- PDB-1i11: SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE -
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基本情報
登録情報
データベース: PDB / ID: 1i11
タイトル
SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN, SOX-5 HMG BOX FROM MOUSE
要素
TRANSCRIPTION FACTOR SOX-5
キーワード
DNA BINDING PROTEIN / HMG BOX / DNA BENDING / DNA RECOGNITION / CHROMATIN / DNA SEQUENCE SPECIFIC / TESTIS DETERMINING.
機能・相同性
機能・相同性情報
regulation of timing of neuron differentiation / positive regulation of chondrocyte differentiation / central nervous system neuron differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment / chondrocyte differentiation / transcription regulator complex / in utero embryonic development ...regulation of timing of neuron differentiation / positive regulation of chondrocyte differentiation / central nervous system neuron differentiation / cartilage development / cartilage condensation / oligodendrocyte differentiation / cell fate commitment / chondrocyte differentiation / transcription regulator complex / in utero embryonic development / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleus 類似検索 - 分子機能
: / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
Text: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND ...Text: This Structure was determined using a combination of 2D and 3D NMR spectra. THE 30 STRUCTURES ARE ALIGNED OVER ALL BACKBONE ATOMS FOR RESIDUES 10-25 AND 32-43. MODEL 1 IS THE MINIMUM ENERGY AND REFERENCE STRUCTURE FOR THE OTHER 29 STRUCTURES.
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試料調製
詳細
タイプ
Solution-ID
内容
Label
溶媒系
solution
1
2-3 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2O
sample_1
90% H2O/10% D2O
solution
2
3 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 100% D2O
sample_2
100% D2O
solution
3
1 mM [U-100% 15N] Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2O
sample_3
90% H2O/10% D2O
solution
4
3 mM Sox-5 HMG Box, 75 mM potassium phosphate buffer, 0.5 mM DTT, 90% H2O/10% D2O
sample_4
90% H2O/10% D2O
試料
濃度 (mg/ml)
単位
構成要素
Isotopic labeling
Conc. range (mg/ml)
Solution-ID
mM
Sox-5 HMG Box
[U-100% 15N]
2-3
1
75mM
potassiumphosphatebuffer
naturalabundance
1
0.5mM
DTT
naturalabundance
1
3mM
Sox-5 HMG Box
naturalabundance
2
75mM
potassiumphosphatebuffer
naturalabundance
2
0.5mM
DTT
naturalabundance
2
1mM
Sox-5 HMG Box
[U-100% 15N]
1
3
75mM
potassiumphosphatebuffer
naturalabundance
3
0.5mM
DTT
naturalabundance
3
3mM
Sox-5 HMG Box
naturalabundance
4
75mM
potassiumphosphatebuffer
naturalabundance
4
0.5mM
DTT
naturalabundance
4
試料状態
イオン強度: 75 mM KPO4 / pH: 6.2 / 圧: Ambient / 温度: 298.00 K
結晶化
*PLUS
手法: other / 詳細: NMR
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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
GE OMEGA
GE
OMEGA
600
1
Bruker AM
Bruker
AM
600
2
Varian UNITYPLUS
Varian
UNITYPLUS
500
3
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解析
NMR software
名称
バージョン
開発者
分類
X-PLOR
3.851
BRUNGER
精密化
Felix
2.3
MolecularSimulations
データ解析
NMRView
3
JOHNSON, BRUCEA.
データ解析
Insight II
97
MolecularSimulations
データ解析
精密化
手法: SIMULATING ANNEALING / ソフトェア番号: 1 詳細: Structures are based on a total of 1383 nonredundant distance NOE restraints, 61 dihedral angle restraints and 24 paired distance restraints for hydrogen bonds.
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 least restraint violations,structures with the lowest energy 計算したコンフォーマーの数: 50 / 登録したコンフォーマーの数: 30