- PDB-7p9y: N-acetylglucosamine kinase from Plesiomonas shigelloides compexed... -
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基本情報
登録情報
データベース: PDB / ID: 7p9y
タイトル
N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine
要素
Ubiquitin-like protein SMT3,N-acetyl-D-glucosamine kinase
キーワード
SUGAR BINDING PROTEIN / N-acetylglucosamine recycling / carbohydrate kinase / ROK kinase.
機能・相同性
機能・相同性情報
N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation ...N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / N-acetylglucosamine metabolic process / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / peptidoglycan turnover / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / protein tag activity / zinc ion binding / ATP binding / identical protein binding / nucleus 類似検索 - 分子機能
N-acetyl-D-glucosamine kinase / : / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin domain profile. ...N-acetyl-D-glucosamine kinase / : / ROK family signature. / ROK family / ROK family / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / ATPase, nucleotide binding domain / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily 類似検索 - ドメイン・相同性
解像度: 1.94→46.136 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.603 / SU ML: 0.122 / 交差検証法: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.138 / 詳細: Hydrogens have not been used
Rfactor
反射数
%反射
Rfree
0.2497
3517
5.132 %
Rwork
0.209
65009
-
all
0.211
-
-
obs
-
68526
99.975 %
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 PLUS MASK
原子変位パラメータ
Biso mean: 55.854 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.288 Å2
0.144 Å2
0 Å2
2-
-
0.288 Å2
0 Å2
3-
-
-
-0.935 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.94→46.136 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
4630
0
143
273
5046
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.012
4918
X-RAY DIFFRACTION
r_angle_refined_deg
1.654
1.641
6627
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.278
5
623
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.908
21.862
247
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.205
15
783
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.51
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.11
0.2
626
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
3690
X-RAY DIFFRACTION
r_nbd_refined
0.227
0.2
2347
X-RAY DIFFRACTION
r_nbtor_refined
0.313
0.2
3315
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.126
0.2
244
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.244
0.2
56
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.114
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
9.215
10.382
2451
X-RAY DIFFRACTION
r_mcangle_it
11.197
19.267
3066
X-RAY DIFFRACTION
r_scbond_it
12.064
11.707
2466
X-RAY DIFFRACTION
r_scangle_it
14.513
21.197
3553
X-RAY DIFFRACTION
r_lrange_it
15.956
102.401
20473
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.085
0.05
9255
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
タイプ
Rms dev position (Å)
Weight position
1
1
AAA
X-RAY DIFFRACTION
Localncs
0.0849
0.05009
1
2
BBB
X-RAY DIFFRACTION
Localncs
0.0849
0.05009
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20