- PDB-4mav: Crystal structure of signaling protein SPB-40 complexed with 5-hy... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mav
Title
Crystal structure of signaling protein SPB-40 complexed with 5-hydroxymethyl oxalanetriol at 2.80 A resolution
Components
Chitinase-3-like protein 1
Keywords
SIGNALING PROTEIN / SPB-40 / TIM barrel / 5-hydroxymethyl oxalanetriol
Function / homology
Function and homology information
response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function
Resolution: 2.79→41.72 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.861 / SU B: 13.766 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23391
535
4.8 %
RANDOM
Rwork
0.18192
-
-
-
all
0.18241
11280
-
-
obs
0.18239
10703
99.56 %
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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: 32.923 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.74 Å2
0 Å2
-0 Å2
2-
-
-1.17 Å2
0 Å2
3-
-
-
1.91 Å2
Refinement step
Cycle: LAST / Resolution: 2.79→41.72 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2894
0
30
110
3034
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.019
3009
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2782
X-RAY DIFFRACTION
r_angle_refined_deg
1.861
1.946
4090
X-RAY DIFFRACTION
r_angle_other_deg
0.849
3.001
6361
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7
5
357
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.309
22.817
142
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.274
15
474
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.704
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
441
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3388
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
759
X-RAY DIFFRACTION
r_mcbond_it
2.227
3.153
1437
X-RAY DIFFRACTION
r_mcbond_other
2.216
3.149
1436
X-RAY DIFFRACTION
r_mcangle_it
3.824
4.718
1791
X-RAY DIFFRACTION
r_mcangle_other
3.828
4.722
1792
X-RAY DIFFRACTION
r_scbond_it
2.464
3.502
1572
X-RAY DIFFRACTION
r_scbond_other
2.463
3.502
1572
X-RAY DIFFRACTION
r_scangle_other
4.146
5.135
2293
X-RAY DIFFRACTION
r_long_range_B_refined
7.658
26.876
3602
X-RAY DIFFRACTION
r_long_range_B_other
7.657
26.88
3603
LS refinement shell
Resolution: 2.792→2.864 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.352
29
-
Rwork
0.233
717
-
obs
-
-
94.31 %
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