TRANSFERASE / Transmembrane protein / Rossmann Fold / CDP-alcohol phosphotransferase
Function / homology
Function and homology information
1L-myo-inositol 1-phosphate cytidylyltransferase / CDP-L-myo-inositol myo-inositolphosphotransferase / phosphotransferase activity, for other substituted phosphate groups / phospholipid biosynthetic process / nucleotidyltransferase activity / membrane / metal ion binding Similarity search - Function
Resolution: 2.66→53.85 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.848 / SU B: 29.957 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.30006
838
5 %
RANDOM
Rwork
0.24281
-
-
-
obs
0.24561
15813
99.66 %
-
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: 61.311 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.44 Å2
-0 Å2
-0 Å2
2-
-
4.09 Å2
0 Å2
3-
-
-
-6.53 Å2
Refinement step
Cycle: LAST / Resolution: 2.66→53.85 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3104
0
39
9
3152
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.019
3203
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
3167
X-RAY DIFFRACTION
r_angle_refined_deg
0.596
1.972
4319
X-RAY DIFFRACTION
r_angle_other_deg
0.504
3
7239
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.046
5
406
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.198
22.846
123
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.83
15
530
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.747
15
21
X-RAY DIFFRACTION
r_chiral_restr
0.038
0.2
507
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.02
3538
X-RAY DIFFRACTION
r_gen_planes_other
0
0.02
721
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.657→2.726 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.389
67
-
Rwork
0.331
1124
-
obs
-
-
98.43 %
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
3.7405
1.8828
0.0865
6.0569
0.1326
8.2245
-0.2623
0.7362
-0.1367
-0.5581
0.7946
0.3296
0.1165
-0.6688
-0.5322
0.0883
0.0177
-0.0395
0.655
-0.0065
0.4067
25.4932
26.2156
79.0078
2
3.1719
0.5502
1.0391
0.2389
0.1693
3.8903
-0.1388
0.7125
-0.048
-0.1195
0.1154
0.147
-0.3993
-0.13
0.0234
0.1275
-0.0234
-0.0604
0.372
-0.0201
0.3254
24.1963
28.3069
79.1969
3
2.5332
-1.4416
-1.4999
6.8159
-2.2893
6.0289
0.0836
0.5646
-0.1914
0.1965
0.1905
-0.1073
-0.067
0.6064
-0.2742
0.0654
0.011
-0.0826
0.6727
-0.1228
0.3458
42.3157
24.3418
81.8839
4
4.6375
-1.3416
-1.0093
0.7005
0.375
0.256
-0.1312
0.7681
-0.524
-0.0414
0.1066
-0.031
0.0554
-0.0526
0.0247
0.1867
0.0019
-0.0713
0.6641
-0.3118
0.3475
41.4877
13.1973
74.6823
5
2.6966
1.824
2.9444
4.3554
0.2044
6.5198
0.296
0.3324
-0.3504
-0.5433
-0.3713
0.1881
0.3332
0.6562
0.0753
0.3329
0.0747
-0.1949
0.6094
-0.2036
0.3866
30.6828
18.0486
64.1915
6
2.9566
-1.4488
-0.6396
1.2514
1.6274
5.4895
-0.1227
0.2113
-0.2047
0.1655
0.1482
0.0931
0.4078
0.4561
-0.0255
0.057
-0.0142
-0.0065
0.2381
-0.0434
0.4041
37.276
20.8387
90.2479
7
9.7211
2.8953
6.2985
2.1228
1.5811
6.5174
0.0124
0.5984
0.0456
0.1691
0.0451
-0.4288
0.2316
0.6142
-0.0575
0.2014
0.019
-0.0161
0.0725
0.0113
0.386
42.0564
28.6883
108.8187
8
2.6669
0.6221
2.3058
3.7167
1.3293
7.0126
0.1947
-0.2013
0.0994
0.8563
-0.2393
0.0073
0.2303
-0.6969
0.0446
0.2067
-0.0468
0.0505
0.0732
-0.0038
0.3878
32.1801
34.8995
118.9308
9
4.5935
1.4277
-1.6833
1.355
-1.3083
26.3679
-0.0209
0.1546
0.3939
0.1376
-0.2684
-0.1182
-0.2187
0.3743
0.2893
0.0806
-0.0287
-0.0319
0.1394
0.0386
0.3487
34.5641
34.0588
102.6233
10
1.3972
0.8342
0.5712
3.6064
0.5044
0.3028
0.1335
0.0702
-0.0985
0.4551
-0.0794
-0.3168
0.1232
0.0895
-0.0541
0.19
0.0476
-0.0463
0.0827
0.0021
0.4165
45.7968
46.009
118.3596
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
72 - 89
2
X-RAY DIFFRACTION
2
A
90 - 175
3
X-RAY DIFFRACTION
3
A
176 - 198
4
X-RAY DIFFRACTION
4
A
199 - 230
5
X-RAY DIFFRACTION
5
A
231 - 260
6
X-RAY DIFFRACTION
6
A
261 - 291
7
X-RAY DIFFRACTION
7
A
295 - 316
8
X-RAY DIFFRACTION
8
A
317 - 355
9
X-RAY DIFFRACTION
9
A
356 - 369
10
X-RAY DIFFRACTION
10
A
370 - 489
+
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