- PDB-5mmt: Inward open PepTSt from Streptococcus thermophilus crystallized i... -
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基本情報
登録情報
データベース: PDB / ID: 5mmt
タイトル
Inward open PepTSt from Streptococcus thermophilus crystallized in space group P3121
要素
Di-or tripeptide:H+ symporter
キーワード
TRANSPORT PROTEIN / Integral membrane protein / Major facilitator superfamily transporter (MFS transporter) / POT PTR or PepT family / proton-coupled peptide transporter
機能・相同性
機能・相同性情報
oligopeptide transport / peptide transmembrane transporter activity / identical protein binding / plasma membrane 類似検索 - 分子機能
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha 類似検索 - ドメイン・相同性
モノクロメーター: Double crystal / 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: 0.9795 Å / 相対比: 1
反射
解像度: 3.4→44.85 Å / Num. obs: 11881 / % possible obs: 74.6 % / 冗長度: 5.3 % / Biso Wilson estimate: 96.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 13.67
反射 シェル
解像度: 3.4→3.49 Å / 冗長度: 0.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.13 / CC1/2: 0.834 / % possible all: 5.8
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
1.9_1692
精密化
XDS
データ削減
XSCALE
データスケーリング
SHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 3.4→44.85 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / 位相誤差: 36.6 詳細: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: 3. ...詳細: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: 3.9 A in the a-direction, 3.7 A in the b-direction and 3.4 A in the best diffracting c-direction of the crystal.
Rfactor
反射数
%反射
Selection details
Rfree
0.2861
589
4.96 %
Random
Rwork
0.2652
-
-
-
obs
0.2662
11292
74.7 %
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溶媒の処理
減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータ
Biso mean: 127.1 Å2
精密化ステップ
サイクル: LAST / 解像度: 3.4→44.85 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
3283
0
0
0
3283
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.005
3377
X-RAY DIFFRACTION
f_angle_d
1.188
4604
X-RAY DIFFRACTION
f_dihedral_angle_d
11.482
1132
X-RAY DIFFRACTION
f_chiral_restr
0.045
538
X-RAY DIFFRACTION
f_plane_restr
0.006
552
LS精密化 シェル
解像度 (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.4-3.7405
0.3994
34
0.3201
641
X-RAY DIFFRACTION
17.4
3.7405-4.2813
0.3216
154
0.2724
2964
X-RAY DIFFRACTION
80
4.2813-5.3926
0.2579
195
0.2334
3768
X-RAY DIFFRACTION
99.9
5.3926-44.85
0.2854
206
0.2802
3916
X-RAY DIFFRACTION
99
精密化 TLS
手法: refined / Origin x: 85.5225 Å / Origin y: -29.2027 Å / Origin z: 25.7457 Å