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- PDB-7kz2: Dihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant ... -

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基本情報

登録情報
データベース: PDB / ID: 7kz2
タイトルDihydrodipicolinate synthase (DHDPS) from C.jejuni, Y110F mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site in C2221 space group
要素4-hydroxy-tetrahydrodipicolinate synthase
キーワードLYASE
機能・相同性
機能・相同性情報


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
類似検索 - 分子機能
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
ACETATE ION / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 4-hydroxy-tetrahydrodipicolinate synthase
類似検索 - 構成要素
生物種Campylobacter jejuni subsp. jejuni serotype O:2 (カンピロバクター)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.9 Å
データ登録者Saran, S. / Sanders, D.A.R.
資金援助 カナダ, 1件
組織認可番号国
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: To Be Published
タイトル: B-FACTOR ANALYSIS SUGGEST THAT L-LYSINE AND R, R-BISLYSINE ALLOSTERICALLY INHIBIT Cj.DHDPS ENZYME BY DECREASING PROTEIN DYNAMICS.
著者: Saran, S. / Sanders, D.A.R.
履歴
登録2020年12月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年12月15日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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
改定 1.22023年11月29日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: 4-hydroxy-tetrahydrodipicolinate synthase
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)209,69456
ポリマ－205,0166
非ポリマー4,67850
水19,7981099
1
A: 4-hydroxy-tetrahydrodipicolinate synthase
D: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,06020
ポリマ－68,3392
非ポリマー1,72218
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-3 kcal/mol
Surface area22620 Å2
手法PISA
2
B: 4-hydroxy-tetrahydrodipicolinate synthase
C: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,94222
ポリマ－68,3392
非ポリマー1,60420
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-7 kcal/mol
Surface area21970 Å2
手法PISA
3
E: 4-hydroxy-tetrahydrodipicolinate synthase
F: 4-hydroxy-tetrahydrodipicolinate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,69114
ポリマ－68,3392
非ポリマー1,35312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-0 kcal/mol
Surface area21970 Å2
手法PISA
単位格子
Length a, b, c (Å)85.580, 231.800, 200.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
11(chain A and (resid 3 through 290 or (resid 291...
21(chain B and (resid 3 through 290 or (resid 291...
31(chain C and (resid 3 through 290 or (resid 291...
41chain D
51(chain E and (resid 3 through 290 or (resid 291...
61(chain F and (resid 3 through 290 or (resid 291...

NCSドメイン領域:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMET(chain A and (resid 3 through 290 or (resid 291...AA3 - 29015 - 302
12LYSLYS(chain A and (resid 3 through 290 or (resid 291...AA291303
13PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
14PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
15PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
16PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
17PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
18PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
19PHEPHE(chain A and (resid 3 through 290 or (resid 291...AA3 - 29815 - 310
21METMET(chain B and (resid 3 through 290 or (resid 291...BB3 - 29015 - 302
22LYSLYS(chain B and (resid 3 through 290 or (resid 291...BB291303
23PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
24PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
25PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
26PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
27PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
28PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
29PHEPHE(chain B and (resid 3 through 290 or (resid 291...BB3 - 29815 - 310
31METMET(chain C and (resid 3 through 290 or (resid 291...CC3 - 29015 - 302
32LYSLYS(chain C and (resid 3 through 290 or (resid 291...CC291303
33PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
34PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
35PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
36PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
37PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
38PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
39PHEPHE(chain C and (resid 3 through 290 or (resid 291...CC3 - 29815 - 310
41PHEPHEchain DDD3 - 29815 - 310
51METMET(chain E and (resid 3 through 290 or (resid 291...EE3 - 29015 - 302
52LYSLYS(chain E and (resid 3 through 290 or (resid 291...EE291303
53PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
54PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
55PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
56PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
57PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
58PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
59PHEPHE(chain E and (resid 3 through 290 or (resid 291...EE3 - 29815 - 310
61METMET(chain F and (resid 3 through 290 or (resid 291...FF3 - 29015 - 302
62LYSLYS(chain F and (resid 3 through 290 or (resid 291...FF291303
63PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
64PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
65PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
66PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
67PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
68PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310
69PHEPHE(chain F and (resid 3 through 290 or (resid 291...FF3 - 29815 - 310

