- PDB-7wgm: Crystal structure of Adenosine triphosphate phosphoribosyltransfe... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 7wgm
Title
Crystal structure of Adenosine triphosphate phosphoribosyltransferase (HisG) from Acinetobacter baumannii at 3.15 A resolution
Components
ATP phosphoribosyltransferase
Keywords
TRANSFERASE / The 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: 3.15→62.027 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 25.633 / SU ML: 0.429 / Cross valid method: FREE R-VALUE / ESU R Free: 0.54 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2709
532
5.315 %
Rwork
0.2154
9478
-
all
0.218
-
-
obs
-
10010
94.756 %
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: 70.727 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.353 Å2
-0 Å2
0 Å2
2-
-
0.681 Å2
0 Å2
3-
-
-
-0.328 Å2
Refinement step
Cycle: LAST / Resolution: 3.15→62.027 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3518
0
4
8
3530
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.013
3567
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.015
3615
X-RAY DIFFRACTION
r_angle_refined_deg
1.533
1.638
4817
X-RAY DIFFRACTION
r_angle_other_deg
1.233
1.584
8314
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.384
5
452
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.778
22.674
172
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.675
15
678
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.815
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.061
0.2
468
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3982
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
750
X-RAY DIFFRACTION
r_nbd_refined
0.212
0.2
684
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.211
0.2
3322
X-RAY DIFFRACTION
r_nbtor_refined
0.158
0.2
1683
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.081
0.2
1773
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.122
0.2
52
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.007
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.19
0.2
12
X-RAY DIFFRACTION
r_nbd_other
0.229
0.2
31
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.143
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
5.133
7.197
1815
X-RAY DIFFRACTION
r_mcbond_other
5.125
7.193
1814
X-RAY DIFFRACTION
r_mcangle_it
8.39
10.779
2264
X-RAY DIFFRACTION
r_mcangle_other
8.392
10.785
2265
X-RAY DIFFRACTION
r_scbond_it
5.176
7.876
1752
X-RAY DIFFRACTION
r_scbond_other
5.175
7.88
1753
X-RAY DIFFRACTION
r_scangle_it
8.639
11.517
2553
X-RAY DIFFRACTION
r_scangle_other
8.638
11.522
2554
X-RAY DIFFRACTION
r_lrange_it
16.041
135.022
13622
X-RAY DIFFRACTION
r_lrange_other
16.041
135.02
13623
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
3.15-3.232
0.324
26
0.277
425
0.28
765
0.772
0.845
58.9543
0.234
3.232-3.32
0.353
34
0.289
534
0.293
746
0.827
0.835
76.1394
0.243
3.32-3.416
0.27
29
0.293
680
0.292
739
0.841
0.83
95.9405
0.254
3.416-3.521
0.278
32
0.298
656
0.297
689
0.867
0.837
99.8549
0.259
3.521-3.636
0.362
45
0.29
641
0.295
687
0.831
0.839
99.8544
0.238
3.636-3.763
0.329
45
0.292
610
0.295
655
0.858
0.87
100
0.244
3.763-3.904
0.284
36
0.26
604
0.261
640
0.895
0.875
100
0.234
3.904-4.063
0.295
36
0.21
576
0.215
612
0.888
0.914
100
0.186
4.063-4.243
0.27
26
0.191
570
0.194
597
0.9
0.941
99.8325
0.164
4.243-4.449
0.242
17
0.183
553
0.185
571
0.92
0.948
99.8249
0.163
4.449-4.688
0.267
26
0.157
523
0.163
550
0.933
0.956
99.8182
0.143
4.688-4.971
0.243
21
0.165
492
0.168
513
0.919
0.954
100
0.155
4.971-5.312
0.239
25
0.17
465
0.173
490
0.941
0.952
100
0.156
5.312-5.734
0.352
25
0.19
433
0.197
458
0.884
0.949
100
0.171
5.734-6.276
0.213
26
0.21
393
0.21
419
0.929
0.94
100
0.19
6.276-7.008
0.29
31
0.192
358
0.199
389
0.917
0.94
100
0.188
7.008-8.075
0.276
26
0.2
325
0.206
351
0.931
0.943
100
0.198
8.075-9.848
0.171
9
0.152
288
0.153
298
0.961
0.974
99.6644
0.167
9.848-13.754
0.157
11
0.166
228
0.165
239
0.985
0.977
100
0.189
13.754-62.027
0.137
6
0.33
124
0.317
156
0.968
0.946
83.3333
0.442
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi