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
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Production, Crystallization and Preliminary X-Ray Analysis of Ctp:Inositol-1-Phosphate Cytidylyltransferase from Archaeoglobus Fulgidus. Authors: Brito, J.A. / Borges, N. / Santos, H. / Archer, M.
Resolution: 1.89→27.67 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
10915
5.02 %
RANDOM
Rwork
0.206
-
-
-
obs
0.208
217329
-
-
Displacement parameters
Biso mean: 45.55 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.1418 Å2
0 Å2
5.7576 Å2
2-
-
5.703 Å2
0 Å2
3-
-
-
-5.8448 Å2
Refine analyze
Luzzati coordinate error obs: 0.33 Å
Refinement step
Cycle: LAST / Resolution: 1.89→27.67 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
19186
0
48
1168
20402
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
19618
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.1
26409
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
7154
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
483
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
2840
HARMONIC
5
X-RAY DIFFRACTION
t_it
19618
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.21
X-RAY DIFFRACTION
t_other_torsion
17.01
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
2507
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
12
HARMONIC
1
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
22541
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.89→1.94 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.382
596
4.89 %
Rwork
0.3507
11603
-
all
0.3523
12199
-
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
1.921
1.1998
-0.0451
3.8499
-0.4178
1.0924
0.0681
-0.1111
-0.1098
0.7646
-0.1064
-0.0695
0.0263
-0.0128
0.0383
0.2357
-0.0147
0.177
-0.2297
-0.0057
-0.1976
81.1243
-119.794
36.4174
2
1.151
-0.0438
0.2734
2.9101
1.4752
2.5554
0.0291
0.0793
0.1077
0.2216
-0.2686
0.6171
0.1108
-0.1841
0.2395
-0.0359
-0.005
0.3072
-0.2184
-0.019
0.0789
57.5917
-100.277
22.9182
3
1.594
0.5659
-0.4613
3.6501
-0.6869
1.1328
0.1536
-0.0442
0.1234
0.4924
-0.0091
0.3568
-0.1656
-0.0001
-0.1445
0.1921
0.0029
0.1886
-0.1793
-0.0143
-0.1819
74.0273
-65.2795
14.0936
4
1.3302
-0.8084
-0.5033
3.0308
0.6685
3.4896
0.1043
0.1263
-0.0622
-0.1405
-0.1483
-0.2448
-0.3757
0.3461
0.044
0.0726
-0.0724
0.0427
-0.1471
0.0132
-0.1665
98.2243
-87.7048
20.0534
5
0.9803
-0.4486
0.2915
2.0104
-0.5044
0.6955
0.0594
0.0924
-0.0262
-0.3348
0.0195
0.1553
0.1114
-0.0181
-0.0789
0.1958
-0.0275
0.124
-0.1161
-0.0088
-0.1519
34.2177
-89.842
53.8073
6
1.2513
0.7323
-0.1106
4.0498
-0.0624
1.9593
0.0294
-0.1381
-0.0336
0.2739
-0.1446
-0.4774
0.1929
0.3282
0.1152
0.0645
-0.0077
0.1764
-0.1557
0.0159
-0.1462
58.9784
-68.3377
53.8835
7
1.5819
-0.6584
-0.1274
2.7961
-0.5631
0.8833
0.1187
0.0978
-0.0089
-0.532
-0.0387
-0.0125
0.0052
-0.0871
-0.0801
0.2448
-0.0301
0.2034
-0.1812
-0.0182
-0.1814
46.7471
-35.2897
34.3259
8
1.4026
-0.3489
-0.5093
4.0981
1.0982
1.5696
0.0589
0.0746
0.0489
-0.5748
-0.0902
0.5131
-0.0823
-0.133
0.0313
0.1142
-0.036
-0.063
-0.2204
0.0213
-0.0891
20.2419
-54.5259
41.5621
9
0.5567
-0.4132
-0.3418
3.0386
1.0632
1.6047
0.008
0.0137
-0.0469
-0.3772
-0.0283
0.0081
-0.3154
-0.0689
0.0202
0.12
-0.0108
0.1602
-0.1511
0.0082
-0.0893
40.6305
-0.1532
52.1243
10
1.7823
0.5744
0.4815
3.2956
-0.5485
2.7816
0.0646
-0.2077
0.0798
0.1773
-0.1355
0.2938
-0.0498
-0.1522
0.0708
-0.1066
-0.0133
0.1448
-0.1502
-0.0292
-0.0028
19.619
-22.4397
64.9547
11
2.7681
-0.9613
-1.7835
4.5862
-0.2652
3.4867
0.0303
0.4928
-0.4522
-0.4191
-0.4622
0.4926
0.1547
-0.4079
0.4319
-0.1622
0.0208
0.1285
-0.1647
-0.1505
0.0091
62.7569
-5.0323
-0.1254
12
0.8167
0.0935
-0.41
3.0059
0.4181
1.8781
-0.0183
0.0335
0.0607
0.2268
0.0024
0.0564
0.0721
-0.0431
0.0158
0.104
-0.0171
0.2938
-0.1985
-0.0122
-0.0549
79.6143
-27.6191
17.6214
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINA)
2
X-RAY DIFFRACTION
2
(CHAINB)
3
X-RAY DIFFRACTION
3
(CHAINC)
4
X-RAY DIFFRACTION
4
(CHAIND)
5
X-RAY DIFFRACTION
5
(CHAINE)
6
X-RAY DIFFRACTION
6
(CHAINF)
7
X-RAY DIFFRACTION
7
(CHAING)
8
X-RAY DIFFRACTION
8
(CHAINH)
9
X-RAY DIFFRACTION
9
(CHAINI)
10
X-RAY DIFFRACTION
10
(CHAINJ)
11
X-RAY DIFFRACTION
11
(CHAINK)
12
X-RAY DIFFRACTION
12
(CHAINL)
+
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