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
4-hydroxy-tetrahydrodipicolinate synthase / HTPA synthase


分子量: 34169.258 Da / 分子数: 6 / 変異: Y110F / 由来タイプ: 組換発現
由来: (組換発現) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (カンピロバクター)
株: ATCC 700819 / NCTC 11168 / 遺伝子: dapA, Cj0806 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q9PPB4, 4-hydroxy-tetrahydrodipicolinate synthase

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非ポリマー , 7種, 1149分子

#2: 化合物
ChemComp-LYS / LYSINE / 2-アンモニオ-2-デアミノ-L-リシンアニオン


タイプ: L-peptide linking / 分子量: 147.195 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H15N2O2
#3: 化合物
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 13 / 由来タイプ: 合成 / 式: C4H10O3
#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 17 / 由来タイプ: 合成 / 式: C2H6O2
#5: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H3O2
#6: 化合物
ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C6H14O4
#7: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1099 / 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: 2.43 Å3/Da / 溶媒含有率: 49.31 %
結晶化温度: 288.15 K / 手法: マイクロバッチ法 / pH: 7.4
詳細: 0.3 M Magnesium acetate, 10 % PEG8000, 0.1 M Sodium acetate (pH 7.4), 60 mM L-lysine

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年12月12日
放射モノクロメーター: double beam / 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: 0.9795 Å / 相対比: 1
反射解像度: 1.9→46.03 Å / Num. obs: 156294 / % possible obs: 99.9 % / 冗長度: 15 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.06741 / Net I/σ(I): 8.43
反射 シェル解像度: 1.9→1.968 Å / Rmerge(I) obs: 1.078 / Num. unique obs: 15421 / CC1/2: 0.273 / CC star: 0.655 / % possible all: 99.59

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHENIX1.17.1_3660精密化
PDB_EXTRACT3.27データ抽出
HKL-3000データ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4LY8

