- PDB-4nrd: Crystal structure of a putative GDSL-like lipase (BACOVA_04955) f... -
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基本情報
登録情報
データベース: PDB / ID: 4nrd
タイトル
Crystal structure of a putative GDSL-like lipase (BACOVA_04955) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
要素
Uncharacterized protein
キーワード
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipase_GDSL_lke protein / PF16255 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
A: Uncharacterized protein B: Uncharacterized protein C: Uncharacterized protein D: Uncharacterized protein E: Uncharacterized protein F: Uncharacterized protein ヘテロ分子
THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 21-228 OF THE TARGET SEQUENCE.
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: 0.97937 Å / 相対比: 1
反射
解像度: 2.1→29.391 Å / Num. all: 61839 / Num. obs: 61839 / % possible obs: 82.2 % / 冗長度: 2.3 % / Rsym value: 0.102 / Net I/σ(I): 6
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
2.1-2.15
2.3
0.463
1.9
10781
4744
0.463
84.3
2.15-2.21
2.3
0.365
2.2
10179
4433
0.365
82.3
2.21-2.28
2.3
0.336
2.4
9093
4010
0.336
76.1
2.28-2.35
2.2
0.296
2.6
8654
3866
0.296
75.4
2.35-2.42
2.3
0.277
2.8
9829
4268
0.277
86.3
2.42-2.51
2.3
0.229
3.3
9609
4162
0.229
86.4
2.51-2.6
2.3
0.187
3.7
8770
3864
0.187
83.7
2.6-2.71
2.3
0.172
4.2
8332
3654
0.172
81.3
2.71-2.83
2.3
0.143
5
6912
3057
0.143
71.8
2.83-2.97
2.3
0.117
5.9
7989
3491
0.117
85.2
2.97-3.13
2.3
0.093
7.1
7733
3331
0.093
86.1
3.13-3.32
2.3
0.084
8.1
7293
3180
0.084
86
3.32-3.55
2.3
0.071
9.5
6522
2862
0.071
82.5
3.55-3.83
2.2
0.059
11.8
5428
2415
0.059
76
3.83-4.2
2.3
0.058
13
6199
2668
0.058
89.7
4.2-4.7
2.3
0.058
13.4
5361
2320
0.058
86.7
4.7-5.42
2.2
0.055
13
4003
1788
0.055
75.8
5.42-6.64
2.3
0.063
11.9
3961
1720
0.063
87.4
6.64-9.39
2.3
0.058
12.9
3041
1316
0.058
84.9
9.39-29.391
2.3
0.064
15.4
1584
690
0.064
82.3
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位相決定
位相決定
手法: 分子置換
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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
PHASER
2.3.0
位相決定
SCALA
3.3.20
データスケーリング
BUSTER-TNT
2.10.0
精密化
MOSFLM
データ削減
BUSTER
2.10.0
精密化
精密化
構造決定の手法: 分子置換 / 解像度: 2.1→29.391 Å / Cor.coef. Fo:Fc: 0.9478 / Cor.coef. Fo:Fc free: 0.9277 / Occupancy max: 1 / Occupancy min: 0.5 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF ...詳細: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 7. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.