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- PDB-6day: Xanthomonas albilineans Dihydropteroate synthase with 4-aminobenz... -

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基本情報

登録情報
データベース: PDB / ID: 6day
タイトルXanthomonas albilineans Dihydropteroate synthase with 4-aminobenzoic acid at 1.65 A
要素Dihydropteroate synthase
キーワードTRANSFERASE / pABA
機能・相同性
機能・相同性情報


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol
類似検索 - 分子機能
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
類似検索 - ドメイン・相同性
4-AMINOBENZOIC ACID / Dihydropteroate synthase
類似検索 - 構成要素
生物種Xanthomonas albilineans GPE PC73 (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: 1.65 Å
データ登録者Oliveira, A.A. / Guido, R.V.C. / Lima, G.M.A. / Bueno, R.V. / Maluf, F.V.
資金援助 ブラジル, 1件
組織認可番号国
Sao Paulo Research Foundation (FAPESP)2015/07005-3 ブラジル
引用ジャーナル: To Be Published
タイトル: Xanthomonas albilineans Dihydropteroate synthase with 4-aminobenzoic acid
著者: Oliveira, A.A. / Guido, R.V.C. / Lima, G.M.A. / Maluf, F.V. / Bueno, R.V.
履歴
登録2018年5月2日登録サイト: RCSB / 処理サイト: RCSB
置き換え2018年6月6日ID: 5UUR
改定 1.02018年6月6日Provider: repository / タイプ: Initial release
改定 1.12020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22023年10月4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
改定 1.32024年12月25日Group: Advisory / Derived calculations / Structure summary
カテゴリ: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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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: Dihydropteroate synthase
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)129,48421
ポリマ－127,5344
非ポリマー1,95017
水11,818656
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-79 kcal/mol
Surface area20710 Å2
手法PISA
2
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,13416
ポリマ－95,6513
非ポリマー1,48313
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-45 kcal/mol
Surface area21620 Å2
手法PISA
単位格子
Length a, b, c (Å)82.589, 75.387, 89.106
Angle α, β, γ (deg.)90.000, 101.102, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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
11SERSERILEILE(chain 'A' and ((resid 5 and (name N or name...AA5 - 255 - 25
12VALVALTHRTHR(chain 'A' and ((resid 5 and (name N or name...AA28 - 2928 - 29
13THRTHRGLYGLY(chain 'A' and ((resid 5 and (name N or name...AA41 - 4941 - 49
14LEULEUGLUGLU(chain 'A' and ((resid 5 and (name N or name...AA52 - 6552 - 65
15VALVALMETMET(chain 'A' and ((resid 5 and (name N or name...AA74 - 14674 - 146
16PROPROILEILE(chain 'A' and ((resid 5 and (name N or name...AA157 - 182157 - 182
17ARGARGPHEPHE(chain 'A' and ((resid 5 and (name N or name...AA185 - 193185 - 193
18GLYGLYLEULEU(chain 'A' and ((resid 5 and (name N or name...AA196 - 237196 - 237
19GLNGLNVALVAL(chain 'A' and ((resid 5 and (name N or name...AA240 - 281240 - 281
21SERSERILEILE(chain 'B' and (resid 5 through 26 or resid 28...BB5 - 255 - 25
22VALVALTHRTHR(chain 'B' and (resid 5 through 26 or resid 28...BB28 - 2928 - 29
23THRTHRGLYGLY(chain 'B' and (resid 5 through 26 or resid 28...BB41 - 4941 - 49
24LEULEUGLUGLU(chain 'B' and (resid 5 through 26 or resid 28...BB52 - 6552 - 65
25VALVALMETMET(chain 'B' and (resid 5 through 26 or resid 28...BB74 - 14674 - 146
26PROPROILEILE(chain 'B' and (resid 5 through 26 or resid 28...BB157 - 182157 - 182
27ARGARGPHEPHE(chain 'B' and (resid 5 through 26 or resid 28...BB185 - 193185 - 193
28GLYGLYLEULEU(chain 'B' and (resid 5 through 26 or resid 28...BB196 - 237196 - 237
29GLNGLNVALVAL(chain 'B' and (resid 5 through 26 or resid 28...BB240 - 281240 - 281
31SERSERILEILE(chain 'C' and ((resid 5 and (name N or name...CC5 - 255 - 25
32VALVALTHRTHR(chain 'C' and ((resid 5 and (name N or name...CC28 - 2928 - 29
33THRTHRGLYGLY(chain 'C' and ((resid 5 and (name N or name...CC41 - 4941 - 49
34LEULEUGLUGLU(chain 'C' and ((resid 5 and (name N or name...CC52 - 6552 - 65
35VALVALMETMET(chain 'C' and ((resid 5 and (name N or name...CC74 - 14674 - 146
36PROPROILEILE(chain 'C' and ((resid 5 and (name N or name...CC157 - 182157 - 182
37ARGARGPHEPHE(chain 'C' and ((resid 5 and (name N or name...CC185 - 193185 - 193
38GLYGLYLEULEU(chain 'C' and ((resid 5 and (name N or name...CC196 - 237196 - 237
39GLNGLNVALVAL(chain 'C' and ((resid 5 and (name N or name...CC240 - 281240 - 281
41SERSERILEILE(chain 'D' and ((resid 5 and (name N or name...DD5 - 255 - 25
42VALVALTHRTHR(chain 'D' and ((resid 5 and (name N or name...DD28 - 2928 - 29
43THRTHRGLYGLY(chain 'D' and ((resid 5 and (name N or name...DD41 - 4941 - 49
44LEULEUGLUGLU(chain 'D' and ((resid 5 and (name N or name...DD52 - 6552 - 65
45VALVALMETMET(chain 'D' and ((resid 5 and (name N or name...DD74 - 14674 - 146
46PROPROILEILE(chain 'D' and ((resid 5 and (name N or name...DD157 - 182157 - 182
47ARGARGPHEPHE(chain 'D' and ((resid 5 and (name N or name...DD185 - 193185 - 193
48GLYGLYLEULEU(chain 'D' and ((resid 5 and (name N or name...DD196 - 237196 - 237
49GLNGLNVALVAL(chain 'D' and ((resid 5 and (name N or name...DD240 - 281240 - 281

