- PDB-1vr8: Crystal structure of GTP binding regulator (TM1622) from Thermoto... -
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基本情報
登録情報
データベース: PDB / ID: 1vr8
タイトル
Crystal structure of GTP binding regulator (TM1622) from Thermotoga Maritima at 1.75 A resolution
要素
GTP binding regulator
キーワード
SIGNALING PROTEIN / TM1622 / GTP BINDING REGULATOR / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
機能・相同性
機能・相同性情報
TM1622-like / Protein of unknown function DUF3242 / TM1622-like superfamily / Protein of unknown function (DUF3242) / Protein Transport Mog1p; Chain A / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED ...SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 25-154 OF THE PREDICTED TM1622 GENE PRODUCT. IN ORDER TO REMOVE A PREDICTED TRANSMEMBRANE HELIX, THE FIRST 24 RESIDUES WERE NOT INCLUDED IN THE CONSTRUCT.
解像度: 1.75→29.31 Å / Num. obs: 16407 / % possible obs: 93.2 % / 冗長度: 4.4 % / Biso Wilson estimate: 25.41 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.4
反射 シェル
解像度: 1.75→1.85 Å / 冗長度: 1.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1586 / Rsym value: 0.339 / % possible all: 63.9
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解析
ソフトウェア
名称
バージョン
分類
MOSFLM
データ削減
SCALA
5
データスケーリング
SHELXD
位相決定
autoSHARP
位相決定
REFMAC
5.2.0005
精密化
CCP4
(SCALA)
データスケーリング
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.75→29.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.433 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 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. LOOP 93-96 IS DISORDERED. THERE IS SOME EXTRA UNKNOWN DENSITY NEARBY WHICH IS NOT MODELED AS WELL.
Rfactor
反射数
%反射
Selection details
Rfree
0.18179
832
5.1 %
RANDOM
Rwork
0.1486
-
-
-
obs
0.15019
15549
93.16 %
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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: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 23.241 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.02 Å2
-0.01 Å2
0 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0.04 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.75→29.31 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1098
0
24
172
1294
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
1160
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1054
X-RAY DIFFRACTION
r_angle_refined_deg
1.49
1.931
1560
X-RAY DIFFRACTION
r_angle_other_deg
0.738
3
2433
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.627
5
135
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.444
22.885
52
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.467
15
197
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.793
15
6
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
164
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1244
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
250
X-RAY DIFFRACTION
r_nbd_refined
0.195
0.2
201
X-RAY DIFFRACTION
r_nbd_other
0.171
0.2
1049
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
705
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.15
0.2
115
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.164
0.2
10
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.245
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.225
0.2
26
X-RAY DIFFRACTION
r_mcbond_it
2.299
3
716
X-RAY DIFFRACTION
r_mcbond_other
0.554
3
278
X-RAY DIFFRACTION
r_mcangle_it
2.897
5
1092
X-RAY DIFFRACTION
r_scbond_it
3.196
5
562
X-RAY DIFFRACTION
r_scangle_it
4.192
5
467
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.2
548
LS精密化 シェル
解像度: 1.75→1.797 Å / Total num. of bins used: 20
Rfactor
反射数
%反射
Rfree
0.252
37
5.52 %
Rwork
0.224
633
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obs
-
-
53.09 %
精密化 TLS
手法: refined / Origin x: 36.8774 Å / Origin y: -12.4241 Å / Origin z: -16.2932 Å