4ly8


解像度: 1.9→46.03 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 22.37 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2177 7814 5 %
Rwork0.186 148416 -
obs0.1875 156230 99.91 %
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 max: 89.67 Å2 / Biso mean: 33.6192 Å2 / Biso min: 12.36 Å2
精密化ステップサイクル: final / 解像度: 1.9→46.03 Å
タンパク質核酸リガンド溶媒全体
原子数13641 0 248 1099 14988
Biso mean--20.12 41.61 -
残基数----1782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5358X-RAY DIFFRACTION4.026TORSIONAL
12B5358X-RAY DIFFRACTION4.026TORSIONAL
13C5358X-RAY DIFFRACTION4.026TORSIONAL
14D5358X-RAY DIFFRACTION4.026TORSIONAL
15E5358X-RAY DIFFRACTION4.026TORSIONAL
16F5358X-RAY DIFFRACTION4.026TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.920.36922530.3447479199
1.92-1.940.36012600.33864934100
1.94-1.970.3382570.31354870100
1.97-1.990.3252600.30454937100
1.99-2.020.31722560.28554870100
2.02-2.050.32590.27154925100
2.05-2.080.29992590.26214915100
2.08-2.110.28122580.2544908100
2.11-2.140.28392610.23834957100
2.14-2.170.25472580.22764897100
2.17-2.210.28592580.21934900100
2.21-2.250.25192620.21954977100
2.25-2.30.26192570.21324878100
2.3-2.340.24562580.20714916100
2.34-2.390.22162600.20024943100
2.39-2.450.24462600.19754931100
2.45-2.510.2292600.18484939100
2.51-2.580.21622590.1794928100
2.58-2.650.21032590.17584917100
2.65-2.740.22762620.17674981100
2.74-2.840.19642600.17694928100
2.84-2.950.22092620.17774976100
2.95-3.090.2292600.1784948100
3.09-3.250.20322620.1744970100
3.25-3.450.20142610.16774966100
3.45-3.720.17672620.16274971100
3.72-4.090.19372630.15425012100
4.09-4.680.16232640.14595016100
4.68-5.90.18752680.16645077100
5.9-100.1942760.16525238100
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)
12.3286-0.0185-1.27152.43210.14383.27740.226-0.17790.0230.39780.02080.2514-0.3806-0.1388-0.27640.2430.05570.0210.26320.06090.3542-76.157-67.21418.583
21.59811.23250.05522.9812-1.47492.1132-0.111-0.13690.19010.0480.12520.4145-0.1133-0.182-0.05740.29830.06460.01170.30550.07330.3217-76.468-64.54220.447
31.06790.20220.1963.61620.74790.9778-0.0204-0.02970.01750.00840.04760.5087-0.0356-0.37820.06840.21020.0420.0110.32790.08460.3489-83.007-72.19413.573
40.31510.0638-0.3741.11230.01710.4069-0.05990.04830.043-0.04450.06730.10940.0315-0.02090.00920.22910.0153-0.02020.24130.05590.2623-67.57-76.5815.962
52.23890.42480.2241.6137-0.70453.1130.0220.09540.28860.02430.0572-0.076-0.20450.1377-0.05760.22580.0075-0.0010.20130.00340.3011-57.683-59.46213.375
61.56660.1925-0.08910.6665-0.33440.3282-0.0495-0.27830.1050.57160.0968-0.1758-0.2943-0.0252-0.06230.35690.02990.01450.31710.01270.2683-65.381-65.95431.275
71.8705-1.1203-0.91694.3110.97412.90830.10090.13180.1054-0.4420.0007-0.6472-0.02540.1075-0.12590.1636-0.03310.03670.31910.07450.3247-27.776-78.317-1.321
81.2371-0.61480.85022.8959-0.8851.5708-0.01430.2337-0.0099-0.1875-0.0045-0.1619-0.01810.19970.05520.2323-0.03420.03040.27710.06990.3312-27.45-78.532-4.631
90.06980.24150.0981.4906-0.59963.04240.0506-0.0680.0773-0.0496-0.0256-0.30660.0480.22060.05920.1727-0.01320.00210.31590.07060.4149-20.863-76.4415.37
