- PDB-3k8r: Crystal structure of protein of unknown function (YP_427503.1) fr... -
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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: 3k8r
タイトル
Crystal structure of protein of unknown function (YP_427503.1) from Rhodospirillum rubrum ATCC 11170 at 2.75 A resolution
要素
Uncharacterized protein
キーワード
Structural Genomics / Unknown function / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
Uncharacterised protein PF10387, DUF2442 / Protein of unknown function DUF2442 / Protein of unknown function (DUF2442) / NE0471 N-terminal domain-like / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
CRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.66 Å3/Da / 溶媒含有率: 53.72 %
結晶化
温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: 20.0000% PEG-6000, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
モノクロメーター: Single crystal Si(111) bent monochromator (horizontal focusing) プロトコル: MAD / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
ID
波長 (Å)
相対比
1
0.91837
1
2
0.97932
1
反射
解像度: 2.75→28.855 Å / Num. obs: 7459 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 75.246 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.8
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
2.75-2.85
0.616
1.5
2732
1391
1
94.9
2.85-2.96
0.43
2.2
2627
1353
1
99.2
2.96-3.1
0.272
3.2
2878
1481
1
98.3
3.1-3.26
0.197
4.4
2736
1393
1
98.7
3.26-3.46
0.123
6.2
2717
1396
1
98.5
3.46-3.73
0.076
9.6
2792
1424
1
98.5
3.73-4.1
0.069
10.9
2756
1407
1
97.8
4.1-4.69
0.046
14.4
2761
1410
1
98.1
4.69-5.88
0.045
16
2726
1393
1
97.9
5.88-28.855
0.034
19.2
2836
1442
1
97.6
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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
5.5.0053
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: 2.75→28.855 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 24.86 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.474 / ESU R Free: 0.278 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 RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.235
344
4.6 %
RANDOM
Rwork
0.213
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-
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obs
0.214
7458
99.52 %
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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