- PDB-1zma: Crystal Structure of the Bacterocin Transport Accessory Protein f... -
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基本情報
登録情報
データベース: PDB / ID: 1zma
タイトル
Crystal Structure of the Bacterocin Transport Accessory Protein from Streptococcus pneumoniae
要素
bacterocin transport accessory protein
キーワード
TRANSPORT PROTEIN / alpha-beta-alpha-sandwich / bacterocin transport / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
機能・相同性
Bacteriocin transport accessory protein / bacteriocin biosynthetic process / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Bacterocin transport accessory protein
解像度: 1.25→1.29 Å / 冗長度: 4.2 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 6.8 / % possible all: 51.6
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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
HKL-3000
位相決定
SHELXCD
位相決定
SHELXD
位相決定
SHELXE
モデル構築
MLPHARE
位相決定
SOLVE
位相決定
RESOLVE
位相決定
ARP/wARP
モデル構築
精密化
構造決定の手法: 単波長異常分散 / 解像度: 1.25→25.5 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.533 / SU ML: 0.031 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.062 / ESU R Free: 0.055 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS FOR THE REFINEMENT.
Rfactor
反射数
%反射
Selection details
Rfree
0.16686
2516
10.1 %
RANDOM
Rwork
0.12748
-
-
-
all
0.13138
22451
-
-
obs
0.13138
22451
89.7 %
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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: 9.835 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.42 Å2
0 Å2
-0.74 Å2
2-
-
-0.46 Å2
0 Å2
3-
-
-
0.32 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.25→25.5 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1092
0
0
256
1348
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
1129
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
998
X-RAY DIFFRACTION
r_angle_refined_deg
1.434
1.949
1547
X-RAY DIFFRACTION
r_angle_other_deg
0.863
3
2358
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.06
5
156
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.537
25
54
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.846
15
210
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.11
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
166
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1363
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
236
X-RAY DIFFRACTION
r_nbd_refined
0.258
0.2
286
X-RAY DIFFRACTION
r_nbd_other
0.197
0.2
1134
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
0.083
0.2
655
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.219
0.2
206
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
0.252
0.2
16
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.312
0.2
44
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.208
0.2
58
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
1.249
1.5
885
X-RAY DIFFRACTION
r_mcbond_other
0.512
1.5
282
X-RAY DIFFRACTION
r_mcangle_it
1.556
2
1168
X-RAY DIFFRACTION
r_scbond_it
2.466
3
465
X-RAY DIFFRACTION
r_scangle_it
3.277
4.5
379
X-RAY DIFFRACTION
r_rigid_bond_restr
1.1
3
2463
X-RAY DIFFRACTION
r_sphericity_free
6.077
3
253
X-RAY DIFFRACTION
r_sphericity_bonded
2.849
3
2093
LS精密化 シェル
解像度: 1.253→1.286 Å / Total num. of bins used: 20 /