- PDB-1vlh: Crystal structure of Phosphopantetheine adenylyltransferase (TM07... -
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Basic information
Entry
Database: PDB / ID: 1vlh
Title
Crystal structure of Phosphopantetheine adenylyltransferase (TM0741) from Thermotoga maritima at 2.20 A resolution
Components
Phosphopantetheine adenylyltransferase
Keywords
TRANSFERASE / TM0741 / PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information
pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function
Resolution: 2.2→68.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.196 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. EACH CHAIN CONTAINS ONE BOUND MOLECULE OF 4'-PHOSPHOPANTETHEINE (PNS). THE MODEL ALSO CONTAINS A MOLECULE OF MPD FROM CRYSTALLIZATION SOLUTION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22687
2497
5.1 %
RANDOM
Rwork
0.17051
-
-
-
obs
0.17332
46254
94.36 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 41.497 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.92 Å2
0 Å2
-1.41 Å2
2-
-
-1.44 Å2
0 Å2
3-
-
-
2.3 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→68.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7520
0
140
258
7918
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
7802
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
7481
X-RAY DIFFRACTION
r_angle_refined_deg
1.716
2.001
10546
X-RAY DIFFRACTION
r_angle_other_deg
0.9
3
17408
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.716
5
943
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.939
24.369
309
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.255
15
1468
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.308
15
36
X-RAY DIFFRACTION
r_chiral_restr
0.096
0.2
1242
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
8299
X-RAY DIFFRACTION
r_gen_planes_other
0.003
0.02
1459
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
1633
X-RAY DIFFRACTION
r_nbd_other
0.184
0.2
7801
X-RAY DIFFRACTION
r_nbtor_other
0.092
0.2
5151
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.164
0.2
324
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.085
0.2
3
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.227
0.2
12
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.274
0.2
45
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.182
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
1.835
3
5055
X-RAY DIFFRACTION
r_mcbond_other
0.493
3
1924
X-RAY DIFFRACTION
r_mcangle_it
2.681
5
7654
X-RAY DIFFRACTION
r_scbond_it
5.857
8
3386
X-RAY DIFFRACTION
r_scangle_it
7.412
11
2892
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
916
tightpositional
0.06
0.05
2
B
916
tightpositional
0.05
0.05
3
C
916
tightpositional
0.05
0.05
4
D
916
tightpositional
0.05
0.05
5
E
916
tightpositional
0.05
0.05
6
F
916
tightpositional
0.06
0.05
1
A
1553
loosepositional
0.67
5
2
B
1553
loosepositional
0.76
5
3
C
1553
loosepositional
0.69
5
4
D
1553
loosepositional
0.75
5
5
E
1553
loosepositional
0.7
5
6
F
1553
loosepositional
0.73
5
1
A
916
tightthermal
0.17
0.5
2
B
916
tightthermal
0.18
0.5
3
C
916
tightthermal
0.16
0.5
4
D
916
tightthermal
0.16
0.5
5
E
916
tightthermal
0.16
0.5
6
F
916
tightthermal
0.16
0.5
1
A
1553
loosethermal
2.42
10
2
B
1553
loosethermal
2.75
10
3
C
1553
loosethermal
2.6
10
4
D
1553
loosethermal
2.45
10
5
E
1553
loosethermal
2.42
10
6
F
1553
loosethermal
2.72
10
LS refinement shell
Resolution: 2.2→2.257 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.327
133
5.19 %
Rwork
0.232
2428
-
obs
-
-
67.32 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
5.3034
0.2765
0.8907
1.8581
-0.3011
2.3653
-0.0206
-0.2211
0.0055
0.2613
0.0435
0.1133
0.2868
-0.3799
-0.0228
-0.0424
-0.0373
0.0319
-0.1457
0.0457
-0.1961
40.6075
1.1487
24.5336
2
3.9712
1.9225
-0.3409
2.7517
-0.2607
1.6161
-0.1906
0.4537
0.0211
-0.2938
0.204
-0.0135
0.3014
0.2022
-0.0134
-0.1159
0.0453
0.0521
-0.0804
-0.0487
-0.1414
58.1107
5.4531
0.8859
3
3.0527
0.955
0.6252
4.2227
0.358
2.005
0.0182
-0.5037
0.2107
0.4368
-0.1145
0.1762
-0.0875
-0.3764
0.0963
-0.1308
0.0528
0.0606
0.0418
-0.0252
-0.1085
21.2424
27.9106
18.5988
4
3.6344
-1.15
1.2388
2.3127
-0.6723
2.9479
-0.0763
0.2824
0.3451
-0.1357
-0.1183
-0.229
-0.4083
0.1845
0.1946
-0.1146
-0.0699
0.0366
-0.123
0.1128
-0.0371
52.2938
38.0993
-1.3713
5
2.1717
-0.765
0.6223
3.9615
-0.8606
2.2607
-0.0496
-0.1638
0.1644
0.2939
-0.0885
-0.0953
-0.1863
0.0267
0.1381
-0.0551
-0.0114
-0.0942
-0.1448
-0.0606
-0.1001
52.8705
32.0107
27.7493
6
2.7232
-1.2898
0.0969
3.5841
0.1426
2.2913
0.0309
0.3861
-0.0489
-0.2544
-0.0282
-0.0785
0.3074
-0.0524
-0.0027
-0.0891
-0.0309
-0.0098
-0.0397
0.0106
-0.1782
27.8845
16.4309
-8.1927
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 157
2
X-RAY DIFFRACTION
2
B
1 - 158
3
X-RAY DIFFRACTION
3
C
1 - 158
4
X-RAY DIFFRACTION
4
D
1 - 158
5
X-RAY DIFFRACTION
5
E
1 - 157
6
X-RAY DIFFRACTION
6
F
1 - 157
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