- PDB-2lxf: Solution NMR structure of a potential acylphosphatase from Giardi... -
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基本情報
登録情報
データベース: PDB / ID: 2lxf
タイトル
Solution NMR structure of a potential acylphosphatase from Giardia lamblia, Seattle Structural Genomics Center for Infectious Disease target GilaA.01396.a
要素
Uncharacterized protein
キーワード
Structural Genomics / Unknown Function / Beaver fever / giardiasis / Seattle Structural Genomics Center for Infectious Disease / SSGCID
1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 93% H2O/7% D2O
93% H2O/7% D2O
2
1.5 mM [U-99% 13C; U-99% 15N] protein, 100 mM sodium chloride, 20 mM TRIS, 1 mM DTT, 100% D2O
100% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
1.5mM
entity-1
[U-99% 13C; U-99% 15N]
1
100mM
sodium chloride-2
1
20mM
TRIS-3
1
1mM
DTT-4
1
1.5mM
entity-5
[U-99% 13C; U-99% 15N]
2
100mM
sodium chloride-6
2
20mM
TRIS-7
2
1mM
DTT-8
2
試料状態
イオン強度: 0.12 / pH: 7 / 圧: ambient / 温度: 293 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
Varian INOVA
Varian
INOVA
600
1
Varian INOVA
Varian
INOVA
750
2
Varian INOVA
Varian
INOVA
800
3
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解析
NMR software
名称
バージョン
開発者
分類
Sparky
3.115
Goddard
データ解析
Sparky
3.115
Goddard
peakpicking
CYANA
2.1
Guntert, MumenthalerandWuthrich
構造決定
Felix
2007
AccelrysSoftwareInc.
解析
CNS
1.1
Brunger, Adams, Clore, Gros, NilgesandRead
精密化
PSVS
1.3
BhattacharyaandMontelione
データ解析
精密化
手法: DGSA-distance geometry simulated annealing / ソフトェア番号: 1 詳細: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...詳細: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 5% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS.
NMR constraints
NOE constraints total: 1232 / NOE intraresidue total count: 285 / NOE long range total count: 388 / NOE medium range total count: 148 / NOE sequential total count: 411 / Hydrogen bond constraints total count: 78 / Protein phi angle constraints total count: 69 / Protein psi angle constraints total count: 69
代表構造
選択基準: closest to the average
NMRアンサンブル
コンフォーマー選択の基準: target function / 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