- PDB-2l05: Solution NMR Structure of the Ras-binding domain of Serine/threon... -
+
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: 2l05
タイトル
Solution NMR Structure of the Ras-binding domain of Serine/threonine-protein kinase B-raf from Homo sapiens, Northeast Structural Genomics Consortium Target HR4694F
2D 1H-13C HSQC high resolution (L/V methyl stereoassignment)
1
7
1
3D HNCO
1
8
1
3DHN(CA)CO
1
9
1
3DHN(CO)CA
1
10
1
3D HNCA
1
11
1
3DCBCA(CO)NH
1
12
1
3D HN(CA)CB
1
13
1
3DHBHA(CO)NH
1
14
1
3D (H)CCH-TOCSY
1
15
1
3D (H)CCH-COSY
1
16
1
3D CCH-TOCSY
1
17
1
3D HNHA
1
18
1
2D 1H-15N hetNOE
1
19
1
1D15NT1andT2
NMR実験の詳細
Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CROYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING N-TERMINAL TAG): BACKBONE, 98.3%, SIDE CHAIN, 98.1%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 147 TO 232, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 154-228: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.9%, ADDITIONALLY ALLOWED, 8.0%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.36/-1.10, ALL, -0.15/-0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.54/-0.97 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 147 TO 232): RECALL, 0.979, PRECISION, 0.933, F-MEASURE, 0.956, DP-SCORE, 0.808. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE MAJORITY OF THE N-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (MGHHHHHHS) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION.
-
試料調製
詳細
Solution-ID
内容
溶媒系
1
0.84 mM [U-100% 13C; U-100% 15N] HR4694F, 20 mM ammonium acetate, 100 mM sodium chloride-3, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.69 mM [U-5% 13C; U-100% 15N] HR4694F, 20 mM ammonium acetate, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS-14, 90% H2O/10% D2O
90% H2O/10% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
0.84mM
HR4694F-1
[U-100% 13C; U-100% 15N]
1
20mM
ammonium acetate-2
1
100mM
sodium chloride-3
1
5mM
calcium chloride-4
1
10mM
DTT-5
1
0.02 %
sodium azide-6
1
50uM
DSS-7
1
0.69mM
HR4694F-8
[U-5% 13C; U-100% 15N]
2
20mM
ammonium acetate-9
2
100mM
sodium chloride-10
2
5mM
calcium chloride-11
2
10mM
DTT-12
2
0.02 %
sodium azide-13
2
50uM
DSS-14
2
試料状態
イオン強度: 0.1 / pH: 4.5 / 圧: ambient / 温度: 298 K
-
NMR測定
NMRスペクトロメーター
タイプ
製造業者
モデル
磁場強度 (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker Avance
Bruker
AVANCE
600
2
-
解析
NMR software
名称
バージョン
開発者
分類
CNS
1.2
Brunger, Adams, Clore, Gros, NilgesandRead
精密化
CYANA
3
Guntert, MumenthalerandWuthrich
精密化
CYANA
3
Guntert, MumenthalerandWuthrich
構造決定
AutoStructure
2.2.1
Huang, Tejero, PowersandMontelione
rpfanalysis
PSVS
1.4
BhattacharyaandMontelione
structurequalityanalysis
NMRPipe
2.3
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
MolProbity
3.17
Richardson
structurequalityanalysis
TopSpin
2.1
BrukerBiospin
collection
TopSpin
2.1
BrukerBiospin
データ解析
PdbStat
5.1
Tejero & Montelione
pdbcoordinateanalysis
PINE
1
Bahrami, Markley, Assadi, andEghbalnia
chemicalshiftassignment
Sparky
3.112
Goddard
データ解析
Sparky
3.112
Goddard
peakpicking
TALOS+
Shen, Cornilescu, DelaglioandBax
dihedralangleconstraints
精密化
手法: simulated annealing / ソフトェア番号: 1 詳細: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1750 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (22.1 ...詳細: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 1750 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (22.1 CONSTRAINTS PER RESIDUE, 6.4 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 147 TO 232 BY PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19.
NMR constraints
NOE constraints total: 1750 / NOE intraresidue total count: 455 / NOE long range total count: 546 / NOE medium range total count: 256 / NOE sequential total count: 493
代表構造
選択基準: lowest energy
NMRアンサンブル
コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 20