- PDB-2gpj: CRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_... -
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基本情報
登録情報
データベース: PDB / ID: 2gpj
タイトル
CRYSTAL STRUCTURE OF A SIDEROPHORE-INTERACTING PROTEIN (SPUTCN32_0076) FROM SHEWANELLA PUTREFACIENS CN-32 AT 2.20 A RESOLUTION
要素
Siderophore-interacting protein
キーワード
FAD-BINDING PROTEIN / SIDEROPHORE-INTERACTING PROTEIN / STRUCTURAL GENOMICS (構造ゲノミクス) / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: 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.
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: 0.97917 Å / 相対比: 1
反射
解像度: 2.2→28.76 Å / Num. obs: 18135 / % possible obs: 96.8 % / Biso Wilson estimate: 43.254 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.13
反射 シェル
Diffraction-ID: 1
解像度 (Å)
最高解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.2-2.28
0.763
2
12638
3065
89.3
2.28-2.37
0.669
2.3
13194
3093
93.8
2.37-2.48
0.597
2.6
13950
3259
95
2.48-2.61
0.478
3.3
13703
3195
96.4
2.61-2.77
0.374
4.1
13796
3222
97.8
2.77-2.98
0.265
5.6
14000
3262
98.2
2.98-3.28
0.164
8.4
14335
3350
99.1
3.28-3.76
0.099
12.2
14372
3382
99.4
3.76
0.066
17.4
13942
3325
99.8
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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
5.2.0005
精密化
XSCALE
データスケーリング
PDB_EXTRACT
1.701
データ抽出
XDS
データ削減
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: 2.2→28.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.732 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.183 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). ACETATE, CHLORIDE, AND CALCIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 3). AN ACETATE AND A CA ION ...詳細: 1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2). ACETATE, CHLORIDE, AND CALCIUM IONS FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 3). AN ACETATE AND A CA ION WERE TENTATIVELY MODELED INTO DENSITY NEAR HIS 213. 4). SEVERAL MOLECULES OF ETHYLENE GLYCOL, USED AS A CRYOPROTECTANT, WERE MODELED INTO THE STRUCTURE. 5). 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 SE-MET INCORPORATION. 6). A FLAVIN ADENINE DINUCLEOTIDE MOLECULE WAS OBSERVED IN THE ACTIVE SITE OF THE PROTEIN. 7). UNEXPLAININED ELECTRON DENSITIES ALONG CRYSTALLOGRAPHIC SYMMETRY AXES WERE NOT MODELED. 8). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
Rfactor
反射数
%反射
Selection details
Rfree
0.232
923
5.1 %
RANDOM
Rwork
0.176
-
-
-
obs
0.179
18093
99.93 %
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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
原子変位パラメータ
Biso mean: 42.581 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.18 Å2
0 Å2
0 Å2
2-
-
-0.18 Å2
0 Å2
3-
-
-
0.37 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.2→28.76 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1910
0
112
95
2117
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
2091
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1885
X-RAY DIFFRACTION
r_angle_refined_deg
1.233
2.002
2838
X-RAY DIFFRACTION
r_angle_other_deg
0.624
3
4381
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.84
5
247
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.657
24.457
92
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.204
15
318
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.343
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.068
0.2
302
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
2278
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
388
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.2
395
X-RAY DIFFRACTION
r_nbd_other
0.217
0.2
1847
X-RAY DIFFRACTION
r_nbtor_refined
0.191
0.2
937
X-RAY DIFFRACTION
r_nbtor_other
0.092
0.2
1123
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.148
0.2
92
X-RAY DIFFRACTION
r_metal_ion_refined
0.127
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.176
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.282
0.2
33
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.181
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
3.04
3
1291
X-RAY DIFFRACTION
r_mcbond_other
0.813
3
494
X-RAY DIFFRACTION
r_mcangle_it
4.163
5
2006
X-RAY DIFFRACTION
r_scbond_it
7.289
8
956
X-RAY DIFFRACTION
r_scangle_it
8.873
11
832
LS精密化 シェル
解像度: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.384
83
-
Rwork
0.293
1229
-
obs
-
1312
99.85 %
精密化 TLS
手法: refined / Origin x: 0.815 Å / Origin y: 27.82 Å / Origin z: 4.719 Å