- PDB-3mbh: Crystal structure of a putative phosphomethylpyrimidine kinase (B... -
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基本情報
登録情報
データベース: PDB / ID: 3mbh
タイトル
Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)
要素
Putative phosphomethylpyrimidine kinase
キーワード
TRANSFERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Kinase
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.
モノクロメーター: Double crystal monochromator / 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: 0.97911 Å / 相対比: 1
反射
解像度: 2→29.814 Å / Num. obs: 125843 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.527 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.12
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
2-2.07
0.554
1.5
44417
23259
1
97.5
2.07-2.15
0.373
2.3
44718
23311
1
98.7
2.15-2.25
0.283
3.1
46721
24394
1
97.6
2.25-2.37
0.205
4.1
46678
24312
1
98.4
2.37-2.52
0.152
5.4
47066
24419
1
99.1
2.52-2.71
0.103
7.8
45701
23660
1
98.9
2.71-2.99
0.066
11.6
47997
24763
1
99
2.99-3.42
0.038
18.6
46384
23878
1
98.7
3.42-4.3
0.022
29.8
45999
23659
1
97.7
4.3-29.814
0.018
37.1
46748
23956
1
97.5
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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
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: 単波長異常分散 / 解像度: 2→29.814 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 8.244 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.15 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. PYRIDOXAL (PXL) MOLECULES FROM THE CRYSTALLIZATION DROP ADDITIVE AND CHLORIDE ANIONS (CL) FROM CRYSTALLIZATION CONDITIONS ARE MODELED IN THE STRUCTURE.
Rfactor
反射数
%反射
Selection details
Rfree
0.206
6306
5 %
RANDOM
Rwork
0.167
-
-
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obs
0.169
125765
99.57 %
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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