- PDB-3sc3: Crystal structure of a Putative DNA replication regulator Hda (Sa... -
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基本情報
登録情報
データベース: PDB / ID: 3sc3
タイトル
Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution
要素
Putative DNA replication regulator Hda
キーワード
HYDROLASE REGULATOR / DNA BINDING PROTEIN / P-loop containing nucleoside triphosphate hydrolases / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / HYDROLASE
機能・相同性
機能・相同性情報
DNA replication origin binding / DNA replication initiation / negative regulation of DNA-templated DNA replication initiation / nucleotide binding / metal ion binding / plasma membrane 類似検索 - 分子機能
ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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要素
#1: タンパク質
PutativeDNAreplicationregulatorHda / Regulatory inactivation of DnaA Hda protein
THE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
タイプ: MARMOSAIC 325 mm CCD / 検出器: CCD / 日付: 2008年11月15日 詳細: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
放射
モノクロメーター: single crystal Si(111) bent / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.97799 Å / 相対比: 1
反射
解像度: 3→46.881 Å / Num. obs: 14422 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 91.955 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.68
反射 シェル
Rmerge(I) obs: 0.014 / Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
3-3.17
1.6
16285
2175
99.9
3.17-3.28
2.7
8745
1163
100
3.28-3.41
3.6
9113
1211
100
3.41-3.57
4.9
9140
1222
100
3.57-3.76
7.5
9312
1239
100
3.76-3.99
9.8
8967
1199
100
3.99-4.29
13.1
8984
1200
99.9
4.29-4.72
16.3
9219
1230
100
4.72-5.39
18.2
9077
1218
100
5.39-6.75
17.7
9191
1246
100
6.75
27.2
9314
1324
99.4
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位相決定
位相決定
手法: 単波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
MolProbity
3beta29
モデル構築
PDB_EXTRACT
3.1
データ抽出
SHELX
位相決定
SHARP
位相決定
XSCALE
December6, 2007
データスケーリング
PHENIX
1.4
精密化
XDS
データ削減
SHELXD
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 3.001→46.881 Å / Occupancy max: 1 / Occupancy min: 0.66 / SU ML: 1.17 / σ(F): 1.39 / 位相誤差: 27.67 / 立体化学のターゲット値: MLHL 詳細: 1. 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 ...詳細: 1. 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. 2. SULFATE (SO4) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITION.
Rfactor
反射数
%反射
Rfree
0.2532
1449
10.06 %
Rwork
0.2237
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obs
0.2267
14406
99.9 %
溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 83.041 Å2 / ksol: 0.351 e/Å3