- PDB-6kkw: Crystal structure of the complex of phosphopantetheine adenylyl t... -
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Basic information
Entry
Database: PDB / ID: 6kkw
Title
Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.
Components
Phosphopantetheine adenylyltransferase
Keywords
TRANSFERASE
Function / homology
Function and homology information
pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function
Resolution: 3.202→49.497 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.406 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.643 / ESU R Free: 0.354 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2327
334
4.801 %
Rwork
0.175
6623
-
all
0.178
-
-
obs
-
6957
92.378 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Biso mean: 76.279 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 3.202→49.497 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1305
0
45
22
1372
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.013
1381
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
1266
X-RAY DIFFRACTION
r_angle_refined_deg
1.821
1.644
1874
X-RAY DIFFRACTION
r_angle_other_deg
1.317
1.57
2925
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.41
5
162
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.545
21.392
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.833
15
224
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.835
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.07
0.2
176
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1531
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
310
X-RAY DIFFRACTION
r_nbd_refined
0.23
0.2
336
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.219
0.2
1225
X-RAY DIFFRACTION
r_nbtor_refined
0.185
0.2
668
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.084
0.2
678
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.191
0.2
38
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.246
0.2
13
X-RAY DIFFRACTION
r_nbd_other
0.3
0.2
77
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.075
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
7.499
7.589
651
X-RAY DIFFRACTION
r_mcbond_other
7.461
7.584
650
X-RAY DIFFRACTION
r_mcangle_it
11.489
11.368
812
X-RAY DIFFRACTION
r_mcangle_other
11.485
11.378
813
X-RAY DIFFRACTION
r_scbond_it
9.2
8.741
730
X-RAY DIFFRACTION
r_scbond_other
9.194
8.749
731
X-RAY DIFFRACTION
r_scangle_it
13.69
12.741
1061
X-RAY DIFFRACTION
r_scangle_other
13.683
12.75
1062
X-RAY DIFFRACTION
r_lrange_it
17.222
91.649
1554
X-RAY DIFFRACTION
r_lrange_other
17.225
91.721
1552
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.202-3.285
0.676
1
0.409
13
X-RAY DIFFRACTION
2.5878
3.285-3.375
0.281
22
0.241
472
X-RAY DIFFRACTION
93.5606
3.375-3.473
0.32
29
0.236
481
X-RAY DIFFRACTION
100
3.473-3.579
0.26
20
0.21
471
X-RAY DIFFRACTION
100
3.579-3.697
0.287
25
0.216
461
X-RAY DIFFRACTION
100
3.697-3.826
0.283
22
0.191
448
X-RAY DIFFRACTION
100
3.826-3.971
0.164
27
0.16
423
X-RAY DIFFRACTION
100
3.971-4.132
0.192
18
0.154
422
X-RAY DIFFRACTION
99.7732
4.132-4.316
0.197
17
0.143
402
X-RAY DIFFRACTION
100
4.316-4.526
0.143
18
0.122
378
X-RAY DIFFRACTION
100
4.526-4.771
0.182
21
0.113
375
X-RAY DIFFRACTION
100
4.771-5.06
0.181
15
0.134
350
X-RAY DIFFRACTION
100
5.06-5.409
0.314
9
0.151
340
X-RAY DIFFRACTION
100
5.409-5.841
0.228
17
0.178
316
X-RAY DIFFRACTION
100
5.841-6.397
0.266
15
0.191
289
X-RAY DIFFRACTION
100
6.397-7.15
0.311
13
0.201
262
X-RAY DIFFRACTION
100
7.15-8.251
0.265
18
0.194
238
X-RAY DIFFRACTION
100
8.251-10.095
0.223
11
0.143
211
X-RAY DIFFRACTION
100
10.095-14.229
0.176
13
0.183
160
X-RAY DIFFRACTION
98.2955
14.229-49.497
0.825
3
0.48
111
X-RAY DIFFRACTION
92.6829
+
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