101.232-0.5254-0.2961.6843-0.32951.4908-0.1231-0.08250.15460.1110.0481-0.1142-0.05940.10720.0830.2187-0.0026-0.04060.24140.0290.2892-30.681-76.52416.595
110.3851-0.30550.41020.77350.25941.9188-0.0974-0.02290.12550.14050.0706-0.05640.0089-0.02470.01370.2451-0.0126-0.02030.24460.03650.298-40.474-69.0410.454
121.2610.0501-0.02043.7535-0.28421.2037-0.03410.12390.1211-0.36080.08910.1520.0048-0.0848-0.06370.2177-0.01010.00690.27270.0550.2659-46.304-70.123-5.439
130.9037-0.42591.10212.3048-0.59091.71420.08760.0117-0.23-0.2598-0.0798-0.1790.30.0293-0.03850.30370.00830.03060.25690.00360.27-34.901-90.571-5.973
142.18240.9306-0.58635.68-1.79551.8695-0.22150.47380.01-0.91980.20340.14760.2618-0.2382-0.06120.3810.0023-0.03820.39510.010.2954-43.802-85.893-13.143
151.01020.371-0.04731.95650.14061.04940.0494-0.07250.0050.1639-0.0612-0.2019-0.01420.1093-0.03040.25910.0261-0.0330.32160.0770.3029-24.556-100.70330.245
162.3228-0.20780.40276.0605-2.41913.1982-0.0917-0.1925-0.1061-0.10940.033-0.74260.10190.07820.0070.24950.04010.00140.31980.01630.3988-17.44-101.27324.011
170.6567-0.42531.05951.6629-1.39912.9662-0.00460.0783-0.06760.105-0.0071-0.16480.04880.28760.06360.2530.04330.00810.27940.04270.351-22.934-104.86517.728
181.01770.3163-0.37141.4556-0.22470.923-0.0909-0.0029-0.0951-0.13910.06610.00810.16090.0020.02850.2860.01060.00040.24920.03150.269-37.535-105.22713.778
191.29970.19530.3031.0114-0.0110.56830.0911-0.2187-0.21870.06-0.0815-0.05670.085-0.0214-0.02770.26620.0230.00010.27740.0690.2637-40.435-108.19833.392
202.76171.3861-0.17165.7232-0.06661.45610.0796-0.3314-0.1210.2795-0.05430.14370.2032-0.07290.16470.27970.0413-0.00230.34560.06090.2434-45.147-102.12437.893
210.21180.6469-0.2082.0216-1.17341.7033-0.0795-0.1247-0.02840.3222-0.0865-0.2023-0.19490.12240.20870.3466-0.031-0.05320.37110.04220.3032-29.062-87.62734.584
222.6841-0.82590.10424.3896-0.91122.5136-0.0764-0.48120.0711.07970.08750.034-0.6016-0.0524-0.05730.45890.00520.00160.42850.00980.2595-36.278-91.14643.997
232.26060.23761.22772.0758-0.2833.07390.0334-0.1546-0.1495-0.12480.26420.2634-0.055-0.3759-0.27020.23580.00690.04010.32820.09390.3258-78.234-104.49822.761
241.4946-1.1147-0.31572.6954-0.70371.89770.04470.1473-0.0956-0.00450.04530.3180.1362-0.265-0.00290.29-0.0448-0.02810.36320.08760.3805-79.316-107.18621.122
251.20610.82410.07942.41070.6211.284-0.0308-0.0438-0.01330.13250.04760.34950.0074-0.3890.01040.26520.00420.07130.44160.10940.3835-82.76-98.81629.285
260.6444-0.03110.29921.2185-0.25490.8526-0.0369-0.1157-0.05650.18280.05260.0679-0.0313-0.1259-0.02580.26740.02230.03130.27270.07150.2335-65.359-96.64732.38
271.60770.2009-0.40771.4236-1.52862.2603-0.0293-0.0676-0.22270.0021-0.0859-0.02540.15590.11150.05710.2486-0.02030.00850.21140.01740.2931-60.348-114.78622.681
281.0511-0.38220.4313.8717-0.73511.5310.04730.2081-0.0743-0.48950.1230.18340.1801-0.1181-0.11410.2838-0.0248-0.05030.29190.02090.2962-71.619-106.9717.63
291.6052-0.72-0.2591.58260.54362.63730.10380.3966-0.1471-0.0743-0.45380.3218-0.1741-0.84730.39090.2419-0.0169-0.03880.3836-0.01610.317-28.815-135.05839.763
