- PDB-7ug8: Crystal structure of a solute receptor from Synechococcus CC9311 ... -
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Basic information
Entry
Database: PDB / ID: 7ug8
Title
Crystal structure of a solute receptor from Synechococcus CC9311 in complex with alpha-ketovaleric and calcium
Components
Ketoacid-binding protein
Keywords
TRANSPORT PROTEIN / Substrate-binding protein / marine cyanobacteria / ketoacid-binding protein
Function / homology
Function and homology information
organic acid transport / tripartite ATP-independent periplasmic transporter complex / organic acid binding / transmembrane transport / periplasmic space / metal ion binding Similarity search - Function
Method to determine structure: SAD / Resolution: 1.796→50.277 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.728 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.121 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1898
2454
4.834 %
Rwork
0.1687
48308
-
all
0.17
-
-
obs
-
50762
89.014 %
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: 44.394 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.341 Å2
-1.224 Å2
-0.948 Å2
2-
-
-1.642 Å2
1.715 Å2
3-
-
-
-0.183 Å2
Refinement step
Cycle: LAST / Resolution: 1.796→50.277 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5159
0
26
255
5440
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.013
5356
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.015
5010
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
1.643
7258
X-RAY DIFFRACTION
r_angle_other_deg
1.375
1.578
11483
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.345
5
667
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.739
21.391
302
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.109
15
851
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.801
15
43
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
648
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
6219
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1359
X-RAY DIFFRACTION
r_nbd_refined
0.201
0.2
1070
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.181
0.2
4380
X-RAY DIFFRACTION
r_nbtor_refined
0.169
0.2
2576
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.082
0.2
2276
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.152
0.2
214
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.111
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
0.108
0.2
7
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.129
0.2
13
X-RAY DIFFRACTION
r_nbd_other
0.205
0.2
50
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.263
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
3.873
4.377
2650
X-RAY DIFFRACTION
r_mcbond_other
3.867
4.375
2649
X-RAY DIFFRACTION
r_mcangle_it
5.008
6.539
3314
X-RAY DIFFRACTION
r_mcangle_other
5.008
6.542
3315
X-RAY DIFFRACTION
r_scbond_it
4.753
4.852
2706
X-RAY DIFFRACTION
r_scbond_other
4.748
4.85
2703
X-RAY DIFFRACTION
r_scangle_it
6.79
7.066
3941
X-RAY DIFFRACTION
r_scangle_other
6.79
7.066
3942
X-RAY DIFFRACTION
r_lrange_it
8.05
50.073
6111
X-RAY DIFFRACTION
r_lrange_other
8.054
49.96
6080
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.097
0.05
10497
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
Rms dev position (Å)
Weight position
1
1
A
X-RAY DIFFRACTION
Localncs
0.09743
0.05008
1
2
B
X-RAY DIFFRACTION
Localncs
0.09743
0.05008
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.796-1.843
0.374
147
0.383
2702
X-RAY DIFFRACTION
67.3682
1.843-1.893
0.324
157
0.343
3246
X-RAY DIFFRACTION
82.1187
1.893-1.948
0.321
183
0.315
3148
X-RAY DIFFRACTION
83.5675
1.948-2.008
0.325
164
0.274
3050
X-RAY DIFFRACTION
83.9165
2.008-2.073
0.252
142
0.238
3112
X-RAY DIFFRACTION
86.153
2.073-2.146
0.215
152
0.209
2982
X-RAY DIFFRACTION
86.6464
2.146-2.227
0.225
141
0.188
2954
X-RAY DIFFRACTION
87.9012
2.227-2.318
0.209
146
0.175
2871
X-RAY DIFFRACTION
89.0759
2.318-2.421
0.193
131
0.156
2797
X-RAY DIFFRACTION
90.2033
2.421-2.539
0.206
139
0.149
2710
X-RAY DIFFRACTION
92.0517
2.539-2.676
0.23
128
0.168
2617
X-RAY DIFFRACTION
93.1772
2.676-2.838
0.208
132
0.155
2486
X-RAY DIFFRACTION
94.7864
2.838-3.033
0.195
134
0.158
2433
X-RAY DIFFRACTION
96.2505
3.033-3.275
0.203
117
0.178
2235
X-RAY DIFFRACTION
98.2456
3.275-3.587
0.173
88
0.167
2159
X-RAY DIFFRACTION
99.778
3.587-4.008
0.185
92
0.152
1932
X-RAY DIFFRACTION
100
4.008-4.624
0.142
96
0.128
1704
X-RAY DIFFRACTION
100
4.624-5.654
0.158
75
0.148
1441
X-RAY DIFFRACTION
100
5.654-7.957
0.194
51
0.172
1114
X-RAY DIFFRACTION
100
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