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要素

#1: タンパク質
Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase


分子量: 31883.580 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: CTC + Natural source
由来: (組換発現) Xanthomonas albilineans GPE PC73 (バクテリア)
株: GPE PC73 / CFBP 7063 / 遺伝子: folP, XALc_1165 / プラスミド: pETTrx / 詳細 (発現宿主): Thioredoxin + 6xHis / 細胞株 (発現宿主): DE3 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Rosetta 2 / 参照: UniProt: D2UDM3, dihydropteroate synthase
#2: 化合物
ChemComp-PAB / 4-AMINOBENZOIC ACID / 4-アミノ安息香酸


分子量: 137.136 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C7H7NO2
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 6 / 由来タイプ: 合成 / 式: SO4
#4: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C3H8O3
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 656 / 由来タイプ: 天然 / 式: H2O
Has protein modificationN

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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: 2.13 Å3/Da / 溶媒含有率: 42.37 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: Polyethylene glycol 3.350, Bis-tris pH 6.5, Lithium sulfate

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データ収集

回折平均測定温度: 100 K / Ambient temp details: Liquid Nitrogen
放射光源由来: シンクロトロン / サイト: LNLS / ビームライン: W01B-MX2 / 波長: 1.4567 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2014年10月28日
放射モノクロメーター: 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: 1.4567 Å / 相対比: 1
反射解像度: 1.65→32.75 Å / Num. obs: 127875 / % possible obs: 98.95 % / 冗長度: 2 % / Biso Wilson estimate: 23.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02261 / Rpim(I) all: 0.02261 / Rrim(I) all: 0.03197 / Net I/σ(I): 13.89
反射 シェル解像度: 1.65→1.71 Å / 冗長度: 1.9 % / Rmerge(I) obs: 0.2204 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 12436 / CC1/2: 0.937 / Rpim(I) all: 0.2204 / Rrim(I) all: 0.3117 / % possible all: 96.89

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解析

ソフトウェア
名称バージョン分類
PHENIX1.13_2998精密化
XDSデータ削減
Aimless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: 1AJ0