300.77160.2885-0.4521.15070.08492.12960.05530.04930.2854-0.2198-0.02070.2970.089-0.28640.01760.2716-0.0069-0.07970.3399-0.00520.3155-29.923-131.99138.542
311.91860.00210.75072.3091-0.76475.80820.1251-0.2355-0.06840.2538-0.08040.40940.4105-1.4168-0.01980.3251-0.0891-0.04610.4787-0.00670.3831-36.465-137.60243.567
321.3925-0.10120.41781.1681-0.13991.58920.0090.1681-0.2561-0.03790.00260.18210.3729-0.2367-0.02540.3234-0.0885-0.00360.3424-0.04690.3131-27.399-149.58544.803
331.6473-0.85820.89571.5501-0.05523.5901-0.053-0.0468-0.1316-0.16760.01520.0010.0601-0.1898-0.03860.3427-0.0227-0.02860.283-0.01020.3051-19.226-148.27643.108
340.52830.1534-0.59040.99950.02160.9867-0.05970.0839-0.0932-0.0874-0.0091-0.0030.2605-0.10880.06060.3624-0.0456-0.04450.3033-0.00640.2835-15.132-147.7233.777
351.9805-0.1436-0.08451.75070.72862.2421-0.01550.35910.0711-0.2533-0.03840.0529-0.0959-0.10510.0390.2689-0.0049-0.04390.31630.07390.2858-13.408-132.63326.249
360.03720.1303-0.39841.7065-0.76443.25550.0060.03820.0939-0.0082-0.1062-0.0522-0.2126-0.11230.10590.33540.0356-0.03890.28930.00150.3166-21.14-123.98846.469
373.1679-0.06541.23321.679-0.11944.3575-0.18610.26040.57360.0443-0.0899-0.1056-0.43230.22380.35150.30890.0238-0.03180.25190.05050.3492-15.15-118.57137.113
381.8030.80940.86252.34680.23181.93910.1433-0.0579-0.31470.2234-0.0558-0.07420.4576-0.2404-0.04120.4142-0.03210.05250.3258-0.02830.2743-20.664-150.14172.891
392.3838-0.64621.36471.6410.29432.7621-0.037-0.249-0.41960.33780.03270.23670.194-0.14430.0420.3661-0.0580.04140.24950.01660.2916-21.016-152.99374.454
402.8829-0.05482.26982.7568-0.81457.0491-0.0653-0.3310.23050.0729-0.16540.1224-0.0397-0.97140.15190.3329-0.02520.04830.3679-0.00110.3279-29.212-147.26372.975
410.5534-0.26091.10281.8438-2.39274.78740.0908-0.1104-0.00310.0979-0.02980.30550.0341-0.1588-0.12750.3179-0.0260.04970.3242-0.02780.3137-25.025-139.31272.17
421.39410.1664-0.30381.36860.34120.5931-0.0103-0.20690.12680.06270.01560.1510.00080.02460.02010.27960.0014-0.00260.237-0.01340.2358-14.625-133.25666.163
431.53710.1934-0.32142.0237-0.88760.9748-0.0182-0.006-0.00680.1119-0.0221-0.06880.0460.11780.05960.32370.0043-0.0260.27350.00930.2287-3.353-140.99273.019
442.73790.32620.19521.88320.04272.0071-0.0238-0.4636-0.30220.27610.0967-0.18510.21190.1073-0.02190.41480.04060.01130.31990.06590.342-0.719-152.3877.688
451.2553-0.23250.84881.3959-0.59642.22370.088-0.0165-0.45760.03990.07760.0450.4991-0.0082-0.14420.5127-0.0542-0.00320.29460.00350.413-13.289-163.37465.721
460.492-0.32230.51190.366-0.63110.5206-0.0203-0.1011-0.0324-0.04440.11130.09260.0835-0.0185-0.0380.35720.03980.00170.195-0.08150.316-43.28-105.97730.268
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:23 )A3 - 23
2X-RAY DIFFRACTION2( CHAIN A AND RESID 24:55 )A24 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:98 )A56 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:214 )A99 - 214
5X-RAY DIFFRACTION5( CHAIN A AND RESID 215:248 )A215 - 248
6X-RAY DIFFRACTION6( CHAIN A AND RESID 249:298 )A249 - 298
