- PDB-4ej7: Crystal structure of the aminoglycoside phosphotransferase APH(3'... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4ej7
Title
Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, ATP-bound
Components
Aminoglycoside 3'-phosphotransferase AphA1-IAB
Keywords
TRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / ALPHA/BETA PROTEIN / PHOSPHOTRANSFERASE / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDES / KANAMYCIN / GTP / INTRACELLULAR
Function / homology
Function and homology information
kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M CA ACETATE, 16% PEG3350, 2 MM ATP, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2.29→43.669 Å / Num. obs: 91198 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Net I/σ(I): 12.552
Reflection shell
Resolution: 2.29→2.3 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.5298 / % possible all: 69.4
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Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
SHELXS
phasing
PHENIX
(phenix.refine: 1.7.3_928)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.29→43.669 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.86 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2516
3790
4.19 %
random
Rwork
0.2134
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-
-
obs
0.215
90409
96.27 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.351 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
4.8067 Å2
-0 Å2
0 Å2
2-
-
31.4101 Å2
-0 Å2
3-
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20.1465 Å2
Refinement step
Cycle: LAST / Resolution: 2.29→43.669 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6472
0
112
294
6878
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
6879
X-RAY DIFFRACTION
f_angle_d
0.694
9395
X-RAY DIFFRACTION
f_dihedral_angle_d
12.75
2535
X-RAY DIFFRACTION
f_chiral_restr
0.043
980
X-RAY DIFFRACTION
f_plane_restr
0.003
1215
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2903-2.3722
0.3448
359
0.3205
8391
X-RAY DIFFRACTION
93
2.3722-2.4672
0.3291
383
0.2955
8699
X-RAY DIFFRACTION
97
2.4672-2.5794
0.3729
381
0.2927
8801
X-RAY DIFFRACTION
97
2.5794-2.7154
0.3343
382
0.2662
8735
X-RAY DIFFRACTION
97
2.7154-2.8855
0.3103
388
0.2519
8662
X-RAY DIFFRACTION
97
2.8855-3.1082
0.2985
383
0.2502
8756
X-RAY DIFFRACTION
97
3.1082-3.4209
0.3134
391
0.2232
8656
X-RAY DIFFRACTION
97
3.4209-3.9157
0.2244
375
0.201
8768
X-RAY DIFFRACTION
97
3.9157-4.9323
0.2131
379
0.1634
8650
X-RAY DIFFRACTION
96
4.9323-43.6765
0.1933
369
0.1961
8501
X-RAY DIFFRACTION
94
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
0.1426
0.0236
0.0704
0.0644
-0.0114
0.1188
0.093
0.0342
-0.4693
-0.186
0.1506
-0.034
-0.065
-0.0895
0.2115
-0.1448
0.187
-0.24
0.0749
0.156
0.1742
84.1093
25.0009
47.5867
2
0.1336
-0.11
0.0046
0.1338
0.0415
0.1559
-0.028
-0.08
-0.0447
-0.0171
0.0761
-0.03
-0.0155
-0.149
0.0039
0.2077
-0.0066
0.0229
0.1811
-0.0016
0.1512
73.9944
47.6784
56.6634
3
0.1989
-0.0059
0.167
0.1977
-0.0443
0.4835
0.3711
0.1106
-0.18
-0.15
0.2106
0.3177
0.1586
-0.0572
0.3098
0.2063
0.0024
-0.0866
0.2145
0.1775
0.3849
33.1321
73.401
75.7129
4
0.0862
-0.1129
-0.0835
0.0738
0.082
0.0971
0.0668
0.0498
-0.0066
0.0435
-0.0737
0.1161
0.1217
0.0347
-0.0006
0.2774
0.0263
-0.0133
0.1835
-0.0127
0.1722
56.0076
64.4034
67.8521
5
0.0509
-0.0249
0.0156
0.0803
-0.026
0.1734
0.1806
0.0408
0.1764
-0.0386
-0.0686
0.0003
0.1725
-0.0459
0.0152
0.1674
0.0039
0.0063
0.2642
-0.017
0.2219
44.0698
29.7781
47.9276
6
0.1241
0.0377
0.0483
0.1216
0.0324
0.1298
0.1276
-0.2442
-0.4124
0.0038
-0.0391
-0.0535
0.0094
0.0997
0.0834
0.2703
-0.0692
-0.1513
0.3143
0.0673
0.2764
54.1111
7.0148
56.7389
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chainAandresid1:102
2
X-RAY DIFFRACTION
2
chainAandresid103:271
3
X-RAY DIFFRACTION
3
chainBandresid1:102
4
X-RAY DIFFRACTION
4
chainBandresid103:271
5
X-RAY DIFFRACTION
5
chainCandresid1:102
6
X-RAY DIFFRACTION
6
chainCandresid103:271
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