- PDB-3ky8: Crystal structure of Putative riboflavin biosynthesis protein (YP... -
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基本情報
登録情報
データベース: PDB / ID: 3ky8
タイトル
Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution
要素
Putative riboflavin biosynthesis protein
キーワード
BIOSYNTHETIC PROTEIN / Putative riboflavin biosynthesis protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
機能・相同性情報
5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process 類似検索 - 分子機能
CRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
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要素
#1: タンパク質
Putativeriboflavinbiosynthesisprotein / Bifunctional deaminase-reductase domain protein
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
0.97917
1
3
0.9787
1
反射
解像度: 2.12→30.029 Å / Num. obs: 24676 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.549 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.7
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
2.12-2.2
0.948
1.5
17588
4765
1
99.2
2.2-2.28
0.769
2
15836
4140
1
99.3
2.28-2.39
0.634
2.4
18413
4788
1
99.5
2.39-2.51
0.465
3.2
16865
4373
1
99.9
2.51-2.67
0.362
4.1
17749
4589
1
99.7
2.67-2.88
0.228
6.2
17926
4640
1
99.8
2.88-3.16
0.131
10.3
17126
4421
1
99.8
3.16-3.62
0.069
18.3
17829
4595
1
99.9
3.62-4.55
0.037
30.4
17713
4559
1
99.9
4.55-30.029
0.029
37.9
17902
4615
1
99.4
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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
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: 2.12→30.029 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 10.193 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.182 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. SULFATE (SO4) IONS AND GLYCEROL (GOL) MOLECULES ARE MODELED BASED ON CRYSTALLIZATION CONDITION. 5. UNIDENTIFIED LIGANDS (UNL) HAVE BEEN MODELED IN ELECTRON DENSITY FOUND NEAR THE PUTATIVE ACTIVE SITES.
Rfactor
反射数
%反射
Selection details
Rfree
0.231
1256
5.1 %
RANDOM
Rwork
0.181
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-
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obs
0.184
24610
99.69 %
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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