- PDB-1yx2: Crystal Structure of the Probable Aminomethyltransferase from Bac... -
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基本情報
登録情報
データベース: PDB / ID: 1yx2
タイトル
Crystal Structure of the Probable Aminomethyltransferase from Bacillus subtilis
要素
Aminomethyltransferase
キーワード
TRANSFERASE / aminomethyltransferase / glycine cleavage system T protein / alpha-beta / beta-barrel / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
機能・相同性
機能・相同性情報
aminomethyltransferase / aminomethyltransferase activity / glycine decarboxylation via glycine cleavage system / transaminase activity / cytosol 類似検索 - 分子機能
Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 ...Glycine cleavage system T protein, bacteria / Aminomethyltransferase fragment / Aminomethyltransferase fragment / Glycine cleavage system T protein / Aminomethyltransferase beta-barrel domains / Aminomethyltransferase beta-barrel domains / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / Gyrase A; domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta 類似検索 - ドメイン・相同性
解像度: 2.08→2.18 Å / 冗長度: 4 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.4 / % possible all: 81.7
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.2.0000
精密化
SBC-Collect
データ収集
HKL-2000
データスケーリング
SHARP
位相決定
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.08→41.2 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.205 / SU ML: 0.198 / 交差検証法: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.262 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.28797
4121
9.9 %
RANDOM
Rwork
0.21165
-
-
-
obs
0.21916
37355
95.97 %
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all
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37355
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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: 31.376 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.29 Å2
0 Å2
0.15 Å2
2-
-
-1.99 Å2
0 Å2
3-
-
-
4.35 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.08→41.2 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
5954
0
4
524
6482
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
6099
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.447
1.973
8276
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.276
5
804
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.355
24.719
267
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.061
15
1134
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.849
15
35
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
903
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
4666
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.333
0.2
3566
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.171
0.2
540
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.206
0.2
76
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.152
0.2
27
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
0.505
1.5
3953
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.856
2
6181
X-RAY DIFFRACTION
r_scbond_it
1.195
3
2439
X-RAY DIFFRACTION
r_scangle_it
1.852
4.5
2095
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: 2.079→2.133 Å / Total num. of bins used: 20 /