518223277447-0.1326539074040.0350513895180.0001301689148840.237402203972-0.01270566104340.01734652851210.195529291355-0.03483356416660.244215505345-19.958251811665.239223231879.1393171108
110.0668696813964-0.02584183102080.1069569241930.0937763672682-0.007545324111120.194444131339-0.02646488137970.3554299960930.579577891902-0.1753859205150.0486499013098-0.137640961655-0.1582174527930.03622798303880.002055919846540.27911894666-0.007794731044390.02101803872710.201881564062-0.002570817110910.228415117084-17.400577883960.762759207268.6423142053
120.987971142559-0.0669672047596-0.1063428158410.788810995559-0.4469846245240.506759270458-0.03011716904580.007491265982830.365680171474-0.0145291028055-0.111245533749-0.0321157201729-0.1233518067210.04714238073160.0006088605450910.257831693425-0.0420857057361-0.02295973560540.235684891420.02726950415560.2926008605977.3049504857264.934553935337.5738709585
130.0506559760125-0.0361152264011-0.0317546164360.097277618703-0.05042018338930.0654644123411-0.04196061777280.07415969934270.209630683258-0.297695877568-0.0877903412712-0.3458714545340.1217144128560.522285686622-0.002984233290460.272625681054-0.01714905986650.06522243111160.3446346115250.0694752268870.32245560659715.524063254860.206027982629.3374387591
140.2162544443630.216695781558-0.06132824673930.190789368581-0.05015424250870.0623407484664-0.122220689020.0889020042902-0.0508267830004-0.06810249417010.0185171197271-0.0407942216977-0.05431194024480.0333806188594-2.62290399725E-50.251466344251-0.0215582000486-0.007672518472980.219090321025-0.002505663821440.201673197392-2.9763780469651.73155381233.0513951933
150.1613262892010.173496005088-0.2303483941430.539917377363-0.3147472421770.3551614523430.0184915040862-0.343718818518-0.2568292989210.0689166065133-0.105891908304-0.1616511680830.001492522162330.1284532873695.69688759262E-50.194411540129-0.000660070783567-0.03077180135610.2146448193320.05126030126930.1924163885334.9625828195351.524050216848.7401341255
160.310092607610.0740020980977-0.05848628805290.1413113366550.09268792595770.0980794148504-0.114619189310.07554481979070.005941939319520.03229339936450.0800605341255-0.0870703834979-0.0518869688403-0.111362980415-0.0005737486080990.2086631970430.00426490192351-0.02076323101810.208372204733-0.006336076580750.209684809695-16.574120678251.567404053238.6506143261
170.179372702937-0.06640018611160.09232381486260.106422228960.008649394824720.0507097036958-0.01441966175560.833760716966-0.306733073138-0.2765047451170.13472903945-0.0167547655712-0.0573770381150.005756845388780.0003847065617550.4271853739410.018331398374-0.05918584028210.3530664837970.05354146061520.434949597327-27.009777763565.040208023729.2074968348
180.195905677188-0.1417386708780.01194887806820.20534880836-0.0559620991610.377893814745-0.0935132732087-0.205083205130.3757794762720.05626924744220.1194682960890.162144221878-0.208541951791-0.2572453099420.006138694258010.258999345820.0526860323213-0.0006429110140270.2042513043680.01304192045110.352818124704-25.649110606466.482392426937.9358744338
190.0808858781698-0.03248738628130.03852306068690.15682064659-0.2057202741340.2443799534230.0935400570012-0.0692375595160.4380907540530.2904827805580.02965964158420.10432802692-0.0651419246357-0.09967320364610.001750544139860.3356327174740.007360850103370.001856012469780.220792933896-0.04674263002080.337852514469-11.099825503667.628391203744.4562222217
200.0350486960289-0.0370429877237-0.01898587476730.0560612217598-0.06076296299130.2756385160010.065958862397-0.409252248250.08170121317510.168571878691-0.034768681530.0830260337066-0.184498695042-0.170184482319-2.92875695388E-60.2686813756870.02771796486810.007617677439150.211841377340.003118985575320.187812348042-15.925215455557.335259449648.0874082334
210.108800286045-0.06599779562790.1409466287680.189626177965-0.01290553253430.1727549498230.143326965469-0.132593031656-0.488267416448-0.0242906270079-0.146350784345-0.0559817007170.340923365868-0.007644727238920.0005518499533870.290447999226-0.0724610540790.01109833790510.267405156123-0.008413992811990.365147056162-32.022082072272.5308187882104.838530522
220.05662179906950.02383691732320.08033527274260.116013880127-0.05946853353160.242143518678-0.1417496214750.258343539995-0.356389718354-0.377889387883-0.0109537502828-0.00583652434760.00503581121518-0.06244892535910.0001190805451310.317485033997-0.0591436544207-0.02910925347330.430723779346-0.07877144294940.381811237904-28.331226771577.146994895690.9236318545
230.212240525445-0.160864934413-0.04067468443020.128262051083-0.0404882120690.376233518802-0.1662111723360.1382056436560.0573819396143-0.1820083818250.08329463219660.0630380756585-0.102695766438-0.242858050671-0.0002779031529620.259412394663-0.0251093764875-0.04893661814770.302303729067-0.02131612465320.292318163675-33.51544933385.003135926596.0003460131
