- PDB-4q7f: 1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from ... -
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Basic information
Entry
Database: PDB / ID: 4q7f
Title
1.98 Angstrom Crystal Structure of Putative 5'-Nucleotidase from Staphylococcus aureus in complex with Adenosine.
Components
5' nucleotidase family protein
Keywords
METAL BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / 5'-nucleotidase / C-terminal domain / phosphoesterase / metal ion binding
Function / homology
Function and homology information
nucleotidase activity / nucleotide catabolic process / hydrolase activity, acting on ester bonds / outer membrane-bounded periplasmic space / DNA recombination / nucleotide binding / metal ion binding Similarity search - Function
Resolution: 1.98→29.36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.663 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21788
2236
5 %
RANDOM
Rwork
0.1869
-
-
-
obs
0.18846
42209
97.96 %
-
all
-
42209
-
-
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: 31.592 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.29 Å2
-0 Å2
0.88 Å2
2-
-
5.7 Å2
0 Å2
3-
-
-
-4.25 Å2
Refinement step
Cycle: LAST / Resolution: 1.98→29.36 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4092
0
20
380
4492
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.019
4355
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3971
X-RAY DIFFRACTION
r_angle_refined_deg
1.493
1.954
5940
X-RAY DIFFRACTION
r_angle_other_deg
0.746
3
9136
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.116
5
537
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.566
24.786
234
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.598
15
669
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.416
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.088
0.2
638
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
5128
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1077
X-RAY DIFFRACTION
r_mcbond_it
1.154
1.502
2109
X-RAY DIFFRACTION
r_mcbond_other
1.154
1.502
2108
X-RAY DIFFRACTION
r_mcangle_it
1.875
2.25
2659
X-RAY DIFFRACTION
r_mcangle_other
1.875
2.25
2660
X-RAY DIFFRACTION
r_scbond_it
1.423
1.69
2246
X-RAY DIFFRACTION
r_scbond_other
1.422
1.69
2246
X-RAY DIFFRACTION
r_scangle_other
2.218
2.484
3282
X-RAY DIFFRACTION
r_long_range_B_refined
6.308
13.621
5279
X-RAY DIFFRACTION
r_long_range_B_other
6.143
13.011
5122
LS refinement shell
Resolution: 1.98→2.031 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.371
180
-
Rwork
0.326
3073
-
obs
-
3073
97.08 %
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
2.4692
0.5534
-0.1487
0.7461
-0.0444
0.6765
-0.1764
0.016
-0.0026
0.0081
0.0628
-0.0804
0.0249
0.0046
0.1136
0.1025
0.0847
0.0246
0.0826
0.0174
0.0663
-33.7231
31.2062
99.3925
2
1.5356
-0.3596
-0.5642
0.8161
0.2401
1.3497
-0.0971
-0.2902
0.2345
0.1177
0.1351
-0.1603
-0.082
0.1255
-0.038
0.1212
0.1122
-0.0219
0.1476
-0.0284
0.1409
-29.65
40.1148
113.3138
3
2.1762
-0.3652
0.0051
0.551
0.2521
1.3021
-0.1152
0.0886
-0.1512
-0.0412
0.0097
-0.06
0.0937
-0.0281
0.1055
0.1337
0.0497
0.0291
0.0824
0.0148
0.072
-40.8349
31.0617
95.8146
4
0.7954
-0.1644
-0.5368
2.1633
0.7465
1.1457
-0.0314
0.1386
-0.0279
-0.0972
0.0547
0.1763
0.0196
-0.1705
-0.0233
0.1197
0.1051
0.0184
0.1895
0.0214
0.0865
-60.9439
44.3453
106.6494
5
2.097
-1.1361
0.4291
2.9549
0.1307
1.295
0.032
0.1637
0.1448
-0.0323
0.0091
-0.0983
0.037
0.1061
-0.0411
0.1202
0.1437
0.0424
0.1896
0.0362
0.124
-57.0935
59.0973
106.2002
6
1.717
0.2871
-0.8348
2.7952
-0.1869
2.4944
-0.0297
0.0049
0.0808
0.186
-0.0901
0.1871
0.0799
-0.0562
0.1198
0.1324
0.1265
0.0613
0.1689
0.021
0.0997
-60.0985
44.2702
117.0322
7
3.9633
3.789
-1.9119
11.1925
-2.7149
1.1436
-0.2948
0.4485
0.2056
-0.7595
0.4195
1.0647
0.128
-0.3537
-0.1247
0.1265
0.0765
-0.0846
0.2506
-0.03
0.1903
-70.4878
48.9161
102.4288
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 69
2
X-RAY DIFFRACTION
2
A
70 - 263
3
X-RAY DIFFRACTION
3
A
264 - 315
4
X-RAY DIFFRACTION
4
A
316 - 389
5
X-RAY DIFFRACTION
5
A
390 - 449
6
X-RAY DIFFRACTION
6
A
450 - 495
7
X-RAY DIFFRACTION
7
A
496 - 511
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