- PDB-3tdq: Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_P... -
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基本情報
登録情報
データベース: PDB / ID: 3tdq
タイトル
Crystal structure of a fimbrial biogenesis protein PilY2 (PilY2_PA4555) from Pseudomonas aeruginosa PAO1 at 2.10 A resolution
要素
PilY2 protein
キーワード
CELL ADHESION / fimbiria / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
機能・相同性
Type 4 fimbrial biogenesis protein PilY2 / Type 4 fimbrial biogenesis protein PilY2 / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / type IV pilus-dependent motility / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / PilY2 protein
THE CONSTRUCT (RESIDUES 19-115) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 19-115) 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: 2.33 Å3/Da / 溶媒含有率: 47.15 % 解説: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND .
タイプ: MARMOSAIC 325 mm CCD / 検出器: CCD / 日付: 2011年7月20日 詳細: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
放射
モノクロメーター: single crystal Si(111) bent / 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
0.97901
1
2
0.91162
1
3
0.97876
1
反射
解像度: 2.1→25.556 Å / Num. obs: 12753 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.782 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.94
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
2.1-2.17
0.33
2.4
3708
1968
1
86.7
2.17-2.26
0.299
2.8
4710
2447
1
99.1
2.26-2.36
0.232
3.6
4491
2346
1
99.4
2.36-2.49
0.196
4.4
4772
2480
1
99.2
2.49-2.64
0.147
5.6
4441
2299
1
99.1
2.64-2.85
0.115
7.2
4747
2458
1
99
2.85-3.13
0.064
11.7
4503
2332
1
99.3
3.13-3.59
0.04
17.3
4624
2392
1
98.4
3.59-4.51
0.024
25.5
4526
2329
1
97.6
4.51-25.556
0.024
28.4
4565
2329
1
95.5
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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
December6, 2010
データスケーリング
BUSTER-TNT
2.8.0
精密化
XDS
データ削減
SHELXD
位相決定
BUSTER
2.8.0
精密化
精密化
構造決定の手法: 多波長異常分散 / 解像度: 2.1→25.556 Å / Cor.coef. Fo:Fc: 0.9463 / Cor.coef. Fo:Fc free: 0.9366 / 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. CHLORIDE, SODIUM, GLYCEROL AND ACETATE MODELED ARE PRESENT IN CRYSTALLIZATION/PROTEIN BUFFER CONDITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).