- PDB-3u80: 1.60 Angstrom Resolution Crystal Structure of a 3-Dehydroquinate ... -
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Basic information
Entry
Database: PDB / ID: 3u80
Title
1.60 Angstrom Resolution Crystal Structure of a 3-Dehydroquinate Dehydratase-like Protein from Bifidobacterium longum
Components
3-dehydroquinate dehydratase, type II
Keywords
UNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information
3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 1.6→29.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.912 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2027
1772
5 %
RANDOM
Rwork
0.17642
-
-
-
obs
0.17783
33629
99.79 %
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all
-
33629
-
-
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: 22.278 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.04 Å2
0 Å2
0 Å2
2-
-
-1.15 Å2
0 Å2
3-
-
-
1.12 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→29.94 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1930
0
0
214
2144
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.02
2128
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1373
X-RAY DIFFRACTION
r_angle_refined_deg
1.329
1.962
2926
X-RAY DIFFRACTION
r_angle_other_deg
0.791
3
3414
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.435
5
291
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.18
25.361
97
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.698
15
377
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.909
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
342
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2399
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
394
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: 1.6→1.639 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.266
109
-
Rwork
0.227
2235
-
obs
-
-
98.2 %
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
0.3007
0.1017
-0.0672
0.396
-0.348
0.3093
-0.0663
0.0011
-0.0189
0.1293
0.0616
-0.0079
-0.1204
-0.0495
0.0046
0.0855
0.0192
0.0134
0.044
-0.0219
0.0208
-0.7001
54.0719
18.3557
2
2.3799
-0.1658
-0.8418
0.7786
-0.1836
0.6345
-0.1791
-0.0244
0.0658
0.3556
0.0807
-0.0442
-0.001
0.0464
0.0983
0.1751
0.042
-0.0029
0.0481
0.009
0.0534
5.0141
51.7013
22.5485
3
0.5032
-0.2235
-0.1239
0.3719
-0.1779
0.2401
-0.036
-0.007
0.0177
0.0201
0.0238
-0.0035
0.0083
-0.0167
0.0122
0.0195
0.0032
0.0009
0.0372
-0.0059
0.0388
-3.755
55.9195
7.4727
4
0.6321
0.1862
-0.3497
0.7109
0.1122
0.4447
-0.0641
-0.0068
-0.013
0.0872
0.0225
-0.0209
0.0132
0.0445
0.0416
0.0523
0.0031
-0.0013
0.0298
0.0062
0.0324
7.6361
47.3402
10.7447
5
0.1305
0.2543
0.0362
1.5118
-0.8322
0.814
-0.0308
-0.0008
-0.0946
-0.1363
-0.017
-0.2652
0.0641
0.015
0.0478
0.0346
0.0171
0.0285
0.0246
-0.0055
0.0791
17.6699
31.2181
-0.2258
6
0.1409
0.2514
-0.2256
1.2612
-0.0689
0.5271
-0.0317
0
-0.0367
-0.0272
-0.0104
-0.0598
0.0769
0.0174
0.0421
0.0301
0.0134
0.0037
0.0177
-0.0105
0.032
13.5978
27.5186
2.4322
7
5.7775
2.0652
8.2268
1.0019
2.4168
12.7744
-0.2126
0.1768
0.1596
-0.0862
0.0397
0.1008
-0.2686
0.2818
0.1729
0.0314
-0.0255
0.001
0.0261
-0.0166
0.0826
-0.4547
22.9537
0.9956
8
0.3571
0.008
0.1204
1.4329
-0.2837
0.0983
0.0045
0.0106
0.006
0.0971
0.0063
0.0565
-0.0146
0.0014
-0.0108
0.0408
-0.0007
0.0122
0.0273
-0.0009
0.0266
7.4289
36.6631
6.4074
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 25
2
X-RAY DIFFRACTION
2
A
26 - 49
3
X-RAY DIFFRACTION
3
A
50 - 120
4
X-RAY DIFFRACTION
4
A
121 - 148
5
X-RAY DIFFRACTION
5
B
1 - 32
6
X-RAY DIFFRACTION
6
B
33 - 80
7
X-RAY DIFFRACTION
7
B
81 - 92
8
X-RAY DIFFRACTION
8
B
93 - 148
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