- PDB-8hqq: Crystal structure of the glucose-binding protein SAR11_0769 from ... -
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Basic information
Entry
Database: PDB / ID: 8hqq
Title
Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose
Components
Probable binding protein component of ABC sugar transporter
Keywords
TRANSPORT PROTEIN / ABC transporter / glucose transporter / periplasmic binding protein / solute-binding protein
Function / homology
carbohydrate transport / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / beta-D-glucopyranose / Probable binding protein component of ABC sugar transporter
Journal: To Be Published Title: Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose Authors: Clifton, B.E. / Laurino, P.
Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold Resolution: 1.86→38.4 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.36 / Stereochemistry target values: ML Details: Initial refinement by simulated annealing in Phenix, followed by iterative real-space and reciprocal-space refinement in COOT and Refmac. Final rounds of reciprocal-space refinement ...Details: Initial refinement by simulated annealing in Phenix, followed by iterative real-space and reciprocal-space refinement in COOT and Refmac. Final rounds of reciprocal-space refinement including TLS refinement were performed in Phenix.
Rfactor
Num. reflection
% reflection
Rfree
0.2369
1608
4.87 %
Rwork
0.2037
-
-
obs
0.2054
33030
98.79 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.86→38.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2960
0
12
99
3071
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
f_bond_d
0.007
X-RAY DIFFRACTION
f_angle_d
0.931
X-RAY DIFFRACTION
f_dihedral_angle_d
6.348
X-RAY DIFFRACTION
f_chiral_restr
0.054
X-RAY DIFFRACTION
f_plane_restr
0.008
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.86-1.92
0.3913
97
0.333
2543
X-RAY DIFFRACTION
90
1.92-1.99
0.3801
129
0.2956
2772
X-RAY DIFFRACTION
98
1.99-2.07
0.3047
127
0.2672
2824
X-RAY DIFFRACTION
99
2.07-2.17
0.2841
134
0.2401
2819
X-RAY DIFFRACTION
100
2.17-2.28
0.2986
165
0.2275
2832
X-RAY DIFFRACTION
100
2.28-2.42
0.2339
128
0.2296
2873
X-RAY DIFFRACTION
100
2.42-2.61
0.2706
146
0.2192
2879
X-RAY DIFFRACTION
100
2.61-2.87
0.2603
159
0.2092
2877
X-RAY DIFFRACTION
100
2.87-3.29
0.2361
147
0.2086
2910
X-RAY DIFFRACTION
100
3.29-4.14
0.2185
162
0.176
2959
X-RAY DIFFRACTION
100
4.14-38.4
0.1914
214
0.1678
3134
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.673
-0.4124
-0.126
0.4788
0.203
0.1809
0.1704
-0.1714
0.3742
0.4978
-0.1319
0.4982
-0.0909
-0.2614
-0.0397
0.4196
-0.1249
0.144
0.458
-0.0953
0.3825
-20.8855
8.0377
-15.8174
2
1.3607
0.2926
-0.1624
1.8404
-0.6364
1.7086
0.2385
-0.2944
0.4292
0.4758
-0.1713
0.1349
-0.5424
-0.0282
-0.13
0.4337
-0.0786
0.111
0.3267
-0.0587
0.3301
-10.1024
17.2134
-16.7316
3
1.2762
-0.3078
-0.174
1.8061
0.5703
1.6962
0.3591
-0.5698
0.0652
0.8867
-0.3244
-0.183
-0.0152
0.1068
-0.0902
0.6283
-0.2282
-0.0219
0.5114
-0.0136
0.3104
-3.4941
4.8033
-6.8018
4
0.7605
0.5366
0.1461
1.0863
0.2177
2.0818
0.0003
0.0332
0.018
0.0506
0.0883
0.016
0.0893
0.0917
-0.0786
0.2625
-0.057
0.0169
0.2415
-0.0042
0.2537
-7.4212
-1.4809
-36.5917
5
1.6914
0.6323
0.0644
1.1787
0.0571
1.3698
0.0013
0.0575
-0.0601
-0.0209
0.0508
-0.025
0.0493
0.1534
-0.0544
0.2473
-0.0575
0.0129
0.2772
0.0107
0.232
0.1252
5.7771
-38.3367
6
1.5935
0.5336
-0.0556
1.3225
0.4372
1.6191
0.1418
-0.1839
0.0261
0.4143
-0.1444
0.1347
0.1921
-0.26
0.0307
0.3976
-0.1135
0.0561
0.2884
0.0073
0.2567
-13.2264
-0.8041
-22.4091
7
1.7458
0.0612
-0.0699
1.0287
-0.4536
1.094
0.0974
0.102
-0.1895
0.3051
-0.1103
-0.128
0.1386
0.0248
0.0145
0.3582
-0.078
-0.0032
0.3179
-0.0164
0.2564
-1.1477
-3.3761
-25.4221
8
0.5677
-0.2118
0.5608
0.6867
0.3927
1.3155
0.0922
0.2321
0.0708
-0.013
0.0066
0.079
-0.216
0.0224
-0.1061
0.2781
-0.1282
0.0275
0.2961
0.0204
0.2593
5.7104
15.654
-37.6393
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid21through50 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid51through96 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid97through126 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid127through188 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid189through257 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid258through352 )
7
X-RAY DIFFRACTION
7
chain 'A' and (resid353through382 )
8
X-RAY DIFFRACTION
8
chain 'A' and (resid383through418 )
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