- PDB-3due: CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 ... -
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基本情報
登録情報
データベース: PDB / ID: 3due
タイトル
CRYSTAL STRUCTURE OF A PUTATIVE PERIPLASMIC PROTEIN FROM DUF2874 FAMILY (BVU_2987) FROM BACTEROIDES VULGATUS ATCC 8482 AT 1.85 A RESOLUTION
要素
Putative periplasmic protein
キーワード
UNKNOWN FUNCTION / PUTATIVE PERIPLASMIC PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
機能・相同性
Inhibitor of vertebrate lysozyme, Ivy - #30 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Inhibitor of vertebrate lysozyme, Ivy / 3-Layer(aba) Sandwich / Alpha Beta / CACODYLATE ION / Putative periplasmic protein
THE CONSTRUCT (RESIDUES 20-145) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 20-145) 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 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
0.97926
1
3
0.97876
1
反射
解像度: 1.85→29.361 Å / Num. obs: 11519 / % possible obs: 100 % / 冗長度: 3.5 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 5.4
反射 シェル
解像度 (Å)
冗長度 (%)
Rmerge(I) obs
Mean I/σ(I) obs
Rsym value
Diffraction-ID
% possible all
1.85-1.9
3.6
0.588
1.3
0.588
1
100
1.9-1.95
3.6
0.447
1.7
0.447
1
100
1.95-2.01
3.6
0.38
2
0.38
1
100
2.01-2.07
3.6
0.294
2.6
0.294
1
100
2.07-2.14
3.6
0.255
3
0.255
1
100
2.14-2.21
3.6
0.222
3.4
0.222
1
100
2.21-2.29
3.6
0.203
3.5
0.203
1
100
2.29-2.39
3.6
0.175
4.3
0.175
1
100
2.39-2.49
3.6
0.167
4.5
0.167
1
100
2.49-2.62
3.6
0.135
5.4
0.135
1
100
2.62-2.76
3.6
0.128
5.3
0.128
1
100
2.76-2.93
3.6
0.109
6.3
0.109
1
100
2.93-3.13
3.5
0.096
6.9
0.096
1
100
3.13-3.38
3.5
0.077
8
0.077
1
100
3.38-3.7
3.5
0.066
8
0.066
1
100
3.7-4.14
3.5
0.052
11.8
0.052
1
100
4.14-4.78
3.4
0.057
10.5
0.057
1
100
4.78-5.85
3.4
0.069
8.5
0.069
1
100
5.85-8.27
3.2
0.064
10.3
0.064
1
100
8.27-29.37
2.8
0.052
10.9
0.052
1
97.1
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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
REFMAC
5.2.0019
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
SCALA
データスケーリング
PDB_EXTRACT
3.004
データ抽出
MOSFLM
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: 1.85→29.361 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.13 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.144 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORAT 4. THE CACODYLATE MOLECULE WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS AND IS SUPPORTED BY AN ANOMALOUS DIFFERENCE FOURIER MAP CALCULATED AT THIS WAVELENGTH.
Rfactor
反射数
%反射
Selection details
Rfree
0.23321
549
4.8 %
RANDOM
Rwork
0.19234
-
-
-
obs
0.19432
10931
99.96 %
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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: 19.076 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.71 Å2
0 Å2
0 Å2
2-
-
0.68 Å2
0 Å2
3-
-
-
0.03 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.85→29.361 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1019
0
5
133
1157
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
1070
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
693
X-RAY DIFFRACTION
r_angle_refined_deg
1.654
1.934
1460
X-RAY DIFFRACTION
r_angle_other_deg
0.94
3
1710
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.367
5
132
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.168
26.364
55
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.88
15
180
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
5.69
15
1
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
158
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1199
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
203
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.2
192
X-RAY DIFFRACTION
r_nbd_other
0.193
0.2
667
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
519
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
512
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.194
0.2
95
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.335
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.25
0.2
17
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.244
0.2
24
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.204
0.2
19
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.422
2
665
X-RAY DIFFRACTION
r_mcbond_other
0.343
2
254
X-RAY DIFFRACTION
r_mcangle_it
1.964
3
1056
X-RAY DIFFRACTION
r_scbond_it
1.502
2
475
X-RAY DIFFRACTION
r_scangle_it
2.237
3
401
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS精密化 シェル
解像度: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.401
40
-
Rwork
0.218
789
-
obs
-
-
100 %
精密化 TLS
手法: refined / Origin x: 9.6413 Å / Origin y: 49.8873 Å / Origin z: 7.6608 Å