1aj0


解像度: 1.65→32.75 Å / SU ML: 0.1905 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.5706
Rfactor反射数%反射
Rfree0.2161 6370 4.99 %
Rwork0.1775 --
obs0.1794 127623 98.97 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 39.55 Å2
精密化ステップサイクル: LAST / 解像度: 1.65→32.75 Å
タンパク質核酸リガンド溶媒全体
原子数7668 0 128 656 8452
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01077926
X-RAY DIFFRACTIONf_angle_d1.168610818
X-RAY DIFFRACTIONf_chiral_restr0.07441328
X-RAY DIFFRACTIONf_plane_restr0.00771412
X-RAY DIFFRACTIONf_dihedral_angle_d6.31565544
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.32132100.28183881X-RAY DIFFRACTION95.94
1.67-1.690.31642090.26873912X-RAY DIFFRACTION97.22
1.69-1.710.3082190.25283982X-RAY DIFFRACTION97.52
1.71-1.730.34381880.25793935X-RAY DIFFRACTION97.47
1.73-1.750.30832130.24373984X-RAY DIFFRACTION96.79
1.75-1.780.27012300.23093993X-RAY DIFFRACTION99.36
1.78-1.80.28622220.214037X-RAY DIFFRACTION99.14
1.8-1.830.25512380.22244011X-RAY DIFFRACTION99.32
1.83-1.860.26452110.21584051X-RAY DIFFRACTION99.28
1.86-1.890.29992060.20054046X-RAY DIFFRACTION99.53
1.89-1.920.25742040.20144047X-RAY DIFFRACTION99.3
1.92-1.960.25691970.20634067X-RAY DIFFRACTION99.49
1.96-1.990.25191900.19164073X-RAY DIFFRACTION99.53
1.99-2.030.25491790.18734097X-RAY DIFFRACTION99.35
2.03-2.080.23491860.18854053X-RAY DIFFRACTION99.55
2.08-2.130.26151930.17864069X-RAY DIFFRACTION99.44
2.13-2.180.23232300.1794061X-RAY DIFFRACTION99.4
2.18-2.240.20871940.18164083X-RAY DIFFRACTION99.23
2.24-2.310.24792090.18573999X-RAY DIFFRACTION99.06
2.31-2.380.21692020.18124104X-RAY DIFFRACTION99.49
2.38-2.460.21982180.1764016X-RAY DIFFRACTION99.06
2.46-2.560.22292330.17994032X-RAY DIFFRACTION99.32
2.56-2.680.19842180.1834076X-RAY DIFFRACTION99.28
2.68-2.820.22332410.18544034X-RAY DIFFRACTION99.56
2.82-30.23412120.18814067X-RAY DIFFRACTION99.35
3-3.230.23512080.17494090X-RAY DIFFRACTION99.49
3.23-3.550.20852050.15984097X-RAY DIFFRACTION99.42
3.55-4.070.17272180.14214101X-RAY DIFFRACTION99.75
4.07-5.120.15642480.13734095X-RAY DIFFRACTION99.56
5.12-33.070.20622390.18754160X-RAY DIFFRACTION98.94
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.87790762622-0.214475889265-0.1233762884692.55491720076-0.9763187142894.68841450549-0.0884768892392-0.08200830286550.2563364101160.00764597474110.1912831948750.0431813176802-0.16490904506-0.416715917238-0.03285644147250.2166565336440.0139470491925-0.01322027529860.1852773197450.01957194431460.230639646789-9.4405405315813.63605561427.67809591807
26.658768098892.3898767411-0.8176351726812.16041824102-0.6436844671081.65986234399-0.320271924524-0.241580536656-0.129327894778-0.07142028702620.2705509806590.0563511577324-0.0878554916098-0.489827845680.06188747031590.3012517483410.06438183850820.004698566594960.3638241841150.09976552782220.277214273537-17.669013986410.86852982410.1525762391
31.91183254573-0.03760435867130.1908898726061.841049678770.7723395813722.655172981830.01339173413810.108608159262-0.1433155056270.08467121748050.1095929738960.1683105107070.0295787577408-0.397538482047-0.1004501976480.2315043912570.0209984612366-0.004251629003880.2930716052910.08143387753380.224411795622-19.02182417858.01900168197-3.05544155011
