D-family DNA polymerase - DP1 subunit (3'-5' proof-reading exonuclease)
Components
DNA polymerase II small subunit
Keywords
TRANSFERASE / DNA polymerase D-family exonuclease
Function / homology
Function and homology information
exodeoxyribonuclease I / single-stranded DNA 3'-5' DNA exonuclease activity / DNA catabolic process / DNA strand elongation involved in DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function
DNA polymerase II small subunit, archaeal / DNA polymerase delta/II small subunit family / DNA polymerase alpha/epsilon subunit B / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Nucleic acid-binding, OB-fold Similarity search - Domain/homology
ACETATE ION / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / : / DNA polymerase II small subunit Similarity search - Component
Biological species
Pyrococcus abyssi (archaea)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9919 Å / Relative weight: 1
Reflection
Resolution: 2.5→48.3 Å / Num. obs: 39885 / % possible obs: 98.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 81.35 Å2 / Rsym value: 0.061 / Net I/σ(I): 6.9
Reflection shell
Resolution: 2.5→2.64 Å / Rsym value: 0.825
-
Processing
Software
Name
Version
Classification
BUSTER
2.10.2
refinement
XDS
datareduction
Aimless
datascaling
AutoSol
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.5→47.42 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.38 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.239
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2248
1998
5.01 %
RANDOM
Rwork
0.1974
-
-
-
obs
0.1988
39885
98.92 %
-
Displacement parameters
Biso mean: 86.01 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-5.6418 Å2
0 Å2
0 Å2
2-
-
-5.1597 Å2
0 Å2
3-
-
-
10.8014 Å2
Refine analyze
Luzzati coordinate error obs: 0.36 Å
Refinement step
Cycle: LAST / Resolution: 2.5→47.42 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7050
0
63
66
7179
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.008
7283
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.08
9902
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
2487
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
177
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
1056
HARMONIC
5
X-RAY DIFFRACTION
t_it
7283
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
0
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_omega_torsion
2.86
X-RAY DIFFRACTION
t_other_torsion
17.81
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
924
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
8075
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.5→2.56 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.2398
129
4.4 %
Rwork
0.2395
2804
-
all
0.2395
2933
-
obs
-
-
99.53 %
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
0.7653
0.3466
0.6831
1.9724
-0.7745
2.9238
-0.3023
0.2307
-0.0158
-0.2413
0.1653
0.09
-0.178
0.0667
0.1371
-0.164
0.0609
0.0326
0.0054
0.0162
-0.2946
67.728
72.516
46.3622
2
2.4121
-0.2365
0.5881
1.9555
0.4673
2.3288
-0.092
-0.1492
-0.4123
-0.0978
-0.0713
-0.2607
0.1903
0.148
0.1633
-0.2313
0.0648
0.0894
-0.2249
0.0847
-0.1129
43.8569
43.061
74.5925
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|* }
2
X-RAY DIFFRACTION
2
{ B|* }
+
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