- PDB-4gfs: 1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratas... -
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Basic information
Entry
Database: PDB / ID: 4gfs
Title
1.8 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 with Nickel Bound at 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
Resolution: 1.8→29.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.311 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24925
2027
5.1 %
RANDOM
Rwork
0.19878
-
-
-
all
0.20136
38018
-
-
obs
0.20136
38018
96.79 %
-
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: 39.789 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-4.16 Å2
-0 Å2
3.37 Å2
2-
-
-1.57 Å2
-0 Å2
3-
-
-
4.81 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3806
0
14
193
4013
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.019
3946
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3893
X-RAY DIFFRACTION
r_angle_refined_deg
1.763
1.964
5362
X-RAY DIFFRACTION
r_angle_other_deg
0.845
3
8955
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.548
5
516
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.231
24.568
162
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.846
15
702
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.992
15
24
X-RAY DIFFRACTION
r_chiral_restr
0.108
0.2
650
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
4465
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
833
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.801→1.848 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.346
124
-
Rwork
0.346
2450
-
obs
-
-
85.4 %
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
2.7044
-6.4617
0.649
16.4325
-1.1025
0.3777
-0.5332
-0.3292
0.0467
0.5267
0.6812
-0.3748
-0.4357
-0.0129
-0.148
0.6881
0.0309
0.0432
0.535
-0.0167
0.1974
-6.7846
-3.4058
35.636
2
3.4524
-0.697
-1.7359
1.5476
1.5505
1.9438
-0.112
-0.1407
-0.1954
0.3356
0.0398
-0.0215
0.2442
0.1594
0.0723
0.2926
-0.0278
-0.1066
0.2439
-0.0107
0.0637
-10.3287
-8.5384
26.0078
3
14.5696
-3.1474
-0.0491
1.127
0.8919
1.9074
-0.0675
0.0025
-0.8555
-0.1093
-0.1784
0.3461
-0.0698
-0.3496
0.2459
0.2316
-0.0317
-0.0947
0.3171
-0.1229
0.154
-28.9773
-15.8066
19.6753
4
5.6779
-0.8022
-0.3983
3.3185
0.7782
0.3314
-0.0305
-0.1406
-0.4267
0.0844
-0.1842
0.4728
0.0599
-0.1665
0.2148
0.2698
-0.0648
-0.0372
0.319
-0.1063
0.1637
-24.2877
-9.8603
23.5371
5
1.5861
-0.4579
-0.4763
2.3223
0.273
1.2012
0.0721
-0.0661
0.0191
0.172
-0.1595
0.237
0.0775
-0.1051
0.0874
0.1915
-0.0356
-0.0302
0.2592
-0.1027
0.0793
-24.339
-2.2205
31.5343
6
1.4347
0.6499
-1.1145
1.6192
-0.4291
1.5269
0.0722
-0.1529
0.1971
0.1468
-0.0743
0.0987
-0.1479
-0.1445
0.0021
0.1821
0.0068
-0.0726
0.2342
-0.081
0.0872
-10.5519
10.9905
22.189
7
0.7844
0.1458
0.4447
2.1692
0.4467
1.5561
0.0077
-0.2117
0.1287
0.0443
-0.117
0.043
0.0618
-0.2058
0.1093
0.2532
-0.0286
-0.0718
0.2964
-0.0363
0.0445
-8.9955
1.1934
18.7697
8
3.1988
-1.7769
-1.5917
3.3638
-1.4181
3.0339
-0.171
0.0504
-0.0877
0.0513
-0.024
-0.123
0.082
-0.0624
0.195
0.2373
-0.0178
-0.0446
0.2585
-0.0402
0.0905
-3.2635
-8.6971
15.1232
9
3.1132
-0.0541
0.6213
2.0071
-0.3359
0.3035
0.0279
0.2116
0.034
-0.2935
-0.0233
0.1606
0.1241
-0.0953
-0.0046
0.327
-0.0056
-0.1155
0.3003
-0.0156
0.0622
8.0094
-0.837
-6.7648
10
6.2608
-1.9775
-0.0972
2.5578
0.3424
1.1526
-0.0777
0.1395
-0.6957
0.0609
-0.0267
0.067
-0.0195
-0.0271
0.1043
0.1953
-0.0171
-0.0593
0.1427
-0.0083
0.1223
21.576
-11.396
-2.6183
11
9.1156
0.4464
-4.3272
3.0569
0.7525
3.7184
0.0092
-0.1269
0.277
0.3176
0.1062
-0.3386
0.2433
0.1856
-0.1155
0.244
0.0293
-0.1147
0.2223
0.0083
0.1064
31.7388
-1.9053
-3.7392
12
3.0496
1.5468
3.6153
4.4038
2.3663
5.3509
0.0723
0.2366
-0.2285
-0.2048
-0.0157
0.0498
0.1242
-0.0882
-0.0566
0.2956
-0.001
-0.1332
0.2569
-0.0628
0.1343
23.6793
-9.9002
-10.6017
13
1.5219
0.1968
-0.4621
2.0389
0.3359
1.1807
0.0592
0.0115
0.0703
-0.0613
-0.0381
-0.12
0.001
-0.0121
-0.0211
0.2194
0.0073
-0.0851
0.1983
0.0057
0.0529
22.8954
7.0017
-7.0113
14
1.55
-0.1331
-0.8835
1.4425
-0.266
0.7811
0.1438
-0.1427
0.2362
0.0558
-0.0171
-0.0186
-0.0669
0.0327
-0.1267
0.2001
-0.0287
-0.0697
0.192
-0.0416
0.087
8.7919
11.9438
5.4161
15
3.301
-1.6223
-1.3299
6.2595
-1.4793
1.5208
-0.006
-0.0119
0.0594
0.1637
0.009
-0.0361
-0.0489
0.1467
-0.003
0.2497
-0.015
-0.0954
0.2448
-0.0068
0.0489
6.7662
-1.1715
5.6148
16
5.7626
-1.1747
2.1094
3.3761
-2.0378
3.0913
-0.2697
-0.1053
-0.2028
0.1502
0.0332
0.3466
0.0262
0.2133
0.2365
0.3055
0.0023
-0.0589
0.3334
0.0347
0.2599
1.9566
-7.1269
5.3735
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 6
2
X-RAY DIFFRACTION
2
A
7 - 23
3
X-RAY DIFFRACTION
3
A
24 - 36
4
X-RAY DIFFRACTION
4
A
37 - 59
5
X-RAY DIFFRACTION
5
A
60 - 139
6
X-RAY DIFFRACTION
6
A
140 - 193
7
X-RAY DIFFRACTION
7
A
194 - 235
8
X-RAY DIFFRACTION
8
A
236 - 252
9
X-RAY DIFFRACTION
9
B
1 - 23
10
X-RAY DIFFRACTION
10
B
24 - 47
11
X-RAY DIFFRACTION
11
B
48 - 60
12
X-RAY DIFFRACTION
12
B
61 - 74
13
X-RAY DIFFRACTION
13
B
75 - 145
14
X-RAY DIFFRACTION
14
B
146 - 213
15
X-RAY DIFFRACTION
15
B
214 - 234
16
X-RAY DIFFRACTION
16
B
235 - 252
+
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