- PDB-3gwr: 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: 3gwr
タイトル
Crystal structure of Putative calcium/calmodulin-dependent protein kinase type II association domain (YP_315894.1) from THIOBACILLUS DENITRIFICANS ATCC 25259 at 2.00 A resolution
要素
Putative calcium/calmodulin-dependent protein kinase type II association domain
キーワード
PROTEIN BINDING / YP_315894.1 / Putative calcium/calmodulin-dependent protein kinase type II association domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / TRANSFERASE
機能・相同性
SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Unknown ligand / SnoaL-like domain-containing protein
A: Putative calcium/calmodulin-dependent protein kinase type II association domain B: Putative calcium/calmodulin-dependent protein kinase type II association domain ヘテロ分子
SEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) WAS EXPRESSED WITH A PURIFICATION TAG ...SEQUENCE THIS CONSTRUCT (WITH MUTATION E14D) 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: 2.63 Å3/Da / 溶媒含有率: 53.16 %
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: 6.2 詳細: 0.2000M NH4F, 20.0000% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
解像度: 2→28.892 Å / Num. obs: 22722 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.968 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.23
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2-2.07
0.586
1.4
7243
3711
1
85.4
2.07-2.15
0.448
1.8
8008
4094
1
96.9
2.15-2.25
0.354
2.3
8591
4346
1
96.7
2.25-2.37
0.257
3.1
8499
4287
1
96.3
2.37-2.52
0.219
3.7
8513
4266
1
96.1
2.52-2.71
0.165
5
8287
4116
1
95.7
2.71-2.99
0.106
7.6
8750
4318
1
95.1
2.99-3.42
0.057
13.1
8408
4140
1
94.9
3.42-4.3
0.029
23.6
8374
4089
1
93.9
4.3-28.892
0.023
30.8
8525
4119
1
92.8
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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
XSCALE
データスケーリング
PDB_EXTRACT
3.006
データ抽出
XDS
データ削減
SHELXD
位相決定
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: 2.01→28.892 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.881 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 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. PG4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. AN UNKNOWN LIGAND (UNL) RESEMBLING BENZOIC ACID OR NITROBENZENE IS MODELED NEAR RESIDUE HIS 122 IN BOTH CHAINS. 6. LOOP REGION RESIDUES 94-98 ARE DISORDRED AND HAVE POOR DENSITY SUPPORT.
Rfactor
反射数
%反射
Selection details
Rfree
0.211
1177
5.2 %
RANDOM
Rwork
0.173
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obs
0.175
22693
97.5 %
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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: BABINET MODEL WITH MASK