- PDB-2nsz: 1.15 Angstrom Crystal Structure of the MA3 domain of Pdcd4 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2nsz
Title
1.15 Angstrom Crystal Structure of the MA3 domain of Pdcd4
Components
Programmed cell death protein 4
Keywords
ANTITUMOR PROTEIN / Pdcd4 / tumor suppressor / translation
Function / homology
Function and homology information
epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / positive regulation of endothelial cell apoptotic process / response to alkaloid / negative regulation of vascular associated smooth muscle cell proliferation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / positive regulation of endothelial cell apoptotic process / response to alkaloid / negative regulation of vascular associated smooth muscle cell proliferation / BMP signaling pathway / negative regulation of cytokine production involved in inflammatory response / response to hormone / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of inflammatory response / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / apoptotic process / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function
Programmed cell death protein 4 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha Similarity search - Domain/homology
Resolution: 1.15→28.6 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.614 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.14959
3093
5.1 %
RANDOM
Rwork
0.13228
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-
-
obs
0.13316
57917
99.94 %
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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: MASK
Displacement parameters
Biso mean: 10.826 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.19 Å2
0.1 Å2
0 Å2
2-
-
0.19 Å2
0 Å2
3-
-
-
-0.29 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.027 Å
0.026 Å
Refinement step
Cycle: LAST / Resolution: 1.15→28.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1037
0
16
170
1223
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
1200
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1116
X-RAY DIFFRACTION
r_angle_refined_deg
1.451
1.987
1649
X-RAY DIFFRACTION
r_angle_other_deg
0.864
3
2624
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.14
5
160
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.557
24.364
55
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.902
15
233
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.331
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
188
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1331
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
231
X-RAY DIFFRACTION
r_nbd_refined
0.241
0.2
304
X-RAY DIFFRACTION
r_nbd_other
0.164
0.2
1137
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
606
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
674
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.152
0.2
92
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
0.228
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.25
0.2
70
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.358
0.2
25
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
1.717
1.5
772
X-RAY DIFFRACTION
r_mcbond_other
0.598
1.5
282
X-RAY DIFFRACTION
r_mcangle_it
2.104
2
1184
X-RAY DIFFRACTION
r_scbond_it
2.974
3
524
X-RAY DIFFRACTION
r_scangle_it
4.036
4.5
448
X-RAY DIFFRACTION
r_rigid_bond_restr
1.491
3
2541
X-RAY DIFFRACTION
r_sphericity_free
6.354
3
170
X-RAY DIFFRACTION
r_sphericity_bonded
3.496
3
2277
LS refinement shell
Resolution: 1.149→1.179 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.165
236
-
Rwork
0.15
4263
-
obs
-
-
99.91 %
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