Yeast Ddi2 Cyanamide Hydratase, T157V mutant, apo structure
Components
DNA damage-inducible protein
Keywords
LYASE / Zn-metalloprotein / HD-domain / hydratase / cyanamide / METAL BINDING PROTEIN
Function / homology
Cyanamide hydratase / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / metal ion binding / DNA damage-inducible protein
#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2)
-
Assembly
Deposited unit
A: DNA damage-inducible protein B: DNA damage-inducible protein C: DNA damage-inducible protein D: DNA damage-inducible protein E: DNA damage-inducible protein F: DNA damage-inducible protein G: DNA damage-inducible protein H: DNA damage-inducible protein I: DNA damage-inducible protein hetero molecules
Resolution: 2.9→39.3 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.07 Details: Iterative maximum likelihood refinement in PHENIX and model building with Coot. The authors state that although Chains H and I are included in the model structure, in general these chains ...Details: Iterative maximum likelihood refinement in PHENIX and model building with Coot. The authors state that although Chains H and I are included in the model structure, in general these chains are considered unreliable due to high B-factors and poor electron density. These chains should not be used for any structural analysis.
Rfactor
Num. reflection
% reflection
Rfree
0.2154
2575
2.53 %
Rwork
0.1926
-
-
obs
0.1932
101864
96.97 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 2.9→39.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
16148
0
169
244
16561
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.006
16653
X-RAY DIFFRACTION
f_angle_d
0.858
22764
X-RAY DIFFRACTION
f_dihedral_angle_d
11.678
9807
X-RAY DIFFRACTION
f_chiral_restr
0.049
2619
X-RAY DIFFRACTION
f_plane_restr
0.006
2916
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.9-2.9558
0.2575
138
0.2309
5554
X-RAY DIFFRACTION
99
2.9558-3.0161
0.2623
123
0.2285
5585
X-RAY DIFFRACTION
98
3.0161-3.0816
0.2459
154
0.224
5551
X-RAY DIFFRACTION
98
3.0816-3.1533
0.2564
158
0.2328
5478
X-RAY DIFFRACTION
98
3.1533-3.2321
0.2811
140
0.2203
5552
X-RAY DIFFRACTION
98
3.2321-3.3195
0.2746
127
0.2272
5566
X-RAY DIFFRACTION
98
3.3195-3.4171
0.2608
150
0.2177
5516
X-RAY DIFFRACTION
98
3.4171-3.5273
0.2711
170
0.214
5505
X-RAY DIFFRACTION
98
3.5273-3.6533
0.2075
171
0.1972
5484
X-RAY DIFFRACTION
98
3.6533-3.7994
0.2144
125
0.1903
5517
X-RAY DIFFRACTION
97
3.7994-3.9722
0.1712
125
0.1739
5529
X-RAY DIFFRACTION
97
3.9722-4.1814
0.1843
142
0.1678
5510
X-RAY DIFFRACTION
97
4.1814-4.4431
0.1678
136
0.1536
5469
X-RAY DIFFRACTION
96
4.4431-4.7856
0.1476
159
0.1502
5473
X-RAY DIFFRACTION
96
4.7856-5.2661
0.1915
120
0.1657
5532
X-RAY DIFFRACTION
96
5.2661-6.0258
0.2176
162
0.1949
5458
X-RAY DIFFRACTION
96
6.0258-7.583
0.2239
123
0.2106
5507
X-RAY DIFFRACTION
95
7.583-39.3209
0.2339
152
0.2008
5503
X-RAY DIFFRACTION
93
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
0.6373
-0.294
0.372
0.7403
-0.429
2.3308
-0.0907
-0.1366
0.0439
0.0013
0.0012
0.0463
-0.2197
-0.5063
0.0818
0.3971
0.2251
-0.0261
0.7497
-0.0057
0.3897
34.8554
85.208
127.3827
2
0.7736
-0.0903
-0.2478
1.5546
-0.0573
1.3712
-0.0378
-0.111
-0.0129
0.1839
0.0568
0.1205
-0.2854
-0.3842
-0.0046
0.3485
0.2247
-0.0179
0.6047
0.0307
0.3813
20.7474
104.8121
95.6159
3
0.8457
0.0286
-0.1126
1.2864
-0.4224
2.155
-0.0031
-0.0496
-0.0508
-0.0444
-0.0011
0.0033
0.0819
0.0188
0.0042
0.2449
0.1139
-0.0369
0.3893
0.019
0.3287
39.125
88.4496
78.4018
4
0.6282
0.0165
-0.2294
1.5009
0.1463
1.6418
0.0091
-0.1074
0.0585
0.1306
0.034
0.0516
-0.1293
-0.1398
-0.0326
0.3072
0.153
-0.0208
0.3879
0.0258
0.4108
19.8238
133.7064
67.8311
5
0.7786
-0.2643
-0.073
1.5369
-0.1498
1.6162
0.0245
-0.0136
-0.0019
-0.0566
-0.0206
-0.0513
-0.0014
0.0901
-0.013
0.235
0.0979
-0.0226
0.3227
0.0235
0.3279
33.7927
114.8582
49.0252
6
1.2138
0.2611
-0.218
1.8038
0.2242
0.7277
-0.0216
-0.0188
0.033
-0.1177
-0.0546
-0.028
-0.0819
0.1288
0.0572
0.513
0.0364
-0.0588
0.2868
0.0101
0.4038
32.4785
165.0476
46.6497
7
1.0627
0.0889
0.1133
1.9179
0.4459
1.3651
-0.0989
0.1402
-0.0895
-0.7285
0.0336
-0.1758
-0.1234
0.1673
0.0584
0.7155
0.0308
0.0911
0.427
0.0008
0.4038
41.4967
146.0842
25.128
8
0.7792
0.0136
-0.4374
0.8977
-0.3446
0.8372
-0.2349
0.2087
0.5423
-0.7791
0.2216
-0.0372
-0.4933
0.2444
0.0145
1.405
-0.2827
-0.059
0.7114
0.1757
1.0019
57.2897
192.7988
33.7994
9
0.1858
0.177
0.2046
0.1545
0.1058
0.5674
-0.6282
0.8079
0.0658
-1.2505
0.423
-0.5405
-0.3803
0.6313
0.2242
1.9305
-0.5953
0.341
1.4813
0.169
1.0542
61.8684
176.8589
8.823
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid -3 through 225)
2
X-RAY DIFFRACTION
2
chain 'B' and (resid -3 through 225)
3
X-RAY DIFFRACTION
3
chain 'C' and (resid -3 through 225)
4
X-RAY DIFFRACTION
4
chain 'D' and (resid -3 through 225)
5
X-RAY DIFFRACTION
5
chain 'E' and (resid -3 through 225)
6
X-RAY DIFFRACTION
6
chain 'F' and (resid -4 through 225)
7
X-RAY DIFFRACTION
7
chain 'G' and (resid -3 through 225)
8
X-RAY DIFFRACTION
8
chain 'H' and (resid0through225)
9
X-RAY DIFFRACTION
9
chain 'I' and (resid1through225)
+
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