240.15268274862-0.0148038268277-0.0222192146350.2282183176520.3034756198940.351606130581-0.0653639497858-0.0006585347206450.0399692777404-0.0192001953538-0.01956536910070.134207096334-0.115202225397-0.0392140292051-1.8420839933E-50.20612313928-0.0134110864724-0.02700363703950.233956394355-0.02561327870930.254800107346-25.681751887487.7755108655103.449232776
251.04025787949-0.3020984105560.08445660670720.6137947219060.07887795720610.4762526965880.0784445510146-0.5315935417650.05757249930120.31006726569-0.1477094764410.1476449372840.107720107631-0.226910383816-0.1960822148360.257468485956-0.07038754174810.08621354587870.340804792155-0.02152778214680.187330246251-28.249877314178.7338664059116.053401385
260.7142214087910.0189814215263-0.0920909820730.398919525196-0.004188864887230.206003763692-0.0154210462730.04440614590720.102559845977-0.01740194315740.0715948712839-0.0200896663713-0.03239429743780.0540492776066-0.0001297783327240.200737090864-0.0176022173411-0.01040254687940.210293060626-0.01522194973710.194537847312-5.4114460974184.1107597922104.175308646
270.0481035343323-0.0400000314199-0.03637218591160.03085238180640.02587328201450.02504146168140.1780952527360.4723311069840.3057226309910.02169284722680.05654109513210.05902256369250.05653215988110.1348045058980.003179265407230.267374867462-0.031153234327-0.002916188339130.409307100273-0.05258611293850.2501378574167.7383189228185.898872023495.5406095418
280.110331226120.047959569048-0.09938942847160.04294830470930.009970977393220.2038545819570.06003015729720.0208863402101-0.348665442448-0.135011470477-0.05471948282110.0264028701505-0.01779362258710.192082415039-6.6123825768E-50.235614288172-0.00280115887749-0.02049107312680.3320690432-0.03549954660850.2814208027592.2303753095974.966017673597.8628717232
290.110668902871-0.0764968143079-0.09279015718490.115240140023-0.1007773996660.3644635226810.06437879770950.0640684199662-0.1364943866380.05437486441440.04235179158460.1051993578210.2056797456850.112228208667-6.82062891055E-50.263175555562-0.0142672819561-0.02753752961590.2466056870240.004103957721970.249443118495-12.144882527570.157166648102.219137974
300.4157314244370.4935208915180.176841398830.6002680476360.1302058244020.3787133094090.069981144004-0.0117196292137-0.2328388085390.2159072887580.037241225206-0.2422125779070.2895783508990.2565302848260.03591784331860.2187687770310.0306969310601-0.01001279320610.1438958216070.0182386351280.149838341452-7.2983933673975.1939399304111.872602794
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 27 through 192 )
2X-RAY DIFFRACTION2chain 'B' and (resid 193 through 309 )
3X-RAY DIFFRACTION3chain 'A' and (resid 27 through 54 )
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 76 )
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 113 )
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 144 )
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 231 )
9X-RAY DIFFRACTION9chain 'A' and (resid 232 through 266 )
10X-RAY DIFFRACTION10chain 'A' and (resid 267 through 291 )
11X-RAY DIFFRACTION11chain 'A' and (resid 292 through 309 )
12X-RAY DIFFRACTION12chain 'C' and (resid 27 through 91 )
13X-RAY DIFFRACTION13chain 'C' and (resid 92 through 108 )
14X-RAY DIFFRACTION14chain 'C' and (resid 109 through 144 )
15X-RAY DIFFRACTION15chain 'C' and (resid 145 through 192 )
16X-RAY DIFFRACTION16chain 'C' and (resid 193 through 220 )
17X-RAY DIFFRACTION17chain 'C' and (resid 221 through 244 )
18X-RAY DIFFRACTION18chain 'C' and (resid 245 through 268 )
19X-RAY DIFFRACTION19chain 'C' and (resid 269 through 291 )
20X-RAY DIFFRACTION20chain 'C' and (resid 292 through 309 )
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 54 )
22X-RAY DIFFRACTION22chain 'D' and (resid 55 through 76 )
23X-RAY DIFFRACTION23chain 'D' and (resid 77 through 101 )
24X-RAY DIFFRACTION24chain 'D' and (resid 102 through 144 )
25X-RAY DIFFRACTION25chain 'D' and (resid 145 through 192 )
26X-RAY DIFFRACTION26chain 'D' and (resid 193 through 231 )
27X-RAY DIFFRACTION27chain 'D' and (resid 232 through 245 )
28X-RAY DIFFRACTION28chain 'D' and (resid 246 through 268 )
29X-RAY DIFFRACTION29chain 'D' and (resid 269 through 291 )
30X-RAY DIFFRACTION30chain 'D' and (resid 292 through 309 )

+
万見について

-
お知らせ

-
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://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

+
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

+
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。

-
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