- PDB-2qnl: CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN (CHU... -
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基本情報
登録情報
データベース: PDB / ID: 2qnl
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN (CHU_0679) FROM CYTOPHAGA HUTCHINSONII ATCC 33406 AT 1.50 A RESOLUTION
要素
Uncharacterized protein
キーワード
SIGNALING PROTEIN / PUTATIVE DNA DAMAGE-INDUCIBLE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
DinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / DinB_2 domain-containing protein
BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
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.
モノクロメーター: Single crystal Si(111) bent (horizontal focusing) 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: 0.97895 Å / 相対比: 1
反射
解像度: 1.5→28.061 Å / Num. obs: 29769 / % possible obs: 97 % / Observed criterion σ(I): -3 / 冗長度: 11.33 % / Biso Wilson estimate: 14.54 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 34.13
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
1.5-1.55
0.161
5.6
9779
4223
1
80.5
1.55-1.62
0.148
7.7
20105
6057
1
95.5
1.62-1.69
0.122
11.4
24173
5188
1
98.6
1.69-1.78
0.099
17.6
38219
5630
1
99.9
1.78-1.89
0.073
24.6
41173
5541
1
100
1.89-2.04
0.05
33.6
42311
5746
1
99.9
2.04-2.24
0.035
44.4
39867
5437
1
99.7
2.24-2.56
0.029
53.2
39959
5510
1
99.3
2.56-3.23
0.023
62.8
40938
5593
1
98.5
3.23-28.061
0.019
75.1
40739
5520
1
97.6
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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
5.2.0019
精密化
PHENIX
精密化
SOLVE
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3
データ抽出
MAR345
CCD
データ収集
XDS
データ削減
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.5→28.061 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.967 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 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. TWO CHLORIDE IONS, ONE SULFATE ION AND FIVE GLYCEROL MOLECULES WERE MODELED.
Rfactor
反射数
%反射
Selection details
Rfree
0.185
1519
5.1 %
RANDOM
Rwork
0.159
-
-
-
obs
0.161
29702
98.32 %
-
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: 11.67 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.04 Å2
-0.02 Å2
0 Å2
2-
-
-0.04 Å2
0 Å2
3-
-
-
0.06 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.5→28.061 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1281
0
37
250
1568
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
1431
X-RAY DIFFRACTION
r_bond_other_d
0.006
0.02
955
X-RAY DIFFRACTION
r_angle_refined_deg
1.644
1.968
1955
X-RAY DIFFRACTION
r_angle_other_deg
1.134
3
2337
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.305
5
181
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.042
24.559
68
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.144
15
233
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
8.356
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
213
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1619
X-RAY DIFFRACTION
r_gen_planes_other
0.012
0.02
282
X-RAY DIFFRACTION
r_nbd_refined
0.235
0.3
368
X-RAY DIFFRACTION
r_nbd_other
0.194
0.3
1049
X-RAY DIFFRACTION
r_nbtor_refined
0.188
0.5
730
X-RAY DIFFRACTION
r_nbtor_other
0.094
0.5
665
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.208
0.5
308
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.309
0.3
26
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.268
0.3
67
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.24
0.5
47
X-RAY DIFFRACTION
r_mcbond_it
1.974
3
933
X-RAY DIFFRACTION
r_mcbond_other
0.472
3
341
X-RAY DIFFRACTION
r_mcangle_it
2.55
5
1406
X-RAY DIFFRACTION
r_scbond_it
4.886
8
614
X-RAY DIFFRACTION
r_scangle_it
6.186
11
548
LS精密化 シェル
解像度: 1.5→1.54 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.174
98
-
Rwork
0.162
1835
-
obs
-
1933
89 %
精密化 TLS
手法: refined / Origin x: 19.391 Å / Origin y: 24.279 Å / Origin z: 10.572 Å