D-family DNA polymerase - DP2 subunit (catalytic subunit)
Components
DNA polymerase II large subunit
Keywords
TRANSFERASE / DNA polymerase D-family
Function / homology
Function and homology information
exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / intein-mediated protein splicing / DNA catabolic process / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function
DNA polymerase II large subunit DP2 / DNA polymerase II large subunit DP2, N-terminal / DNA polymerase II large subunit DP2 / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.984 Å / Relative weight: 1
Reflection
Resolution: 2.19→43.8 Å / Num. obs: 63302 / % possible obs: 99.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 49.98 Å2 / Net I/σ(I): 8.5
Reflection shell
Rsym value: 1.151
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.2
refinement
XDS
datareduction
Aimless
datascaling
AutoSol
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.19→43.8 Å / Cor.coef. Fo:Fc: 0.9432 / Cor.coef. Fo:Fc free: 0.9278 / SU R Cruickshank DPI: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.18
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2346
3165
5 %
RANDOM
Rwork
0.199
-
-
-
obs
0.2008
63302
99.34 %
-
Displacement parameters
Biso mean: 53.38 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-7.5119 Å2
0 Å2
0 Å2
2-
-
3.9661 Å2
0 Å2
3-
-
-
3.5458 Å2
Refine analyze
Luzzati coordinate error obs: 0.309 Å
Refinement step
Cycle: LAST / Resolution: 2.19→43.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7525
0
2
242
7769
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
7693
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.09
10407
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2709
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
189
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1095
HARMONIC
5
X-RAY DIFFRACTION
t_it
7693
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
3.08
X-RAY DIFFRACTION
t_other_torsion
18.25
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
965
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
8
HARMONIC
1
X-RAY DIFFRACTION
t_utility_angle
12
HARMONIC
1
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
8589
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.19→2.25 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2752
216
5.01 %
Rwork
0.2393
4094
-
all
0.2411
4310
-
obs
-
-
92.84 %
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
0.6359
0.0242
0.2467
0.7648
-0.019
1.158
-0.039
-0.017
0.1125
-0.0001
0.0216
0.0179
-0.3121
0.0623
0.0174
0.0193
0.0069
-0.0119
-0.0853
-0.0257
-0.0954
61.823
110.737
14.6083
2
1.038
0.4112
-0.5291
0
-0.4874
0.0154
0.0357
0.0251
0.0019
-0.0052
0.0518
-0.1381
0.0078
-0.0037
-0.0875
-0.0073
0.0419
0.0055
-0.0828
-0.0512
0.007
13.9991
108.495
24.909
3
0.9077
-0.1673
-0.4674
0.1691
0.0485
0.3831
-0.0024
0.0502
0.0049
0.0343
0.0006
0.0523
0.008
-0.0812
0.0019
-0.0098
-0.0074
-0.0314
-0.0786
-0.0354
-0.1011
14.0514
97.3364
19.8962
4
1.4631
-0.1061
-0.5286
0.7343
-0.1784
1.355
-0.036
0.0498
-0.0383
-0.0246
0.057
0.1867
0.0308
-0.0126
-0.021
-0.0346
0.0059
-0.0548
-0.1327
0.0209
-0.0526
51.0004
85.5184
14.2578
5
1.1449
-0.3646
-0.2911
0.056
0.022
0
0.0145
0.0014
0.0756
0.0015
-0.0018
0.0675
0.0817
0.0174
-0.0128
-0.0129
-0.0216
0.0265
-0.0568
-0.0154
0.0362
34.5737
110.03
20.3415
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|4 - A|267 }
2
X-RAY DIFFRACTION
2
{ A|268 - A|497 }
3
X-RAY DIFFRACTION
3
{ A|498 - A|730 }
4
X-RAY DIFFRACTION
4
{ A|731 - A|971 }
5
X-RAY DIFFRACTION
5
{ A|972 - A|1034 }
+
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