- PDB-2ojr: Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 2ojr
Title
Structure of ubiquitin solved by SAD using the Lanthanide-Binding Tag
Components
Ubiquitin
Keywords
PROTEIN BINDING / Lanthide-binding tag / Terbium / Tb / SAD phasing
Function / homology
Function and homology information
: / : / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / 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 / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / 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 / Negative regulation of FGFR3 signaling Similarity search - Function
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 ...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 Similarity search - Domain/homology
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.
Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1 Å / Relative weight: 1
Reflection
Redundancy: 5.6 % / Av σ(I) over netI: 9.7 / Number: 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
Highest resolution (Å)
Lowest resolution (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
Reflection
Resolution: 2.6→50 Å / Num. obs: 7214 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 15.8
Reflection shell
Resolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.8 / % possible all: 87.7
-
Phasing
Phasing
Method: SAD
Phasing MAD
D res high: 2.75 Å / D res low: 8.94 Å / FOM : 0.252 / Reflection: 3261
Phasing MAD set
R kraut acentric: 0.128 / Highest resolution: 8.94 Å / Lowest resolution: 2.75 Å / FOM : 0.254 / Power: 0.37 kW
Phasing MAD set
Wavelength: 1.1 Å / F double prime: 8.58 / F prime: -1.77
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SnB
phasing
RESOLVE
phasing
REFMAC
refinement
PDB_EXTRACT
2
dataextraction
Refinement
Method to determine structure: SAD / Resolution: 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 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.355 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.254
285
4.6 %
RANDOM
Rwork
0.216
-
-
-
obs
0.218
6147
100 %
-
all
-
6147
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 48.73 Å2
Baniso -1
Baniso -2
Baniso -3
1-
6 Å2
3 Å2
0 Å2
2-
-
6 Å2
0 Å2
3-
-
-
-8.99 Å2
Refinement step
Cycle: LAST / Resolution: 2.6→30.49 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
871
0
2
17
890
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
884
X-RAY DIFFRACTION
r_bond_other_d
0.008
0.02
592
X-RAY DIFFRACTION
r_angle_refined_deg
1.608
1.975
1197
X-RAY DIFFRACTION
r_angle_other_deg
1.959
3
1459
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.514
5
109
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
45.403
26.444
45
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.897
15
162
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.225
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.18
0.2
135
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
983
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
155
X-RAY DIFFRACTION
r_nbd_refined
0.286
0.3
254
X-RAY DIFFRACTION
r_nbd_other
0.238
0.3
596
X-RAY DIFFRACTION
r_nbtor_refined
0.196
0.5
417
X-RAY DIFFRACTION
r_nbtor_other
0.11
0.5
486
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.258
0.5
46
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.121
0.5
5
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.27
0.3
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.267
0.3
13
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.32
0.5
1
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
0.766
1.5
694
X-RAY DIFFRACTION
r_mcbond_other
0.085
1.5
226
X-RAY DIFFRACTION
r_mcangle_it
0.908
2
877
X-RAY DIFFRACTION
r_scbond_it
1.389
3
391
X-RAY DIFFRACTION
r_scangle_it
2.171
4.5
320
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.6→2.67 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.348
9
-
Rwork
0.345
217
-
obs
-
-
100 %
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi