- PDB-8paf: Crystal structure of human Histidine Triad Nucleotide-Binding Pro... -
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Basic information
Entry
Database: PDB / ID: 8paf
Title
Crystal structure of human Histidine Triad Nucleotide-Binding Protein 1 in complex with 5'-O-[N-(3-Indolepropionic acid)sulfamoyl] 2-aminoethenoadenosine
Components
Histidine triad nucleotide-binding protein 1
Keywords
HYDROLASE / HINT / HIT / histidine triad / phosphoramidase / complex / inhibitor
Function / homology
Function and homology information
purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like superfamily Similarity search - Domain/homology
Histidinetriadnucleotide-bindingprotein1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1
Mass: 13823.931 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→18.486 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.841 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.163 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.1874
592
4.311 %
Rwork
0.1357
13141
-
all
0.138
-
-
obs
-
13733
99.717 %
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: 13.863 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.983 Å2
0 Å2
-0.198 Å2
2-
-
-0.522 Å2
0 Å2
3-
-
-
-1.407 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→18.486 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1762
0
39
291
2092
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.012
1954
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
1834
X-RAY DIFFRACTION
r_angle_refined_deg
1.461
1.657
2657
X-RAY DIFFRACTION
r_angle_other_deg
0.495
1.601
4260
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.852
5
247
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
7.371
5
11
X-RAY DIFFRACTION
r_dihedral_angle_other_2_deg
0.021
5
1
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.259
10
339
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
16.096
10
83
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
279
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2290
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
419
X-RAY DIFFRACTION
r_nbd_refined
0.235
0.2
406
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.194
0.2
1699
X-RAY DIFFRACTION
r_nbtor_refined
0.171
0.2
937
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.081
0.2
1005
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.174
0.2
170
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.049
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.146
0.2
16
X-RAY DIFFRACTION
r_nbd_other
0.147
0.2
51
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.237
0.2
19
X-RAY DIFFRACTION
r_mcbond_it
1.228
1.356
964
X-RAY DIFFRACTION
r_mcbond_other
1.227
1.356
963
X-RAY DIFFRACTION
r_mcangle_it
1.866
2.426
1219
X-RAY DIFFRACTION
r_mcangle_other
1.866
2.425
1220
X-RAY DIFFRACTION
r_scbond_it
1.788
1.567
990
X-RAY DIFFRACTION
r_scbond_other
1.787
1.566
990
X-RAY DIFFRACTION
r_scangle_it
2.902
2.794
1438
X-RAY DIFFRACTION
r_scangle_other
2.901
2.794
1439
X-RAY DIFFRACTION
r_lrange_it
5.041
15.944
2311
X-RAY DIFFRACTION
r_lrange_other
4.787
14.094
2248
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
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
2.1-2.154
0.234
39
0.156
943
0.158
983
0.959
0.983
99.8983
0.135
2.154-2.212
0.168
54
0.137
948
0.138
1002
0.983
0.988
100
0.114
2.212-2.275
0.146
33
0.121
894
0.122
927
0.983
0.991
100
0.101
2.275-2.344
0.158
44
0.117
863
0.119
908
0.984
0.991
99.8899
0.097
2.344-2.42
0.195
40
0.129
855
0.132
895
0.977
0.99
100
0.108
2.42-2.503
0.239
33
0.137
829
0.141
863
0.97
0.988
99.8841
0.114
2.503-2.596
0.232
34
0.139
804
0.143
838
0.963
0.989
100
0.118
2.596-2.7
0.172
36
0.149
788
0.15
824
0.984
0.986
100
0.127
2.7-2.817
0.226
40
0.147
725
0.151
766
0.962
0.987
99.8695
0.128
2.817-2.951
0.191
55
0.141
671
0.145
727
0.974
0.987
99.8624
0.118
2.951-3.106
0.184
31
0.155
675
0.156
708
0.98
0.986
99.7175
0.135
3.106-3.289
0.219
29
0.123
654
0.127
683
0.97
0.991
100
0.115
3.289-3.508
0.181
26
0.14
607
0.142
633
0.976
0.989
100
0.129
3.508-3.778
0.131
25
0.134
565
0.134
590
0.992
0.991
100
0.13
3.778-4.121
0.173
13
0.118
529
0.119
542
0.985
0.992
100
0.114
4.121-4.579
0.234
13
0.107
490
0.11
503
0.981
0.993
100
0.103
4.579-5.234
0.166
20
0.129
425
0.131
445
0.989
0.992
100
0.122
5.234-6.286
0.196
7
0.163
377
0.164
384
0.981
0.987
100
0.156
6.286-8.416
0.197
15
0.171
293
0.172
309
0.98
0.985
99.6764
0.166
8.416-18.486
0.158
5
0.151
206
0.151
215
0.984
0.986
98.1395
0.149
+
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