LIGASE / tetrahydrofolate synthase / ATP binding / magnesium banding / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases (NIAID) / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information
dihydrofolate synthase activity / tetrahydrofolylpolyglutamate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / ATP binding / metal ion binding Similarity search - Function
Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.963 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20238
2423
5.1 %
RANDOM
Rwork
0.176
-
-
-
obs
0.17736
45277
99.45 %
-
all
-
47700
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.091 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.49 Å2
0 Å2
0 Å2
2-
-
0.55 Å2
0 Å2
3-
-
-
-1.05 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3086
0
42
224
3352
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.021
3226
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2129
X-RAY DIFFRACTION
r_angle_refined_deg
1.447
1.968
4398
X-RAY DIFFRACTION
r_angle_other_deg
0.917
3
5192
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.637
5
413
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.959
23.873
142
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.403
15
508
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.989
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
502
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
3621
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
642
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.836
1.5
2029
X-RAY DIFFRACTION
r_mcbond_other
0.245
1.5
830
X-RAY DIFFRACTION
r_mcangle_it
1.428
2
3244
X-RAY DIFFRACTION
r_scbond_it
2.236
3
1197
X-RAY DIFFRACTION
r_scangle_it
3.513
4.5
1149
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.245
170
-
Rwork
0.215
3273
-
obs
-
-
99.11 %
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
2.8329
-0.7229
0.8617
2.2975
-2.3443
6.7748
-0.055
0.1306
-0.2944
-0.3906
0.024
0.0895
1.1002
-0.2513
0.031
0.3531
-0.0284
0.0157
0.0574
-0.0326
0.1346
65.723
41.8621
3.3556
2
1.7799
0.6824
-0.505
2.3146
-0.6114
2.8163
-0.0507
-0.1409
-0.0916
0.3146
-0.0568
-0.4063
0.3046
0.3824
0.1075
0.1482
0.0568
0.0107
0.2031
0.0296
0.183
75.7901
45.2884
18.3113
3
0.2104
-0.3125
-0.3645
0.7813
0.03
1.5571
0.0164
-0.0254
0.0444
-0.0335
0.0313
-0.0846
-0.1452
0.1127
-0.0477
0.1737
-0.0417
-0.0041
0.1598
-0.0035
0.1703
64.613
64.8758
18.5935
4
2.0104
-0.9057
-0.875
0.8793
-0.0077
2.5052
0.073
0.0804
-0.1471
-0.1895
-0.1429
0.0983
0.016
-0.0966
0.0699
0.1619
-0.0118
-0.0152
0.1734
-0.0165
0.1526
63.2987
56.1138
5.7454
5
1.0294
-0.1893
-0.5265
4.203
-1.4313
2.6579
-0.016
0.0277
-0.0494
-0.1092
-0.0708
-0.2651
0.2847
0.3201
0.0868
0.1497
0.0228
0.0165
0.1926
0.008
0.1737
72.9119
48.5893
10.73
6
1.5399
0.3261
-0.5162
1.282
-0.7794
1.5603
-0.0557
-0.1131
-0.034
-0.0569
0.0896
-0.049
0.174
0.0838
-0.0338
0.1776
-0.0062
-0.0153
0.1449
0.001
0.1263
63.6252
54.0578
24.9313
7
1.4624
0.6183
-0.3843
2.6797
-0.5291
1.181
-0.048
-0.298
-0.1381
0.2234
0.0208
-0.0506
0.0622
0.1915
0.0271
0.2005
0.0091
-0.0188
0.1693
0.007
0.1007
63.3769
54.6851
35.8196
8
7.4457
-1.2355
-1.2986
3.0516
0.2765
1.5667
-0.0245
-0.1391
-0.0091
0.3948
0.0867
0.0955
-0.1032
0.0551
-0.0622
0.2263
-0.0233
0.002
0.1338
-0.0646
0.1213
59.2784
69.1394
36.1825
9
0.8182
0.0876
-0.5828
1.2386
-0.0488
0.8731
0.0416
-0.159
0.067
0.0853
0.047
0.0001
-0.2222
0.0525
-0.0886
0.1994
-0.0273
0.0084
0.1332
-0.0441
0.1644
60.1354
74.8974
27.5567
10
4.5659
3.0579
1.9913
2.687
2.1925
2.0717
-0.078
0.2405
0.2428
-0.1818
0.1086
0.0972
-0.2966
0.0122
-0.0306
0.2554
0.0098
0.0115
0.1792
0.019
0.1802
52.7308
71.1658
15.4746
11
3.6612
-0.6985
2.4772
0.5877
-1.849
7.1116
-0.0571
-0.2614
0.188
0.2205
0.2139
0.1248
-0.5834
-0.6272
-0.1568
0.1584
0.0243
0.0226
0.2285
0.055
0.2136
41.4827
62.3224
20.8894
12
4.8594
-3.4526
0.5972
5.2811
-1.8646
4.2749
0.1592
-0.228
-0.5537
0.0945
0.2447
0.7199
-0.0258
-0.6444
-0.4039
0.0355
-0.0542
0.0164
0.2419
0.0441
0.2623
35.7415
55.885
17.883
13
9.5883
-3.1156
3.4283
3.9222
-1.1811
2.7091
0.2228
-0.5433
-0.2491
0.2719
-0.116
-0.0598
-0.0144
-0.4717
-0.1068
0.0959
-0.0741
0.0228
0.2785
0.1014
0.2395
37.8145
52.9527
25.6743
14
3.4069
-0.2927
0.7543
5.047
-2.099
4.7808
0.1194
0.1211
-0.4009
-0.0681
0.053
0.3632
0.2564
-0.6044
-0.1724
0.0245
-0.0647
-0.0171
0.2528
0.0181
0.3277
33.2895
51.6034
13.7034
15
2.0778
-0.3131
-0.199
2.2639
-1.0764
4.9772
0.1058
0.1875
-0.2601
-0.2009
0.041
0.103
0.3197
-0.1362
-0.1468
0.1201
-0.0461
-0.0461
0.1998
-0.0023
0.2237
44.7661
54.9113
9.6989
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
6 - 25
2
X-RAY DIFFRACTION
2
A
26 - 47
3
X-RAY DIFFRACTION
3
A
48 - 82
4
X-RAY DIFFRACTION
4
A
83 - 110
5
X-RAY DIFFRACTION
5
A
111 - 139
6
X-RAY DIFFRACTION
6
A
140 - 176
7
X-RAY DIFFRACTION
7
A
177 - 218
8
X-RAY DIFFRACTION
8
A
219 - 231
9
X-RAY DIFFRACTION
9
A
247 - 286
10
X-RAY DIFFRACTION
10
A
287 - 306
11
X-RAY DIFFRACTION
11
A
307 - 331
12
X-RAY DIFFRACTION
12
A
332 - 352
13
X-RAY DIFFRACTION
13
A
353 - 368
14
X-RAY DIFFRACTION
14
A
369 - 416
15
X-RAY DIFFRACTION
15
A
417 - 434
+
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