- PDB-3vut: Crystal structures of non-phosphorylated MAP2K4 -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3vut
Title
Crystal structures of non-phosphorylated MAP2K4
Components
Dual specificity mitogen-activated protein kinase kinase 4
Keywords
TRANSFERASE / apo form / Kinase
Function / homology
Function and homology information
smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins ...smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cellular response to sorbitol / JUN kinase kinase activity / cell growth involved in cardiac muscle cell development / mitogen-activated protein kinase kinase / negative regulation of motor neuron apoptotic process / positive regulation of nitric-oxide synthase biosynthetic process / Fc-epsilon receptor signaling pathway / Uptake and function of anthrax toxins / JNK cascade / dendrite cytoplasm / MAP3K8 (TPL2)-dependent MAPK1/3 activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of DNA replication / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular response to mechanical stimulus / MAPK cascade / cellular senescence / positive regulation of neuron apoptotic process / perikaryon / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / molecular adaptor activity / protein kinase activity / positive regulation of protein phosphorylation / phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / cytosol Similarity search - Function
Helix Hairpins - #2120 / Helix Hairpins / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Helix Hairpins - #2120 / Helix Hairpins / Helix non-globular / Special / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.847 / Cor.coef. Fo:Fc free: 0.773 / SU B: 46.99 / SU ML: 0.733 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.40666
447
4.9 %
RANDOM
Rwork
0.3312
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-
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all
0.33471
8659
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obs
0.33471
8658
98.19 %
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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: 94.474 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.97 Å2
-0 Å2
-0 Å2
2-
-
1.78 Å2
0 Å2
3-
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-
1.19 Å2
Refinement step
Cycle: LAST / Resolution: 3.5→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3457
0
0
0
3457
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.02
3512
X-RAY DIFFRACTION
r_angle_refined_deg
1.753
1.989
4753
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
9.003
5
452
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.525
25.802
131
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.344
15
605
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.53
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.116
0.2
567
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
2554
LS refinement shell
Resolution: 3.498→3.586 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.424
40
-
Rwork
0.263
600
-
obs
-
-
95.24 %
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