- PDB-3di5: Crystal structure of a dinb-like protein (bce_4655) from bacillus... -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 3di5
タイトル
Crystal structure of a dinb-like protein (bce_4655) from bacillus cereus atcc 10987 at 2.01 A resolution
要素
DinB-like Protein
キーワード
METAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
機能・相同性
DNA damage-inducible protein DinB / DinB family / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / NICKEL (II) ION / Uncharacterized protein
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.
-
実験情報
-
実験
実験
手法: X線回折 / 使用した結晶の数: 1
-
試料調製
結晶
マシュー密度: 2.16 Å3/Da / 溶媒含有率: 43.04 %
結晶化
温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.57 詳細: 0.2M magnesium chloride, 30.5% polyethylene glycol 4000, 0.1M TRIS pH 8.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
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
0.97916
1
3
0.9786
1
反射
解像度: 2.009→28.63 Å / Num. obs: 11180 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / 冗長度: 3.93 % / Biso Wilson estimate: 35.693 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 13.57
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
0.413
2.63
3354
1627
1
77.6
2.07-2.15
0.265
3.9
4326
2043
1
97.3
2.15-2.25
0.197
4.8
4593
2166
1
98.3
2.25-2.37
0.135
6.7
4564
2147
1
96.7
2.37-2.52
0.1
8.8
4557
2134
1
98
2.52-2.71
0.074
11
4459
2091
1
98.5
2.71-2.99
0.048
14.9
4672
2174
1
98
2.99-3.42
0.031
20.6
4539
2118
1
98.8
3.42-4.3
0.022
28
4465
2089
1
97
4.3-28.63
0.021
32.1
4455
2093
1
95.7
-
位相決定
位相決定
手法: 多波長異常分散
-
解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.2.0019
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
3.004
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: 2.009→28.63 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.715 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.185 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. 3.X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS, ANOMALOUS DIFFERENCE FOURIERS AND COORDINATION GEOMETRY SUPPORT THE MODELING OF NI ION IN THE PUTATIVE ACTIVE SITE 4.THE DATA IS ANISOTROPIC ALONG THE B-DIRECTION.
Rfactor
反射数
%反射
Selection details
Rfree
0.266
534
4.8 %
RANDOM
Rwork
0.229
-
-
-
obs
0.231
11168
97.98 %
-
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
原子変位パラメータ
Biso mean: 33.148 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-4.4 Å2
0 Å2
0 Å2
2-
-
5.29 Å2
0 Å2
3-
-
-
-0.88 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.009→28.63 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1146
0
1
55
1202
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1189
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
753
X-RAY DIFFRACTION
r_angle_refined_deg
1.273
1.936
1627
X-RAY DIFFRACTION
r_angle_other_deg
0.924
3
1850
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.035
5
151
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.434
24.348
46
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.892
15
184
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.366
15
3
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
189
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1324
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
235
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.2
280
X-RAY DIFFRACTION
r_nbd_other
0.17
0.2
718
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
608
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
554
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.15
0.2
42
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.147
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.121
0.2
17
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.076
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
0.764
1.5
778
X-RAY DIFFRACTION
r_mcbond_other
0.154
1.5
305
X-RAY DIFFRACTION
r_mcangle_it
1.147
2
1219
X-RAY DIFFRACTION
r_scbond_it
1.641
3
489
X-RAY DIFFRACTION
r_scangle_it
2.259
4.5
408
LS精密化 シェル
解像度: 2.009→2.061 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.356
33
-
Rwork
0.316
699
-
all
-
732
-
obs
-
-
87.56 %
精密化 TLS
手法: refined / Origin x: 22.8597 Å / Origin y: 10.4516 Å / Origin z: 20.6285 Å