- PDB-4gbs: Crystal structure of a putative lipoprotein (BF2707) from Bactero... -
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IDまたはキーワード:
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基本情報
登録情報
データベース: PDB / ID: 4gbs
タイトル
Crystal structure of a putative lipoprotein (BF2707) from Bacteroides fragilis NCTC 9343 at 2.75 A resolution
要素
Putative lipoprotein
キーワード
LIPID BINDING PROTEIN / PF14064 family / transport / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / HEME-BINDING PROTEIN
機能・相同性
HmuY protein / HmuY protein / Putative lipoprotein
1. THE CONSTRUCT (RESIDUES 25-223) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...1. THE CONSTRUCT (RESIDUES 25-223) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
解像度: 2.48→46.676 Å / Num. obs: 21701 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 76.09 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 14.65 / Num. measured all: 137544
反射 シェル
Diffraction-ID: 1
解像度 (Å)
Rmerge F obs
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. possible
Num. unique obs
Rrim(I) all
% possible all
2.48-2.57
0.705
1.17
1.7
14273
2138
2133
1.269
99.8
2.57-2.67
0.785
0.775
2.4
13410
2076
2065
0.843
99.5
2.67-2.79
0.87
0.563
3.2
12508
2089
2079
0.617
99.5
2.79-2.94
0.954
0.297
5.7
13972
2178
2176
0.324
99.9
2.94-3.12
0.986
0.18
9.3
14282
2102
2101
0.195
100
3.12-3.36
0.995
0.105
14.4
14460
2162
2157
0.114
99.8
3.36-3.7
0.998
0.067
20.6
14086
2178
2176
0.072
99.9
3.7-4.23
0.998
0.05
24.8
12596
2186
2174
0.055
99.5
4.23-5.31
0.999
0.044
30.8
14381
2222
2215
0.048
99.7
5.31-46.676
0.998
0.05
30
13576
2483
2441
0.055
98.3
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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
XSCALE
March15, 2012
データスケーリング
BUSTER-TNT
2.10.0
精密化
XDS
データ削減
SHELXD
位相決定
BUSTER
2.10.0
精密化
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.48→46.676 Å / Cor.coef. Fo:Fc: 0.9462 / Cor.coef. Fo:Fc free: 0.9335 / Occupancy max: 1 / Occupancy min: 0.5 / 交差検証法: THROUGHOUT / σ(F): 0 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).5.THE PROTEIN WAS SUBJECTED TO REDUCTIVE METHYLATION PRIOR TO CRYSTALLIZATION. LYSINE 101 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS N-DIMETHYL-LYSINE (MLY). 6. SULFATE MOLECULES(SO4) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE.