- PDB-2ojr: Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag -
+
データを開く
IDまたはキーワード:
読み込み中...
-
基本情報
登録情報
データベース: PDB / ID: 2ojr
タイトル
Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag
要素
Ubiquitin
キーワード
PROTEIN BINDING / Lanthide-binding tag / Terbium / Tb / SAD phasing
機能・相同性
機能・相同性情報
: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation ...: / : / protein modification process => GO:0036211 / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity 類似検索 - 分子機能
Rhinovirus 14, subunit 4 - #180 / Rhinovirus 14, subunit 4 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Rhinovirus 14, subunit 4 - #180 / Rhinovirus 14, subunit 4 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta 類似検索 - ドメイン・相同性
TERBIUM(III) ION / Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 類似検索 - 構成要素
SEQUENCE The inserted residues at the N-terminus of the protein correspond to a 32-residue dSE3 ...SEQUENCE The inserted residues at the N-terminus of the protein correspond to a 32-residue dSE3 lanthide-binding tag The residues numbered 66 to 100 in this entry correspond to residues -4 to 13 and -1' to 15' in the primary citation.
モノクロメーター: SI-111 / 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: 1.1 Å / 相対比: 1
Reflection
冗長度: 5.6 % / Av σ(I) over netI: 9.7 / 数: 36570 / Rmerge(I) obs: 0.106 / Χ2: 1.12 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 6538 / % possible obs: 99.8
Diffraction reflection shell
最高解像度 (Å)
最低解像度 (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.81
50
98.8
1
0.074
0.96
5.2
4.62
5.81
100
1
0.09
1.137
5.7
4.03
4.62
100
1
0.091
1.236
5.8
3.66
4.03
100
1
0.092
1.231
5.9
3.4
3.66
100
1
0.114
1.214
5.9
3.2
3.4
100
1
0.141
1.277
5.4
3.04
3.2
99.8
1
0.199
1.174
5.5
2.91
3.04
100
1
0.267
1.032
5.6
2.8
2.91
99.8
1
0.366
0.944
5.7
2.7
2.8
99.8
1
0.473
0.943
5.4
反射
解像度: 2.6→50 Å / Num. obs: 7214 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / 冗長度: 8.5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 15.8
反射 シェル
解像度: 2.6→2.69 Å / 冗長度: 4.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.8 / % possible all: 87.7
-
位相決定
位相決定
手法: 単波長異常分散
Phasing MAD
D res high: 2.75 Å / D res low: 8.94 Å / FOM : 0.252 / 反射: 3261
Phasing MAD set
R kraut acentric: 0.128 / 最高解像度: 8.94 Å / 最低解像度: 2.75 Å / FOM : 0.254 / Power: 0.37 kW
Phasing MAD set
波長: 1.1 Å / F double prime: 8.58 / F prime: -1.77
-
解析
ソフトウェア
名称
バージョン
分類
NB
DENZO
データ削減
SCALEPACK
データスケーリング
SnB
位相決定
RESOLVE
位相決定
REFMAC
精密化
PDB_EXTRACT
2
データ抽出
精密化
構造決定の手法: 単波長異常分散 / 解像度: 2.6→30.49 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.109 / SU ML: 0.211 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / 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
0.254
285
4.6 %
RANDOM
Rwork
0.216
-
-
-
obs
0.218
6147
100 %
-
all
-
6147
-
-
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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK