- PDB-3h8u: Crystal structure of uncharacterized conserved protein with doubl... -
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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: 3h8u
タイトル
Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution
要素
uncharacterized conserved protein with double-stranded beta-helix domain
キーワード
structural genomics / unknown function / YP_001338853.1 / uncharacterized conserved protein with double-stranded beta-helix domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Cupin domain
機能・相同性
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Cupin_2 domain-containing protein
ジャーナル: To be published タイトル: Crystal structure of uncharacterized conserved protein with double-stranded beta-helix domain (YP_001338853.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.80 A resolution 著者: Joint Center for Structural Genomics (JCSG)
A: uncharacterized conserved protein with double-stranded beta-helix domain B: uncharacterized conserved protein with double-stranded beta-helix domain ヘテロ分子
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
解像度: 1.8→24.953 Å / Num. obs: 21525 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / 冗長度: 2.86 % / Biso Wilson estimate: 19.864 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1
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
1.8-1.86
0.491
1.44
5531
3759
1
92.7
1.86-1.94
0.36
2
6567
4438
1
95.8
1.94-2.03
0.234
2.9
6285
4251
1
96.4
2.03-2.13
0.18
3.7
5722
3870
1
96.3
2.13-2.27
0.133
4.9
6464
4374
1
96.6
2.27-2.44
0.104
5.8
6019
4088
1
96.9
2.44-2.69
0.082
7.3
6326
4295
1
97.7
2.69-3.07
0.055
10.3
6118
4146
1
98
3.07-3.87
0.04
14.5
6273
4258
1
97.7
3.87-24.953
0.033
17.3
6326
4311
1
98.1
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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
5.2.0005
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: 1.8→24.953 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.999 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.115 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 RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. A SULPHATE CATION, GLYCEROL AND PEG FRAGMNET (2PE) MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.196
1044
4.9 %
RANDOM
Rwork
0.152
-
-
-
obs
0.154
21489
99.74 %
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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