- PDB-2kzy: Solution NMR structure of the ZNF216 A20 zinc finger -
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基本情報
登録情報
データベース: PDB / ID: 2kzy
タイトル
Solution NMR structure of the ZNF216 A20 zinc finger
要素
Zfand5 protein (Zinc finger protein 216 (Predicted), isoform CRA_a)
キーワード
METAL BINDING PROTEIN / A20 domain / ZNF216 / Atrogene / zinc finger
機能・相同性
機能・相同性情報
respiratory system process / smooth muscle tissue development / fibroblast migration / vasculature development / skeletal system morphogenesis / face development / platelet-derived growth factor receptor signaling pathway / in utero embryonic development / DNA binding / zinc ion binding / cytoplasm 類似検索 - 分子機能
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. ...: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4770 / Zinc finger, AN1-type / AN1-like Zinc finger / AN1-like Zinc finger / Zinc finger AN1-type profile. / AN1-like Zinc finger / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
手法: 溶液NMR 詳細: NMR structure of ZNF216 residues 1 to 60 containing an A20 type zinc finger from residues 14 to 45, the termini are disordered.
NMR実験
Conditions-ID
Experiment-ID
Solution-ID
タイプ
1
1
1
2D 1H-1H NOESY
1
2
1
2D 1H-1H TOCSY
1
3
2
2D 1H-15N HSQC
1
4
2
3D 1H-15N NOESY
1
5
2
3D 1H-15N TOCSY
1
6
3
3DCBCA(CO)NH
1
7
3
3D HN(CA)CB
1
8
3
3D HNCO
1
9
3
3DHN(CA)CO
1
10
3
3D 1H-13C NOESY
1
11
3
3D (H)CCH-TOCSY
1
12
4
2D 1H-15N HSQCIPAP
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試料調製
詳細
Solution-ID
内容
溶媒系
1
1 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 90% H2O/10% D2O
90% H2O/10% D2O
2
1.2 mM [U-100% 15N] ZNF216-A20-6, 50 uM Zinc-7, 0.1 mM DSS-8, 5 mM TRIS-9, 50 mM sodium chloride-10, 90% H2O/10% D2O
90% H2O/10% D2O
3
0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-11, 50 uM Zinc-12, 0.1 mM DSS-13, 5 mM TRIS-14, 50 mM sodium chloride-15, 90% H2O/10% D2O
90% H2O/10% D2O
4
1.2 mM [U-100% 15N] ZNF216-A20-16, 50 uM Zinc-17, 0.1 mM DSS-18, 5 mM TRIS-19, 50 mM sodium chloride-20, 7 % Polyacrylamide gel-21, 90% H2O/10% D2O
90% H2O/10% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
1mM
ZNF216-A20-1
1
50uM
Zinc-2
1
0.1mM
DSS-3
1
5mM
TRIS-4
1
50mM
sodium chloride-5
1
1.2mM
ZNF216-A20-6
[U-100% 15N]
2
50uM
Zinc-7
2
0.1mM
DSS-8
2
5mM
TRIS-9
2
50mM
sodium chloride-10
2
0.8mM
ZNF216-A20-11
[U-100% 13C; U-100% 15N]
3
50uM
Zinc-12
3
0.1mM
DSS-13
3
5mM
TRIS-14
3
50mM
sodium chloride-15
3
1.2mM
ZNF216-A20-16
[U-100% 15N]
4
50uM
Zinc-17
4
0.1mM
DSS-18
4
5mM
TRIS-19
4
50mM
sodium chloride-20
4
7 %
Polyacrylamide gel-21
4
試料状態
イオン強度: 0.1 / pH: 7 / 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: Bruker Avance / 製造業者: Bruker / モデル: AVANCE / 磁場強度: 600 MHz
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解析
NMR software
名称
バージョン
開発者
分類
TopSpin
2.1
BrukerBiospin
collection
TopSpin
2.1
BrukerBiospin
解析
CcpNMR
1.1.15
CCPN
chemicalshiftassignment
CcpNMR
1.1.15
CCPN
chemicalshiftcalculation
CcpNMR
1.1.15
CCPN
peakpicking
CcpNMR
1.1.15
CCPN
データ解析
X-PLOR NIH
2.14
Schwieters, Kuszewski, TjandraandClore
構造決定
X-PLOR NIH
2.14
Schwieters, Kuszewski, TjandraandClore
精密化
精密化
手法: simulated annealing, molecular dynamics / ソフトェア番号: 1 詳細: using NOE, dihedral and RDC restraints using XPLOR-NIH, incorperating soft restraints (NOE, dihedral and RDC) using XPLOR-NIH
NMR constraints
NOE constraints total: 724 / NOE intraresidue total count: 299 / NOE long range total count: 132 / NOE medium range total count: 110 / NOE sequential total count: 183 / Protein chi angle constraints total count: 12 / Protein other angle constraints total count: 61 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 48
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 計算したコンフォーマーの数: 200 / 登録したコンフォーマーの数: 20 / 代表コンフォーマー: 1