7X-RAY DIFFRACTION7( CHAIN B AND RESID 3:23 )B3 - 23
8X-RAY DIFFRACTION8( CHAIN B AND RESID 24:55 )B24 - 55
9X-RAY DIFFRACTION9( CHAIN B AND RESID 56:98 )B56 - 98
10X-RAY DIFFRACTION10( CHAIN B AND RESID 99:148 )B99 - 148
11X-RAY DIFFRACTION11( CHAIN B AND RESID 149:214 )B149 - 214
12X-RAY DIFFRACTION12( CHAIN B AND RESID 215:248 )B215 - 248
13X-RAY DIFFRACTION13( CHAIN B AND RESID 249:279 )B249 - 279
14X-RAY DIFFRACTION14( CHAIN B AND RESID 280:298 )B280 - 298
15X-RAY DIFFRACTION15( CHAIN C AND RESID 3:55 )C3 - 55
16X-RAY DIFFRACTION16( CHAIN C AND RESID 56:70 )C56 - 70
17X-RAY DIFFRACTION17( CHAIN C AND RESID 71:98 )C71 - 98
18X-RAY DIFFRACTION18( CHAIN C AND RESID 99:191 )C99 - 191
19X-RAY DIFFRACTION19( CHAIN C AND RESID 192:229 )C192 - 229
20X-RAY DIFFRACTION20( CHAIN C AND RESID 230:248 )C230 - 248
21X-RAY DIFFRACTION21( CHAIN C AND RESID 249:279 )C249 - 279
22X-RAY DIFFRACTION22( CHAIN C AND RESID 280:298 )C280 - 298
23X-RAY DIFFRACTION23( CHAIN D AND RESID 3:23 )D3 - 23
24X-RAY DIFFRACTION24( CHAIN D AND RESID 24:55 )D24 - 55
25X-RAY DIFFRACTION25( CHAIN D AND RESID 56:98 )D56 - 98
26X-RAY DIFFRACTION26( CHAIN D AND RESID 99:214 )D99 - 214
27X-RAY DIFFRACTION27( CHAIN D AND RESID 215:248 )D215 - 248
28X-RAY DIFFRACTION28( CHAIN D AND RESID 249:298 )D249 - 298
29X-RAY DIFFRACTION29( CHAIN E AND RESID 3:23 )E3 - 23
30X-RAY DIFFRACTION30( CHAIN E AND RESID 24:55 )E24 - 55
31X-RAY DIFFRACTION31( CHAIN E AND RESID 56:70 )E56 - 70
32X-RAY DIFFRACTION32( CHAIN E AND RESID 71:129 )E71 - 129
33X-RAY DIFFRACTION33( CHAIN E AND RESID 130:148 )E130 - 148
34X-RAY DIFFRACTION34( CHAIN E AND RESID 149:214 )E149 - 214
35X-RAY DIFFRACTION35( CHAIN E AND RESID 215:248 )E215 - 248
36X-RAY DIFFRACTION36( CHAIN E AND RESID 249:279 )E249 - 279
37X-RAY DIFFRACTION37( CHAIN E AND RESID 280:298 )E280 - 298
38X-RAY DIFFRACTION38( CHAIN F AND RESID 3:23 )F3 - 23
39X-RAY DIFFRACTION39( CHAIN F AND RESID 24:55 )F24 - 55
40X-RAY DIFFRACTION40( CHAIN F AND RESID 56:70 )F56 - 70
41X-RAY DIFFRACTION41( CHAIN F AND RESID 71:98 )F71 - 98
42X-RAY DIFFRACTION42( CHAIN F AND RESID 99:171 )F99 - 171
43X-RAY DIFFRACTION43( CHAIN F AND RESID 172:214 )F172 - 214
44X-RAY DIFFRACTION44( CHAIN F AND RESID 215:248 )F215 - 248
45X-RAY DIFFRACTION45( CHAIN F AND RESID 249:298 )F249 - 298
46X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )A301
47X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )C301
48X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )B301
49X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )E301
50X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )D301
51X-RAY DIFFRACTION46( CHAIN A AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN B AND RESID 301:301 ) OR ( CHAIN E AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 ) OR ( CHAIN F AND RESID 301:301 )F301

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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

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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