42.59706601828-0.3364144519811.332936329530.4603527824470.07298994855531.839887285450.07718511643070.551975472161-0.0505326458723-0.03247142934420.02296034694710.00533125398510.03033482917180.204333247733-0.1157236462760.2178330146430.00519358222962-0.0009358921758060.2908812249540.0135704110350.224170756162-2.913501703364.74871152452-5.00678538995
51.525595775760.2280128699060.234637713050.964105752231-1.564708037292.756275193910.2404584883370.446107002302-0.465058389833-0.0786174088646-0.07580696856120.005956547568960.02176470025680.39295908442-0.1312509033350.2470928937320.081590707397-0.03937371914160.418591546572-0.09639751997280.32337753716526.5587868036-4.0280030268212.4164834534
63.164351284691.949711978831.786534934071.777304366671.317316250262.336064426610.06008712258080.365020180811-0.192170192027-0.0777920729704-0.00848730011798-0.00980634655219-0.1755578041420.388114094441-0.05065680311490.2803726909280.0538130993813-0.01920790207750.431332479187-0.1073808336370.27167961711433.60410091570.14534130898316.251641803
72.06349437047-0.07600713318920.4444537040490.712040866214-0.1727417968430.906738065883-0.03912363038581.116959763330.0584753044868-0.0978195053924-0.0276099384721-0.088370929599-0.05153467065680.916123478134-0.1142820735650.243261050999-0.000619060779911-0.005728298909821.06672612647-0.08199393335670.31836289794538.80691212643.633190317595.3842693161
81.38677682585-0.366537395456-0.01247641030660.5602614616890.01253034669530.159250562409-0.09857855187440.1838531934890.206857624317-0.1081543303080.2396225438450.0633624654989-0.004485314096190.3149427871660.2762684859260.258399606597-0.215735165413-0.0773724075671.613261226070.3205206485830.48258111676438.009830331912.5296224775-6.67772122515
92.73240495372-0.774593326492-0.4535000746721.564988269420.2547813968581.71577002749-0.06520874381430.4637731010110.207538857666-0.09983495034440.3067183261860.0217699806074-0.03581439881790.917575189457-0.2945392377890.211263476861-0.0739543211352-0.00488081376760.970873642340.1242912048760.35700872202329.580675465810.5663354296-2.06383197665
103.38907740408-0.743800541424-2.032588851842.781662648120.2253272712453.01804256901-0.2074310167990.7903180052750.4178039658410.05102678696340.0333044798680.068025016788-0.1041248364660.5149491034390.04463886062990.211764243687-0.0842310504229-0.05691441544970.51220484840.03029169572740.30635296894720.563673418411.50929947243.63213204622
111.86434741075-0.0690224836728-0.4044738690351.501511685830.3316491285533.179542706970.04707667086810.9722846765290.120901321278-0.065680197827-0.0394283343937-0.02673520397160.1044156004620.5656461166870.02983313576920.172732838958-0.00255874248474-0.008708543322380.486742239878-0.000993645042520.22138515946218.34347906335.20116374071.51363192653
123.816299049851.807653675595.734951902922.118811911942.339466684318.735566350520.2907419323290.93313975637-0.394768886839-0.354417232403-0.1099007511670.06192882511990.1414840838990.380458192968-0.1588288202990.26317494740.0976038944089-0.03290061902710.524022137656-0.1531428806950.31087757815211.4373276325-2.73318176007-2.90898063044
