- PDB-3qi5: Crystal structure of human alkyladenine DNA glycosylase in comple... -
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Basic information
Entry
Database: PDB / ID: 3qi5
Title
Crystal structure of human alkyladenine DNA glycosylase in complex with 3,N4-ethenocystosine containing duplex DNA
Components
DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3')
DNA-3-methyladenine glycosylase
Keywords
HYDROLASE/DNA / alkyladenine DNA glycosylase fold / AAG / Excision / 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 B: 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*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3') E: DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3') F: DNA (5'-D(*GP*GP*CP*AP*AP*GP*CP*AP*TP*GP*TP*CP*A)-3') hetero molecules
Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal grow
Temperature: 295 K / Method: vapor diffusion, hanging drop Details: The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary ...Details: The 3,N4-ethenocytosine (EDC) containing DNA duplex was prepared by annealing the EDC containing 13-mer crystallization oligonucleotide ('5-GAC ATG (EDC)TT GCC T-3') with its complementary strand that contained G opposite EDC (5'-GGC AAG CAT GTC A-3'). The delta79AAG-EDC complexes were prepared by mixing equimolar ratios of delta79AAG and EDC:G 13-mer DNA duplex at the final 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. The crystals were obtained upon mixing 1 uL of complex and 1 ul of the reservoir solution (100 mM sodium cacodylate pH 6.0, 200 mM manganese chloride and 20% polyethylene glycol (PEG)-3350) over 0.5 ml of the reservoir solution, followed by incubation for 2 days, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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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: 2.2→81 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.824 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28427
1331
5.1 %
RANDOM
Rwork
0.23637
-
-
-
obs
0.23881
24947
96.22 %
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all
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24947
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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: 15.654 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.62 Å2
0.29 Å2
0.21 Å2
2-
-
-1.06 Å2
0.13 Å2
3-
-
-
0.39 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→81 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3249
1024
2
232
4507
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.022
4468
X-RAY DIFFRACTION
r_angle_refined_deg
1.029
2.269
6254
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.709
5
412
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.351
21.895
153
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.213
15
563
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.988
15
44
X-RAY DIFFRACTION
r_chiral_restr
0.058
0.2
682
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
3078
X-RAY DIFFRACTION
r_mcbond_it
0.486
1.5
2070
X-RAY DIFFRACTION
r_mcangle_it
0.888
2
3310
X-RAY DIFFRACTION
r_scbond_it
0.57
3
2398
X-RAY DIFFRACTION
r_scangle_it
0.999
4.5
2944
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
1152
tightpositional
0.29
0.05
1
1
B
184
mediumpositional
0.15
0.5
2
2
C
263
mediumpositional
0.33
0.5
2
2
E
245
mediumpositional
0.13
0.5
1
1
A
1152
tightthermal
0.08
0.5
1
1
B
184
mediumthermal
0.07
2
2
2
D
263
mediumthermal
0.14
2
2
2
F
245
mediumthermal
0.1
2
LS refinement shell
Resolution: 2.2→2.252 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.348
86
-
Rwork
0.289
1734
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obs
-
-
89.61 %
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
2.1497
-1.1267
0.7034
2.4143
-1.1749
2.6896
0.0758
0.1762
0.0561
0.0858
-0.1194
-0.0937
0.0805
-0.0006
0.0436
0.1644
-0.0144
-0.0017
0.0189
0.0031
0.0503
19.5344
10.0103
-41.3271
2
2.3455
-1.2472
-1.2225
2.4382
1.0247
2.6073
-0.1419
0.1152
-0.0961
0.1284
0.0791
0.0643
-0.0568
0.0834
0.0628
0.0225
-0.0293
0.0057
0.2082
-0.0012
0.0578
-0.229
-9.7377
-67.7282
3
0.3987
-0.4108
-0.398
1.9566
0.3612
2.2433
0.0381
-0.0323
-0.1267
0.3619
-0.0794
0.0891
-0.0837
0.0183
0.0414
0.2316
-0.0348
0.0108
0.0233
-0.0008
0.0706
14.8238
5.6987
-21.1756
4
1.6315
-1.2689
-0.9148
7.5473
0.5121
3.3317
0.0261
-0.0565
-0.0623
0.3992
-0.2245
-0.1075
0.1154
-0.1552
0.1984
0.1557
-0.0239
-0.0134
0.0524
0.0305
0.059
15.078
4.0514
-21.6272
5
0.3443
0.26
-0.841
1.46
-0.6971
2.8385
-0.1782
0.155
-0.0593
-0.1711
0.0208
-0.0013
0.1245
-0.2473
0.1574
0.1656
-0.0765
-0.0055
0.2863
-0.0215
0.0662
4.2907
-4.9353
-87.7975
6
9.9932
-1.2419
-0.5354
0.8286
-1.2579
2.6352
0.1526
0.6552
-0.3351
-0.023
-0.1528
0.0544
-0.0159
0.1021
0.0002
0.084
-0.0081
0.0141
0.1335
-0.0303
0.0914
5.9779
-5.3712
-87.3452
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
86 - 198
2
X-RAY DIFFRACTION
1
A
211 - 244
3
X-RAY DIFFRACTION
1
A
256 - 263
4
X-RAY DIFFRACTION
1
A
274 - 289
5
X-RAY DIFFRACTION
2
B
86 - 198
6
X-RAY DIFFRACTION
2
B
211 - 244
7
X-RAY DIFFRACTION
2
B
256 - 263
8
X-RAY DIFFRACTION
2
B
274 - 289
9
X-RAY DIFFRACTION
3
C
1 - 13
10
X-RAY DIFFRACTION
4
D
14 - 25
11
X-RAY DIFFRACTION
5
E
1 - 13
12
X-RAY DIFFRACTION
6
F
14 - 25
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