CHAD domain superfamily / CHAD / CHAD domain / CHAD domain / CHAD domain profile. / metal ion binding / CARBONATE ION / COPPER (II) ION / CHAD domain protein
Function and homology information
Biological species
Streptomyces chartreusis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.037 Å
Journal: FEBS Lett / Year: 2019 Title: Structural and biochemical analysis of a phosin from Streptomyces chartreusis reveals a combined polyphosphate- and metal-binding fold. Authors: Sebastiaan Werten / Nils Hinnerk Rustmeier / Maximilian Gemmer / Marie-Joëlle Virolle / Winfried Hinrichs / Abstract: X-ray crystallographic analysis of a phosin (PptA) from Steptomyces chartreusis reveals a metal-associated, lozenge-shaped fold featuring a 5-10 Å wide, positively charged tunnel that traverses the ...X-ray crystallographic analysis of a phosin (PptA) from Steptomyces chartreusis reveals a metal-associated, lozenge-shaped fold featuring a 5-10 Å wide, positively charged tunnel that traverses the protein core. Two distinct metal-binding sites were identified in which the predominant metal ion was Cu . In solution, PptA forms stable homodimers that bind with nanomolar affinity to polyphosphate, a stress-related biopolymer acting as a phosphate and energy reserve in conditions of nutrient depletion. A single protein dimer interacts with 14-15 consecutive phosphate moieties within the polymer. Our observations suggest that PptA plays a role in polyphosphate metabolism, mobilisation or sensing, possibly by acting in concert with polyphosphate kinase (Ppk). Like Ppk, phosins may influence antibiotic synthesis by streptomycetes.
Method to determine structure: SAD / Resolution: 2.037→46.196 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.617 / SU ML: 0.142 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.155 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
1228
5 %
Random selection
Rwork
0.191
-
-
-
all
0.193
-
-
-
obs
0.193
24546
98.944 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 43.16 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.127 Å2
0 Å2
-0 Å2
2-
-
-2.613 Å2
0 Å2
3-
-
-
-2.515 Å2
Refinement step
Cycle: LAST / Resolution: 2.037→46.196 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2155
0
28
134
2317
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.019
2213
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2112
X-RAY DIFFRACTION
r_angle_refined_deg
1.532
1.962
3008
X-RAY DIFFRACTION
r_angle_other_deg
0.816
3
4827
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.552
5
278
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.157
20.947
95
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.86
15
344
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.948
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
354
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
2454
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
476
X-RAY DIFFRACTION
r_nbd_refined
0.229
0.2
532
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.159
0.2
1975
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
1095
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.083
0.2
1109
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.175
0.2
103
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.055
0.2
2
X-RAY DIFFRACTION
r_metal_ion_refined
0.184
0.2
2
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.076
0.2
9
X-RAY DIFFRACTION
r_nbd_other
0.136
0.2
37
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.079
0.2
4
X-RAY DIFFRACTION
r_mcbond_it
3.243
4.063
1127
X-RAY DIFFRACTION
r_mcbond_other
3.239
4.061
1126
X-RAY DIFFRACTION
r_mcangle_it
4.821
6.048
1400
X-RAY DIFFRACTION
r_mcangle_other
4.82
6.051
1401
X-RAY DIFFRACTION
r_scbond_it
4.205
4.623
1086
X-RAY DIFFRACTION
r_scbond_other
4.202
4.604
1068
X-RAY DIFFRACTION
r_scangle_it
6.456
6.756
1608
X-RAY DIFFRACTION
r_scangle_other
6.471
6.726
1582
X-RAY DIFFRACTION
r_lrange_it
8.252
49.385
2546
X-RAY DIFFRACTION
r_lrange_other
8.249
49.267
2521
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.037-2.09
0.412
82
0.368
1547
X-RAY DIFFRACTION
90.2993
2.09-2.147
0.356
86
0.329
1646
X-RAY DIFFRACTION
97.6875
2.147-2.209
0.264
85
0.273
1603
X-RAY DIFFRACTION
99.8226
2.209-2.277
0.312
83
0.244
1584
X-RAY DIFFRACTION
99.7606
2.277-2.351
0.279
81
0.221
1545
X-RAY DIFFRACTION
99.6324
2.351-2.434
0.239
78
0.192
1475
X-RAY DIFFRACTION
99.7431
2.434-2.525
0.22
75
0.183
1418
X-RAY DIFFRACTION
99.7328
2.525-2.628
0.266
72
0.182
1380
X-RAY DIFFRACTION
99.7938
2.628-2.745
0.211
70
0.185
1334
X-RAY DIFFRACTION
99.7868
2.745-2.878
0.281
67
0.188
1263
X-RAY DIFFRACTION
99.7749
2.878-3.033
0.312
64
0.203
1215
X-RAY DIFFRACTION
100
3.033-3.216
0.243
60
0.19
1148
X-RAY DIFFRACTION
99.8347
3.216-3.437
0.278
57
0.188
1083
X-RAY DIFFRACTION
99.6503
3.437-3.711
0.198
54
0.165
1028
X-RAY DIFFRACTION
100
3.711-4.062
0.237
49
0.156
925
X-RAY DIFFRACTION
99.8974
4.062-4.537
0.191
46
0.151
865
X-RAY DIFFRACTION
100
4.537-5.231
0.206
40
0.164
761
X-RAY DIFFRACTION
99.5031
5.231-6.386
0.215
34
0.202
658
X-RAY DIFFRACTION
100
6.386-8.946
0.176
28
0.142
519
X-RAY DIFFRACTION
99.8175
8.946-46.196
0.153
17
0.185
321
X-RAY DIFFRACTION
99.705
+
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