- PDB-3uby: Crystal structure of human alklyadenine DNA glycosylase in a lowe... -
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Basic information
Entry
Database: PDB / ID: 3uby
Title
Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA
Components
DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
DNA-3-methyladenine glycosylase
Keywords
HYDROLASE/DNA / alkyladenine DNA glycosylase fold / AAG / DNA repair / DNA binding / Nucleus / HYDROLASE-DNA complex
Function / homology
Function and homology information
alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair ...alkylbase DNA N-glycosylase activity / DNA-7-methyladenine glycosylase activity / DNA-3-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase II / DNA-7-methylguanine glycosylase activity / DNA-3-methyladenine glycosylase activity / depurination / DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / DNA alkylation repair / mitochondrial nucleoid / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / base-excision repair / damaged DNA binding / nucleoplasm / cytosol Similarity search - Function
A: DNA-3-methyladenine glycosylase C: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3') D: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop Details: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 ...Details: An equimolar ratio of delta79AAG and 13-mer single-stranded (ss) EDC DNA were mixed to form a protein-DNA complex concentration of 0.3 mM in the complex buffer (20 mM HEPES-NaOH, pH 7.5, 100 mM NaCl, 0.1 mM EDTA, 5% v/v glycerol and 1 mM DTT). The complex was incubated on ice for 15 min and used for crystallization. Crystals were obtained upon mixing 1 uL of protein-DNA complex and 1 uL of reservoir solution (100 mM BIS-TRIS, pH 5.5, 200 mM cesium chloride and 20% polyethylene glycol (PEG) 3350) over 0.5 ml of reservoir solution. Crystals appeared after incubation for 14 days at 22 degrees C, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
Resolution: 2→65.65 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.087 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26545
1375
5.1 %
RANDOM
Rwork
0.2194
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-
-
obs
0.22176
25556
92.12 %
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all
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26998
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 36.01 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.41 Å2
0 Å2
0 Å2
2-
-
0.41 Å2
0 Å2
3-
-
-
-0.82 Å2
Refinement step
Cycle: LAST / Resolution: 2→65.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2967
354
0
250
3571
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
3429
X-RAY DIFFRACTION
r_angle_refined_deg
1.104
2.112
4709
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.055
5
376
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.096
22.029
138
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.599
15
504
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.494
15
38
X-RAY DIFFRACTION
r_chiral_restr
0.068
0.2
513
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2502
X-RAY DIFFRACTION
r_mcbond_it
2.61
1.5
1900
X-RAY DIFFRACTION
r_mcangle_it
3.499
2
3031
X-RAY DIFFRACTION
r_scbond_it
5.26
3
1529
X-RAY DIFFRACTION
r_scangle_it
6.684
4.5
1678
LS refinement shell
Resolution: 2→2.053 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.265
99
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Rwork
0.219
1833
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obs
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-
89.49 %
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
1.8175
-0.756
-0.8565
1.83
0.6659
2.5151
0.0444
0.0808
-0.0785
0.1421
-0.1046
0.0499
-0.0796
0.0603
0.0602
0.2203
0.0217
-0.0121
0.0209
-0.0225
0.1267
3.6984
-5.0095
21.4544
2
1.7615
-0.874
0.8017
3.1614
-0.6637
3.6281
-0.0657
0.184
0.0425
-0.1014
0.1151
-0.0269
0.0369
-0.1413
-0.0493
0.1001
0.0275
0.0268
0.1592
-0.0474
0.1279
-15.1881
-26.4475
-1.8766
3
0.5437
0.9939
1.202
1.8201
2.2202
2.838
0.0469
-0.0752
0.0119
0.1083
-0.1109
0.0343
0.1071
0.1185
0.0641
0.4785
-0.0197
-0.025
0.4773
0.0084
0.218
7.7356
1.8047
40.2028
4
1.8467
0.513
-2.3749
10.8793
-2.1692
12.9283
0.0918
-0.5275
0.355
0.1186
0.4908
-0.4344
-0.3425
0.3405
-0.5826
0.2237
-0.0591
-0.0267
0.2337
-0.1381
0.1711
9.5881
9.3631
38.6698
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
80 - 200
2
X-RAY DIFFRACTION
1
A
209 - 264
3
X-RAY DIFFRACTION
1
A
268 - 290
4
X-RAY DIFFRACTION
2
B
80 - 130
5
X-RAY DIFFRACTION
2
B
144 - 160
6
X-RAY DIFFRACTION
2
B
166 - 198
7
X-RAY DIFFRACTION
2
B
208 - 262
8
X-RAY DIFFRACTION
2
B
274 - 289
9
X-RAY DIFFRACTION
3
C
1 - 11
10
X-RAY DIFFRACTION
4
D
1 - 8
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