- PDB-3h51: Crystal structure of Putative calcium/calmodulin dependent protei... -
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基本情報
登録情報
データベース: PDB / ID: 3h51
タイトル
Crystal structure of Putative calcium/calmodulin dependent protein kinase II association domain (NP_636218.1) from XANTHOMONAS CAMPESTRIS at 1.70 A resolution
要素
Putative calcium/calmodulin dependent protein kinase II association domain
キーワード
PROTEIN BINDING / NP_636218.1 / Putative calcium/calmodulin dependent protein kinase II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
機能・相同性
機能・相同性情報
calmodulin-dependent protein kinase activity / calmodulin binding 類似検索 - 分子機能
Uncharacterised conserved protein UCP028470, steroid isomerase-related / Steroid delta5-4-isomerase / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta 類似検索 - ドメイン・相同性
A: Putative calcium/calmodulin dependent protein kinase II association domain B: Putative calcium/calmodulin dependent protein kinase II association domain ヘテロ分子
THE CONSTRUCT (RESIDUES 20-174) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-174) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.32 Å3/Da / 溶媒含有率: 46.96 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 20.0000% PEG-1000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91837
1
2
0.97901
1
反射
解像度: 1.7→29.488 Å / Num. obs: 33865 / % possible obs: 97.9 % / 冗長度: 3.2 % / Biso Wilson estimate: 22.186 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.464
反射 シェル
Diffraction-ID: 1
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.7-1.74
3.2
0.665
1.2
7906
2496
0.665
97.3
1.74-1.79
3.2
0.525
1.5
7586
2398
0.525
97.4
1.79-1.84
3.2
0.372
2.1
7475
2355
0.372
96.5
1.84-1.9
3.2
0.278
2.8
7228
2285
0.278
98.5
1.9-1.96
3.2
0.231
3.1
7022
2213
0.231
96.9
1.96-2.03
3.2
0.188
4
6846
2158
0.188
97.4
2.03-2.11
3.2
0.158
4.7
6574
2085
0.158
98.6
2.11-2.19
3.2
0.135
5.3
6314
1990
0.135
97.6
2.19-2.29
3.2
0.113
5.5
6106
1931
0.113
97.4
2.29-2.4
3.1
0.098
6.6
5831
1854
0.098
98.8
2.4-2.53
3.2
0.085
7.8
5603
1760
0.085
98.6
2.53-2.69
3.2
0.076
8.7
5253
1662
0.076
98.3
2.69-2.87
3.2
0.07
9.1
4983
1570
0.07
98.3
2.87-3.1
3.2
0.066
9.4
4566
1443
0.066
98.6
3.1-3.4
3.1
0.055
11.7
4300
1367
0.055
98.8
3.4-3.8
3.1
0.047
12.7
3802
1208
0.047
98.7
3.8-4.39
3.1
0.044
13.1
3427
1088
0.044
98.2
4.39-5.38
3.1
0.049
11.9
2837
910
0.049
99.1
5.38-7.6
3.1
0.056
10.5
2199
713
0.056
98.2
7.6-29.49
3.1
0.047
13.3
1157
379
0.047
94.4
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
3.2.5
データスケーリング
PDB_EXTRACT
3.006
データ抽出
MOSFLM
データ削減
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.7→29.488 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.425 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.107 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PEG AND PG4 MOLECULES (FRAGMENTS OF PEG1000 AND PEG200) USED IN THE CRYSTALLIZATION AND CRYOPROTECTION CONDITION HAVE BEEN MODELED. 5. ELECTRON DENSITIES OF RESIDUES OF 30-34 AND 108-112 IN BOTH A AND B CHAINS ARE POOR AND MODELS ARE NOT RELIABLE IN THIS REGION. 6. AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF BOTH A AND B CHAINS.
Rfactor
反射数
%反射
Selection details
Rfree
0.215
1695
5 %
RANDOM
Rwork
0.179
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obs
0.18
33842
97.62 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK