- PDB-7cga: Crystal structure of human unphosphorylated p38gamma -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 7cga
Title
Crystal structure of human unphosphorylated p38gamma
Components
Mitogen-activated protein kinase 12
Keywords
SIGNALING PROTEIN / kinase
Function / homology
Function and homology information
positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase / signal transduction in response to DNA damage ...positive regulation of peptidase activity / myoblast differentiation / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / muscle organ development / positive regulation of muscle cell differentiation / Myogenesis / negative regulation of cell cycle / MAP kinase activity / mitogen-activated protein kinase / signal transduction in response to DNA damage / p38MAPK events / NOD1/2 Signaling Pathway / VEGFA-VEGFR2 Pathway / Negative regulation of MAPK pathway / MAPK cascade / peptidyl-serine phosphorylation / regulation of cell cycle / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function
Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / : / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...Mitogen-activated protein kinase 12 / Mitogen-activated protein (MAP) kinase p38-like / : / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily Similarity search - Domain/homology
A: Mitogen-activated protein kinase 12 B: Mitogen-activated protein kinase 12 C: Mitogen-activated protein kinase 12 D: Mitogen-activated protein kinase 12
Mass: 39907.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK12, ERK6, SAPK3 / Production host: Escherichia coli (E. coli) References: UniProt: P53778, mitogen-activated protein kinase
Resolution: 3.15→19.944 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.579 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 1.094 / ESU R Free: 0.341 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2178
2558
5.037 %
Random
Rwork
0.1603
48225
-
-
all
0.163
-
-
-
obs
-
50783
98.963 %
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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 BULK SOLVENT
Displacement parameters
Biso mean: 65.137 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.069 Å2
-0.034 Å2
-0 Å2
2-
-
-0.069 Å2
-0 Å2
3-
-
-
0.224 Å2
Refinement step
Cycle: LAST / Resolution: 3.15→19.944 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11192
0
0
230
11422
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.013
11432
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
10740
X-RAY DIFFRACTION
r_angle_refined_deg
1.739
1.646
15448
X-RAY DIFFRACTION
r_angle_other_deg
1.278
1.581
24880
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.84
5
1384
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.315
22.166
628
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
23.362
15
2064
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.225
15
80
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
1436
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
12696
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2456
X-RAY DIFFRACTION
r_nbd_refined
0.22
0.2
2632
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.199
0.2
10427
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
5350
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.087
0.2
5833
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.172
0.2
279
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.016
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.183
0.2
42
X-RAY DIFFRACTION
r_nbd_other
0.225
0.2
136
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.162
0.2
7
X-RAY DIFFRACTION
r_mcbond_it
6.054
6.753
5548
X-RAY DIFFRACTION
r_mcbond_other
6.053
6.753
5547
X-RAY DIFFRACTION
r_mcangle_it
9.411
10.129
6928
X-RAY DIFFRACTION
r_mcangle_other
9.41
10.13
6929
X-RAY DIFFRACTION
r_scbond_it
6.264
7.226
5884
X-RAY DIFFRACTION
r_scbond_other
6.263
7.226
5885
X-RAY DIFFRACTION
r_scangle_it
9.84
10.631
8520
X-RAY DIFFRACTION
r_scangle_other
9.84
10.632
8521
X-RAY DIFFRACTION
r_lrange_it
13.935
77.435
12801
X-RAY DIFFRACTION
r_lrange_other
13.931
77.447
12797
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.15-3.23
0.289
167
0.253
3271
X-RAY DIFFRACTION
93.7551
3.23-3.317
0.309
192
0.224
3345
X-RAY DIFFRACTION
99.326
3.317-3.412
0.261
158
0.22
3329
X-RAY DIFFRACTION
100
3.412-3.515
0.278
145
0.203
3230
X-RAY DIFFRACTION
100
3.515-3.628
0.218
151
0.17
3131
X-RAY DIFFRACTION
100
3.628-3.752
0.227
166
0.163
3015
X-RAY DIFFRACTION
100
3.752-3.89
0.192
162
0.155
2943
X-RAY DIFFRACTION
100
3.89-4.045
0.219
149
0.145
2817
X-RAY DIFFRACTION
100
4.045-4.22
0.209
151
0.133
2714
X-RAY DIFFRACTION
100
4.22-4.42
0.171
146
0.124
2607
X-RAY DIFFRACTION
100
4.42-4.651
0.222
115
0.126
2505
X-RAY DIFFRACTION
100
4.651-4.922
0.18
128
0.131
2374
X-RAY DIFFRACTION
100
4.922-5.248
0.206
145
0.148
2214
X-RAY DIFFRACTION
100
5.248-5.647
0.254
123
0.166
2085
X-RAY DIFFRACTION
100
5.647-6.155
0.247
96
0.166
1966
X-RAY DIFFRACTION
100
6.155-6.83
0.227
108
0.151
1787
X-RAY DIFFRACTION
99.9473
6.83-7.79
0.2
82
0.161
1611
X-RAY DIFFRACTION
100
7.79-9.318
0.189
82
0.155
1405
X-RAY DIFFRACTION
100
9.318-12.348
0.161
56
0.136
1161
X-RAY DIFFRACTION
99.9179
12.348-19
0.251
36
0.203
703
X-RAY DIFFRACTION
85.6315
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