- PDB-2ooj: CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3224... -
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基本情報
登録情報
データベース: PDB / ID: 2ooj
タイトル
CRYSTAL STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION FROM DUF3224 FAMILY (SO_1590) FROM SHEWANELLA ONEIDENSIS MR-1 AT 1.84 A RESOLUTION
要素
Hypothetical protein
キーワード
UNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
SO1590-like / Protein of unknown function DUF3224 / SO1590-like superfamily / Protein of unknown function (DUF3224) / AOC barrel-like / Beta Barrel / Mainly Beta / ACETATE ION / Uncharacterized protein
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.
モノクロメーター: Single crystal Si(111) bent (horizontal focusing) 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: 0.97883 Å / 相対比: 1
反射
解像度: 1.84→29.79 Å / Num. obs: 24865 / % possible obs: 99.9 % / 冗長度: 4.7 % / Biso Wilson estimate: 26.88 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10.5
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
1.84-1.89
3.6
0.692
1.4
6465
1805
0.692
100
1.89-1.94
3.6
0.525
1.4
6195
1740
0.525
100
1.94-2
3.6
0.409
1.8
6180
1722
0.409
100
2-2.06
3.6
0.349
2.1
6024
1687
0.349
100
2.06-2.12
3.6
0.281
2.5
5707
1598
0.281
100
2.12-2.2
3.6
0.231
3
5628
1573
0.231
100
2.2-2.28
3.6
0.204
3.4
5430
1527
0.204
100
2.28-2.38
3.6
0.18
3.9
5217
1462
0.18
100
2.38-2.48
3.6
0.169
4.1
5039
1406
0.169
100
2.48-2.6
3.6
0.142
4.7
4794
1348
0.142
100
2.6-2.74
4.9
0.174
3.6
6179
1272
0.174
100
2.74-2.91
7.1
0.17
3.8
8818
1239
0.17
100
2.91-3.11
7.1
0.135
4.6
8072
1138
0.135
100
3.11-3.36
7.1
0.11
5.8
7548
1070
0.11
100
3.36-3.68
7
0.095
6.7
7069
1008
0.095
100
3.68-4.11
6.9
0.086
7.1
6271
903
0.086
100
4.11-4.75
6.8
0.085
7.2
5558
817
0.085
99.9
4.75-5.82
6.7
0.083
7.1
4610
687
0.083
99.8
5.82-8.23
6.5
0.085
7
3531
545
0.085
99.1
8.23-29.83
5.6
0.078
7.7
1794
318
0.078
95.6
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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
SHELX
位相決定
REFMAC
5.2.0019
精密化
SCALA
データスケーリング
PDB_EXTRACT
2
データ抽出
MAR345
CCD
データ収集
MOSFLM
データ削減
CCP4
(SCALA)
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: 単波長異常分散 / 解像度: 1.84→29.788 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.012 / SU ML: 0.091 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.118 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ACETATE IONS (ACT) ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 4. THE SE POSITION FOR RESIDUE MSE B1 WAS ASSIGNED BASED ON THE ANOMALOUS DIFFERENCE FOURIER MAPS AND HEAVY ATOM SUB-STRUCTURE USED FOR PHASING. THE CA, CB AND CG ATOMS WERE NOT MODELED DUE TO DISORDER AT THE N-TERMINUS.
Rfactor
反射数
%反射
Selection details
Rfree
0.206
1258
5.1 %
RANDOM
Rwork
0.178
-
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all
0.18
-
-
-
obs
0.18
24752
99.89 %
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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: BABINET MODEL WITH MASK