- PDB-3dcy: Crystal Structure a TP53-induced glycolysis and apoptosis regulat... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3dcy
Title
Crystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.
Components
REGULATOR PROTEIN
Keywords
apoptosis regulator / OMIM 610775 / C12orf5 / TIGAR / TP53-induced glycolysis and apoptosis regulator / CASP Target / Structural Genomics Medical Relevance / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / Isomerase / Phosphoprotein
Function / homology
Function and homology information
: / regulation of response to DNA damage checkpoint signaling / regulation of pentose-phosphate shunt / intracellular anatomical structure / : / cellular response to cobalt ion / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / positive regulation of hexokinase activity ...: / regulation of response to DNA damage checkpoint signaling / regulation of pentose-phosphate shunt / intracellular anatomical structure / : / cellular response to cobalt ion / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / positive regulation of hexokinase activity / intestinal epithelial cell development / negative regulation of programmed cell death / negative regulation of glucose catabolic process to lactate via pyruvate / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / negative regulation of mitophagy / positive regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA repair / response to ischemia / response to gamma radiation / TP53 Regulates Metabolic Genes / autophagy / cellular response to hypoxia / mitochondrial outer membrane / response to xenobiotic stimulus / apoptotic process / DNA damage response / nucleus / cytoplasm / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS STRUCTURE WAS SUBMITTED AS CASP8 ID T0394.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal grow
Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PROTEIN SOLUTION (10 MG/ML SEMET PROTEIN, 0.050 M NACL, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (20% PEG 3350, 0.10 M MES PH 6.0) CRYOPROTECTED WITH 20% ...Details: PROTEIN SOLUTION (10 MG/ML SEMET PROTEIN, 0.050 M NACL, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (20% PEG 3350, 0.10 M MES PH 6.0) CRYOPROTECTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K
Resolution: 1.748→50 Å / Num. obs: 25927 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.109 / Χ2: 2.108 / Net I/σ(I): 16.223
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. unique all
Χ2
% possible all
1.75-1.81
9.7
0.54
2.369
2514
0.946
98.4
1.81-1.89
13
0.44
2533
0.975
99.8
1.89-1.97
14.3
0.318
2565
1.123
100
1.97-2.07
14.6
0.247
2556
1.157
100
2.07-2.2
14.6
0.188
2555
1.308
100
2.2-2.38
14.7
0.156
2570
1.451
100
2.38-2.61
14.6
0.132
2605
1.645
100
2.61-2.99
14.6
0.109
2610
2.31
100
2.99-3.77
14.5
0.083
2638
2.663
100
3.77-50
13.8
0.068
2781
6.786
99.9
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Phasing
Phasing
Method: SAD
Phasing MAD set
R cullis centric: 0 / Highest resolution: 1.75 Å / Lowest resolution: 36.43 Å / Power centric: 0
ID
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
0
0
22729
3113
ANO_1
0.44
3.003
22626
0
Phasing MAD set shell
R cullis centric: 0 / Power centric: 0
ID
Resolution (Å)
R cullis acentric
Power acentric
Reflection acentric
Reflection centric
ISO_1
7.66-36.43
0
0
215
150
ISO_1
5.48-7.66
0
0
423
154
ISO_1
4.49-5.48
0
0
569
155
ISO_1
3.9-4.49
0
0
695
162
ISO_1
3.49-3.9
0
0
788
149
ISO_1
3.19-3.49
0
0
869
154
ISO_1
2.95-3.19
0
0
962
159
ISO_1
2.76-2.95
0
0
1051
158
ISO_1
2.61-2.76
0
0
1103
161
ISO_1
2.47-2.61
0
0
1182
160
ISO_1
2.36-2.47
0
0
1236
156
ISO_1
2.26-2.36
0
0
1307
156
ISO_1
2.17-2.26
0
0
1360
155
ISO_1
2.09-2.17
0
0
1423
160
ISO_1
2.02-2.09
0
0
1470
162
ISO_1
1.96-2.02
0
0
1506
154
ISO_1
1.9-1.96
0
0
1584
159
ISO_1
1.84-1.9
0
0
1633
160
ISO_1
1.8-1.84
0
0
1673
149
ISO_1
1.75-1.8
0
0
1680
140
ANO_1
7.66-36.43
0.157
8.841
215
0
ANO_1
5.48-7.66
0.159
9.123
423
0
ANO_1
4.49-5.48
0.173
8.153
569
0
ANO_1
3.9-4.49
0.199
7.017
695
0
ANO_1
3.49-3.9
0.252
5.686
788
0
ANO_1
3.19-3.49
0.269
5.401
869
0
ANO_1
2.95-3.19
0.263
5.359
962
0
ANO_1
2.76-2.95
0.281
5.064
1051
0
ANO_1
2.61-2.76
0.31
4.563
1103
0
ANO_1
2.47-2.61
0.359
3.795
1182
0
ANO_1
2.36-2.47
0.377
3.519
1236
0
ANO_1
2.26-2.36
0.434
2.937
1307
0
ANO_1
2.17-2.26
