- PDB-3s42: Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from... -
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Basic information
Entry
Database: PDB / ID: 3s42
Title
Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site
Components
3-dehydroquinate dehydratase
Keywords
LYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TIM BARREL
Function / homology
Function and homology information
3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function
: / 3-dehydroquinate dehydratase, active site / Dehydroquinase class I active site. / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology
BORIC ACID / IMIDAZOLE / MALONIC ACID / NICKEL (II) ION / 3-dehydroquinate dehydratase Similarity search - Component
Resolution: 1.45→28.56 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.035 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.17527
4091
5 %
RANDOM
Rwork
0.14352
-
-
-
obs
0.14515
77604
99.63 %
-
all
-
77604
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 14.752 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.5 Å2
0 Å2
0 Å2
2-
-
1.49 Å2
0 Å2
3-
-
-
-0.99 Å2
Refinement step
Cycle: LAST / Resolution: 1.45→28.56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4026
0
48
563
4637
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.022
4759
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3119
X-RAY DIFFRACTION
r_angle_refined_deg
2.2
1.963
6494
X-RAY DIFFRACTION
r_angle_other_deg
1.056
3
7704
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.612
5
643
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.531
24.65
200
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.533
15
857
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.884
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.134
0.2
764
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.02
5486
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
927
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.494
1.5
3026
X-RAY DIFFRACTION
r_mcbond_other
0.55
1.5
1220
X-RAY DIFFRACTION
r_mcangle_it
2.293
2
4943
X-RAY DIFFRACTION
r_scbond_it
3.397
3
1733
X-RAY DIFFRACTION
r_scangle_it
5.225
4.5
1545
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.45→1.488 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.201
289
-
Rwork
0.179
5399
-
obs
-
-
96.02 %
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
0.5054
0.1563
0.2338
0.4458
0.0601
0.5066
-0.0423
0.0374
0.0693
-0.0227
-0.0107
0.0299
-0.0789
-0.0079
0.053
0.0184
-0.0011
-0.0003
0.016
-0.0084
0.0379
7.1237
9.3073
5.3344
2
0.8298
-0.1858
0.0057
1.2801
0.1241
0.9283
-0.0318
-0.0772
0.0063
0.0605
0.0521
-0.0234
-0.0287
0.0703
-0.0204
0.0064
-0.0023
-0.0008
0.0326
-0.0069
0.0278
17.0242
4.5535
14.4212
3
0.3575
-0.1005
-0.1453
0.3304
0.1741
0.8425
-0.0051
-0.0018
-0.0095
0.0273
0.0013
-0.0063
0.0737
0.0083
0.0038
0.0077
0.0008
-0.0002
0.0002
-0.0006
0.0235
9.7103
-8.1138
2.4793
4
0.7445
0.275
0.0828
1.6782
-0.2388
1.3908
0.0384
0.0424
0.0298
-0.0232
-0.0417
-0.0898
-0.0377
0.0409
0.0033
0.0254
0.0093
0.0049
0.0091
-0.002
0.036
10.9607
6.3723
-8.3592
5
0.5948
0.1765
0.2125
0.2398
-0.2469
0.9165
0.0221
-0.0515
0.1081
0.0466
-0.0274
0.0054
-0.1077
0.1155
0.0053
0.0945
-0.0001
0.0145
0.0741
0.0015
0.0926
12.1291
7.0148
-41.4054
6
1.6481
-0.1401
0.3445
0.9057
-0.1212
1.2228
0.033
0.1544
0.0611
0.0104
-0.0007
0.0574
-0.0506
-0.0932
-0.0323
0.0287
0.0281
0.0175
0.0476
0.0149
0.0276
1.6531
5.4063
-46.3481
7
0.4249
-0.0057
-0.0151
0.1765
-0.1843
1.4781
0.0342
-0.0366
-0.0249
-0.029
-0.0035
-0.0099
0.1283
-0.004
-0.0307
0.0187
-0.0055
-0.0022
0.0053
0.003
0.0125
8.3455
-6.9902
-35.3454
8
2.6359
0.422
1.3772
1.5102
0.1932
3.5379
-0.0869
0.0043
-0.0535
-0.0666
0.0959
0.0611
-0.3686
-0.0631
-0.0089
0.0674
0.0114
0.0145
0.0254
-0.0088
0.0385
7.2843
9.5866
-24.4425
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-7 - 44
2
X-RAY DIFFRACTION
2
A
45 - 102
3
X-RAY DIFFRACTION
3
A
103 - 208
4
X-RAY DIFFRACTION
4
A
209 - 252
5
X-RAY DIFFRACTION
5
B
-23 - 47
6
X-RAY DIFFRACTION
6
B
48 - 91
7
X-RAY DIFFRACTION
7
B
92 - 228
8
X-RAY DIFFRACTION
8
B
229 - 252
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