- PDB-1yz5: The crystal structure of 14-3-3-sigma at 2.8 angstrom resolution -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1yz5
Title
The crystal structure of 14-3-3-sigma at 2.8 angstrom resolution
Components
14-3-3 protein sigma
Keywords
SIGNALING PROTEIN / helix bundle / homodimer
Function / homology
Function and homology information
regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / RHO GTPases activate PKNs / protein sequestering activity / protein kinase A signaling / negative regulation of innate immune response / protein export from nucleus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function
Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.815 / SU B: 16.314 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29158
748
5.1 %
RANDOM
Rwork
0.21933
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all
0.22
13974
-
-
obs
0.22293
13856
99.15 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 37.656 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.51 Å2
0 Å2
0 Å2
2-
-
-2.28 Å2
0 Å2
3-
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-
0.77 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3442
0
0
72
3514
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.021
3473
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3099
X-RAY DIFFRACTION
r_angle_refined_deg
1.232
1.971
4663
X-RAY DIFFRACTION
r_angle_other_deg
0.806
3
7170
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.63
5
446
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.116
25.192
156
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.759
15
594
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.146
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.066
0.2
516
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
3912
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
670
X-RAY DIFFRACTION
r_nbd_refined
0.25
0.2
991
X-RAY DIFFRACTION
r_nbd_other
0.182
0.2
3214
X-RAY DIFFRACTION
r_nbtor_refined
0.187
0.2
1729
X-RAY DIFFRACTION
r_nbtor_other
0.091
0.2
1961
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.22
0.2
105
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.186
0.2
16
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.277
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.263
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
0.48
1.5
2285
X-RAY DIFFRACTION
r_mcbond_other
0.049
1.5
919
X-RAY DIFFRACTION
r_mcangle_it
0.855
2
3521
X-RAY DIFFRACTION
r_scbond_it
0.731
3
1350
X-RAY DIFFRACTION
r_scangle_it
1.225
4.5
1142
LS refinement shell
Resolution: 2.8→2.873 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.404
62
-
Rwork
0.302
982
-
obs
-
-
98.03 %
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