0.473
2.667
1360
0
ANO_1
2.09-2.17
0.529
2.367
1423
0
ANO_1
2.02-2.09
0.586
1.994
1470
0
ANO_1
1.96-2.02
0.637
1.726
1506
0
ANO_1
1.9-1.96
0.691
1.551
1584
0
ANO_1
1.84-1.9
0.766
1.365
1633
0
ANO_1
1.8-1.84
0.843
1.159
1662
0
ANO_1
1.75-1.8
0.907
1.019
1588
0
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
-9.508
-43.389
-30.512
SE
18.06
2.79
2
-3.922
-37.232
-39.334
SE
15.19
2.34
3
-4.411
-61.117
-8.823
SE
18.89
2.36
4
-3.863
-48.1
-39.159
SE
23.82
2.26
5
-1.071
-3.339
-44.033
SE
19.18
2.12
6
-6.683
-46.528
-24.71
SE
31.83
1.97
7
-4.386
-0.724
-75.575
SE
25.62
1.59
8
-10.437
-16.046
-49.611
SE
26.62
1.48
9
-28.627
-45.478
-7.317
SE
22.26
0.42
Phasing dm
Method: Solvent flattening and Histogram matching / Reflection: 25842
Phasing dm shell
Resolution (Å)
Delta phi final
FOM
Reflection
6.81-100
67
0.713
503
5.35-6.81
59.8
0.818
509
4.64-5.35
54.4
0.88
508
4.17-4.64
54.9
0.886
544
3.82-4.17
56.8
0.898
599
3.54-3.82
58.5
0.888
653
3.32-3.54
56.4
0.886
687
3.13-3.32
58.6
0.88
727
2.97-3.13
60
0.871
763
2.84-2.97
56.7
0.901
808
2.72-2.84
53.3
0.882
824
2.61-2.72
57.1
0.904
874
2.52-2.61
55.1
0.886
919
2.43-2.52
53.8
0.896
919
2.36-2.43
56.1
0.899
958
2.29-2.36
53.2
0.898
973
2.22-2.29
54.9
0.91
1044
2.17-2.22
55
0.905
1028
2.11-2.17
56.5
0.883
1086
2.06-2.11
58.5
0.897
1086
2.01-2.06
59.3
0.884
1126
1.97-2.01
58.8
0.889
1137
1.93-1.97
60
0.885
1163
1.89-1.93
63.2
0.885
1216
1.85-1.89
67.9
0.859
1189
1.82-1.85
71.5
0.852
1256
1.79-1.82
71.9
0.819
1234
1.75-1.79
74.6
0.775
1509
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHARP
phasing
DM
5
phasing
REFMAC
5.2.0019
refinement
PDB_EXTRACT
3
dataextraction
HKL-2000
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.748→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.185 / SU B: 2.29 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Additional Fo-Fc density surrounding the loop containing residues 226-230 suggested some structural ambiguity in this region.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.229
1313
5.075 %
RANDOM
Rwork
0.18
-
-
-
obs
0.182
25870
99.511 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 21.653 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.357 Å2
0 Å2
0 Å2
2-
-
0.22 Å2
0 Å2
3-
-
-
0.137 Å2
Refinement step
Cycle: LAST / Resolution: 1.748→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2007
0
5
266
2278
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2056
X-RAY DIFFRACTION
r_angle_refined_deg
1.479
1.977
2782
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.979
5
267
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.426
23.804
92
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.257
15
388
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.907
15
15
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
315
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1532
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
1029
X-RAY DIFFRACTION
r_nbtor_refined
0.304
0.2
1437
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.126
0.2
211
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.17
0.2
28
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.118
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
1.079
1.5
1319
X-RAY DIFFRACTION
r_mcangle_it
1.696
2
2056
X-RAY DIFFRACTION
r_scbond_it
2.686
3
825
X-RAY DIFFRACTION
r_scangle_it
4.022
4.5
716
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection all
% reflection obs (%)
1.748-1.793
0.388
94
0.253
1673
1881
93.939
1.793-1.842
0.248
99
0.228
1739
1846
99.567
1.842-1.896
0.277
104
0.196
1683
1788
99.944
1.896-1.954
0.248
90
0.18
1662
1752
100
1.954-2.018
0.229
73
0.177
1597
1671
99.94
2.018-2.089
0.213
83
0.185
1556
1640
99.939
2.089-2.167
0.225
91
0.172
1505
1596
100
2.167-2.256
0.246
70
0.175
1453
1523
100
2.256-2.356
0.207
61
0.172
1406
1467
100
2.356-2.471
0.216
73
0.176
1326
1399
100
2.471-2.604
0.2
84
0.186
1260
1344
100
2.604-2.761
0.245
73
0.183
1196
1269
100
2.761-2.952
0.244
55
0.186
1159
1214
100
2.952-3.187
0.248
64
0.19
1059
1123
100
3.187-3.49
0.187
43
0.165
981
1024
100
3.49-3.9
0.227
49
0.15
895
944
100
3.9-4.5
0.147
35
0.146
821
856
100
4.5-5.502
0.201
30
0.175
693
723
100
5.502-7.743
0.272
29
0.234
550
579
100
7.743-55.132
0.329
13
0.2
343
358
99.441
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