- PDB-3r13: Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) f... -
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基本情報
登録情報
データベース: PDB / ID: 3r13
タイトル
Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
要素
Deoxyribose-phosphate aldolase
キーワード
LYASE / TIM beta/alpha-barrel / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
機能・相同性
機能・相同性情報
deoxyribose phosphate catabolic process / deoxyribose-phosphate aldolase / deoxyribose-phosphate aldolase activity / deoxyribonucleotide catabolic process / carbohydrate catabolic process / cytoplasm 類似検索 - 分子機能
Deoxyribose-phosphate aldolase type I / Deoxyribose-phosphate aldolase / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 1.83→44.677 Å / Num. obs: 42195 / % possible obs: 100 % / 冗長度: 3.7 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 8.2
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
1.83-1.93
3.7
0.552
2.4
23040
6174
0.552
100
1.93-2.05
3.8
0.4
3.3
21478
5725
0.4
100
2.05-2.19
3.8
0.27
4.7
20571
5482
0.27
100
2.19-2.36
3.8
0.2
6
19024
5059
0.2
100
2.36-2.59
3.8
0.151
7.4
17609
4672
0.151
100
2.59-2.89
3.8
0.108
9.7
16019
4252
0.108
100
2.89-3.34
3.8
0.075
12.4
14093
3754
0.075
100
3.34-4.09
3.7
0.05
16.9
11899
3186
0.05
100
4.09-5.79
3.7
0.039
20.2
9209
2486
0.039
100
5.79-44.677
3.6
0.034
21.6
5003
1405
0.034
99.7
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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
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
SCALA
3.2.5
データスケーリング
REFMAC
5.5.0110
精密化
XDS
データ削減
XSCALE
データスケーリング
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: 1.83→44.677 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.131 / SU ML: 0.088 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12 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. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE ELECTRON DENSITY REVEALS THAT LYSINE 179 HAS BEEN COVALENTLY MODIFIED. IT WAS MODELED AS AN UNKNOWN LIGAND (UNL). 4. ACETATE (ACT) AND GLYCEROL (GOL) MODELED IN THE STRUCTURE ARE PRESENT IN CRYO/PROTEIN BUFFERS. 5. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 6. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
Rfactor
反射数
%反射
Selection details
Rfree
0.1928
2116
5 %
RANDOM
Rwork
0.1545
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obs
0.1564
42154
99.97 %
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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