133.330332932230.108625320656-0.3917790444342.571750075290.9544731372974.7772324172-0.1228099672680.2818628245780.03692178116660.1272771665270.0575192506996-0.04695771993530.05968032275430.07860604530330.05958700044420.2005938133260.00157017161317-0.01513305999150.1569282765610.0396268236820.21004208851742.399418720113.735703524838.0783480416
146.43672106984-2.86686115666-0.4750371968321.854628619510.5623065363821.0603916202-0.1615213005230.20246478415-0.2873944085030.1604374160860.06131375038160.1214695008460.005127010468450.2472103210340.08883348612150.231084461914-0.01588112494940.01087146275550.2593696040850.01745248267590.22035029009750.470979874610.984382374134.8787338497
151.321940459280.214793754089-0.1370763361831.04114775874-0.549414282552.053065648040.0240542731534-0.0559765109747-0.118564787045-0.0595681221099-0.0223160473867-0.03844992812470.1094332861830.205325062076-0.006446710634580.1908483561850.007126615075950.0189283592170.1785205570760.005961837615440.18216044858551.64731756986.9286378655248.3474016863
161.77419739540.3075655765950.681940865970.649953232526-0.04762578414480.924927769050.00112332366617-0.227546108078-0.02781784134050.0508529053593-0.0007222965418240.02321949170010.021212256518-0.00778044822114-0.007732338806130.185244732469-0.003497554683240.02348074762370.2098462435060.0215773131810.17760893506135.74596134335.0062200793150.5072060846
175.479612925693.305897228893.783428558844.097850295212.726605343665.519540238910.22024437177-0.639812160387-0.2751550292290.27758471742-0.07130186227020.1168969868340.66659655355-0.271885647923-0.1186486614280.261355934684-0.00523099045220.01697775401160.3389236528490.09032955178010.2348268365684.1541418729-7.6688359617248.8586754935
180.1524572899460.1237611253050.6319254882050.5573057319391.945925467887.033200344410.07768407643970.1640134520220.0468578227732-0.1039507691340.1083096273080.0497893936669-0.7111325459350.453667061145-0.1618531662450.304920876638-0.01818899281320.01249423989180.2721762800390.03370125596090.2796823963437.005428310491.0895324675725.7052566842
194.39886420303-2.369777850445.613503254993.12237787078-2.880828062047.166364015240.110059638650.238429682102-0.253746222864-0.09551320642930.0877352764548-0.1804430781370.01498730389740.350962801159-0.140618437060.2472305230430.008829467958660.01331978789570.1960772520950.01167173243580.2812671500768.74663186871-5.1260398494726.9035641101
200.657142901244-0.9361985747620.9166360496841.45012570964-1.343533037371.28565702323-0.3420320239170.2854031072490.6517446524190.269749828077-0.0813165062361-0.513951539907-0.6515597160820.1859200889950.2804939920560.3836403334180.00175723172262-0.05857401207060.249399775910.08934323033970.3867153551612.236504959185.3286531249131.9629904875
215.75429638662-4.470919520670.6456302468128.33267026243-1.114678652032.954837495890.08808338152150.285018449164-0.266159842673-0.246887598968-0.02299550175680.117443472211-0.0269929734729-0.225116858635-0.06101286823740.244850764637-0.0159082496060.00602054716420.214428206203-0.001457628478550.202536170044-3.73303853899-3.568967185326.5755943045
221.72874929432-0.567348354024-0.1990327595211.915350661790.7467791983421.63229214567-0.0217772042478-0.122078167630.0129054017892-0.0776067004125-0.008977088797910.0709512576687-0.0162580498605-0.2595909304180.01516528233360.17779489580.006186184426010.01118551351640.2273410504560.03828874538340.203192028343-6.390112252511.508535911837.2915330198
