- PDB-7wgk: Crystal structure of Adenosine triphosphate phosphoribosyltransfe... -
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Basic information
Entry
Database: PDB / ID: 7wgk
Title
Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 3.13 A resolution
Components
ATP phosphoribosyltransferase
Keywords
TRANSFERASE / Catalytic Domain of ATP-PRT / HisG
Function / homology
Function and homology information
ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / ATP binding / cytoplasm Similarity search - Function
ATP phosphoribosyltransferase HisG, short form / ATP phosphoribosyltransferase HisG / ATP phosphoribosyltransferase, catalytic domain / ATP phosphoribosyltransferase, conserved site / ATP phosphoribosyltransferase / ATP phosphoribosyltransferase signature. Similarity search - Domain/homology
Resolution: 3.13→59.488 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.847 / SU B: 26.73 / SU ML: 0.436 / Cross valid method: FREE R-VALUE / ESU R Free: 0.553 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2987
502
4.576 %
Rwork
0.2186
10469
-
all
0.222
-
-
obs
-
10971
99.528 %
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: 70.246 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.037 Å2
0 Å2
0 Å2
2-
-
1.06 Å2
-0 Å2
3-
-
-
-1.023 Å2
Refinement step
Cycle: LAST / Resolution: 3.13→59.488 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3518
0
0
24
3542
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.013
3564
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
3612
X-RAY DIFFRACTION
r_angle_refined_deg
1.573
1.638
4814
X-RAY DIFFRACTION
r_angle_other_deg
1.186
1.584
8308
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.91
5
452
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.693
22.674
172
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.874
15
678
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.808
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.065
0.2
468
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
3978
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
750
X-RAY DIFFRACTION
r_nbd_refined
0.222
0.2
571
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.205
0.2
3196
X-RAY DIFFRACTION
r_nbtor_refined
0.155
0.2
1628
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.08
0.2
1854
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.17
0.2
45
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.048
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.35
0.2
3
X-RAY DIFFRACTION
r_nbd_other
0.182
0.2
34
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.33
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
5
7.148
1814
X-RAY DIFFRACTION
r_mcbond_other
4.97
7.146
1813
X-RAY DIFFRACTION
r_mcangle_it
8.122
10.707
2264
X-RAY DIFFRACTION
r_mcangle_other
8.123
10.712
2265
X-RAY DIFFRACTION
r_scbond_it
5.22
7.828
1750
X-RAY DIFFRACTION
r_scbond_other
5.218
7.83
1751
X-RAY DIFFRACTION
r_scangle_it
8.708
11.45
2550
X-RAY DIFFRACTION
r_scangle_other
8.706
11.453
2551
X-RAY DIFFRACTION
r_lrange_it
15.414
133.321
13251
X-RAY DIFFRACTION
r_lrange_other
15.413
133.318
13252
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
3.13-3.211
0.355
39
0.301
759
0.303
800
0.772
0.796
99.75
0.279
3.211-3.299
0.233
40
0.299
729
0.295
770
0.856
0.804
99.8701
0.266
3.299-3.394
0.321
44
0.298
725
0.3
771
0.828
0.822
99.7406
0.27
3.394-3.498
0.337
35
0.295
677
0.297
713
0.823
0.844
99.8597
0.264
3.498-3.613
0.402
36
0.289
670
0.295
706
0.783
0.839
100
0.256
3.613-3.739
0.444
25
0.322
657
0.326
693
0.774
0.852
98.4127
0.288
3.739-3.88
0.42
32
0.271
627
0.277
681
0.75
0.867
96.7695
0.235
3.88-4.037
0.32
29
0.225
600
0.229
631
0.856
0.893
99.683
0.193
4.037-4.216
0.319
26
0.212
599
0.216
625
0.852
0.908
100
0.186
4.216-4.421
0.347
25
0.201
574
0.208
599
0.912
0.932
100
0.177
4.421-4.658
0.201
19
0.15
553
0.152
573
0.948
0.959
99.8255
0.136
4.658-4.939
0.233
15
0.138
527
0.14
542
0.931
0.97
100
0.13
4.939-5.277
0.238
22
0.162
487
0.166
509
0.965
0.962
100
0.156
5.277-5.696
0.282
20
0.181
452
0.185
472
0.924
0.947
100
0.171
5.696-6.234
0.251
19
0.19
427
0.193
446
0.932
0.945
100
0.18
6.234-6.961
0.291
22
0.187
376
0.192
398
0.925
0.949
100
0.188
6.961-8.019
0.244
20
0.178
341
0.181
361
0.947
0.952
100
0.182
8.019-9.777
0.193
23
0.158
293
0.161
317
0.957
0.969
99.6845
0.176
9.777-13.644
0.474
4
0.175
252
0.178
256
0.648
0.971
100
0.199
13.644-59.488
0.292
7
0.324
143
0.322
158
0.879
0.924
94.9367
0.35
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