Text: THE PROTEIN IS MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. ALL ...Text: THE PROTEIN IS MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE SIDE CHAIN METHYL ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE NUMBERS 1 TO 183, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-12,14-16,18-38,66-106,111-146,152-181: (A) RMSD (ORDERED RESIDUES): BB, 1.0, HEAVY ATOM, 1.5. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.0%, ADDITIONALLY ALLOWED, 10.9%, GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.34/-1.02, ALL, -0.31/-1.83. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 20.78/-2.04 (E) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 55. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,13,17,39-65,107-110,147-151,182-183.
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試料調製
詳細
Solution-ID
内容
溶媒系
1
0.82 mM [U-13C; U-15N; U-2H; ILVFY-1H] WR73, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
2
0.85 mM [U-5% 13C; U-100% 15N] WR73, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
90% H2O/10% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
0.82mM
WR73-1
[U-13C; U-15N; U-2H; ILVFY-1H]
1
20mM
MES-2
1
100mM
sodium chloride-3
1
5mM
calcium chloride-4
1
10mM
DTT-5
1
50uM
DSS-6
1
0.02 %
sodium azide-7
1
0.85mM
WR73-8
[U-5% 13C; U-100% 15N]
2
20mM
MES-9
2
100mM
sodium chloride-10
2
5mM
calcium chloride-11
2
10mM
DTT-12
2
50uM
DSS-13
2
0.02 %
sodium azide-14
2
試料状態
pH: 6.5 / 圧: ambient / 温度: 298 K
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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
Varian INOVA
Varian
INOVA
600
2
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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
CNS
1.2
Brunger, Adams, Clore, Gros, NilgesandRead
構造決定
CNS
1.2
Brunger, Adams, Clore, Gros, NilgesandRead
geometryoptimization
CYANA
3
Guntert, MumenthalerandWuthrich
構造決定
PINE
1
Bahrami, Markley, Assadi, andEghbalnia
chemicalshiftassignment
NMRPipe
2.3
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
解析
Sparky
3
Goddard
データ解析
Sparky
3
Goddard
peakpicking
Sparky
3
Goddard
chemicalshiftassignment
TopSpin
2.1
BrukerBiospin
collection
VnmrJ
Varian
collection
PSVS
1.4
BhattacharyaandMontelione
structurevalidation
TALOS
plus
Cornilescu, DelaglioandBax
dihedralangleconstraints
PdbStat
5.1
TejeroandMontelione
pdbcoordinateanalysis
精密化
手法: simulated annealing / ソフトェア番号: 1 詳細: THE FINAL MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 272 DIHEDRAL ANGLE CONSTRAINTS, AND 126 HYDROGEN BOND CONSTRAINTS (7.6 ...詳細: THE FINAL MINIMAL CONSTRAINT STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING DISTANCE CONSTRAINTS, 272 DIHEDRAL ANGLE CONSTRAINTS, AND 126 HYDROGEN BOND CONSTRAINTS (7.6 CONSTRAINTS PER RESIDUE, 2.3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 183 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: 976 / NOE intraresidue total count: 89 / NOE long range total count: 351 / NOE medium range total count: 248 / NOE sequential total count: 288
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