234.11013054592.471406245741.400687404165.554824903962.098626975642.58241252408-0.111262607403-0.3705918269840.39461529847-0.2188654542920.05116061571180.236804453488-0.205869652858-0.1316059156460.01723338265420.1833690097530.04197883801950.02971278706930.282924624978-0.01005819145850.205301469586-5.6659472719.5288759136144.0693872219
248.08769125864.756034628490.5420412392873.838604221760.4859579581231.240717854450.132103570053-0.5073124759970.6435076171830.3903695535670.06223432004530.179945114093-0.157569779715-0.273254070713-0.240603752690.2355275205980.07822043113430.03609109341890.409801011947-0.07912052872870.288105730558-5.3159063579413.061896001952.3516827134
254.896516378692.77308222285-0.6552017845062.93034188887-0.6269808769421.38603458078-0.0589209646717-0.1836392165170.2724568724560.008674953763520.1447758286350.16453352537-0.01662690719-0.177542753697-0.07975045488490.2085259164350.0177902484040.02352625622770.29061763368-0.03423685336660.2400051601462.7837744843711.320571036347.0645570805
262.943773780220.526055905697-0.2249005041452.47016342677-0.280732939662.09907440189-0.0250840264011-0.1177628672310.269658881089-0.07354168417370.0150563417229-0.0781930721714-0.1123778263830.0101928652411-0.0226186346430.1616540095520.00687740244549-0.007053898552370.1820949848650.008660032462170.20534729780513.04264138249.8888735950342.624344046
276.20459447056-1.456437385174.748011215922.72240415163-1.517730578813.71364712720.182253511032-0.736031708588-0.3796190893750.323848660070.114866243837-0.004276732168880.0251837773434-0.421951706931-0.2655457581840.206389359909-0.02724155524030.01744127444110.3004424491820.07143230158770.23870848431721.1937291649-1.9806861475948.3929556692
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 282 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 54 )
6X-RAY DIFFRACTION6chain 'B' and (resid 55 through 93 )
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 161 )
8X-RAY DIFFRACTION8chain 'B' and (resid 162 through 180 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 241 )
11X-RAY DIFFRACTION11chain 'B' and (resid 242 through 264 )
12X-RAY DIFFRACTION12chain 'B' and (resid 265 through 282 )
13X-RAY DIFFRACTION13chain 'C' and (resid 3 through 54 )
14X-RAY DIFFRACTION14chain 'C' and (resid 55 through 93 )
15X-RAY DIFFRACTION15chain 'C' and (resid 94 through 161 )
16X-RAY DIFFRACTION16chain 'C' and (resid 162 through 282 )
17X-RAY DIFFRACTION17chain 'D' and (resid 4 through 20 )
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 40 )
19X-RAY DIFFRACTION19chain 'D' and (resid 41 through 54 )
20X-RAY DIFFRACTION20chain 'D' and (resid 55 through 75 )
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 93 )
22X-RAY DIFFRACTION22chain 'D' and (resid 94 through 129 )
23X-RAY DIFFRACTION23chain 'D' and (resid 130 through 161 )
24X-RAY DIFFRACTION24chain 'D' and (resid 162 through 179 )
25X-RAY DIFFRACTION25chain 'D' and (resid 180 through 207 )
26X-RAY DIFFRACTION26chain 'D' and (resid 208 through 264 )
27X-RAY DIFFRACTION27chain 'D' and (resid 265 through 282 )

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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