bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function
DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : ...DnaQ-like 3'-5' exonuclease / Monooxygenase - #300 / Ribonuclease H-like motif / DNA-directed DNA polymerase T4 type / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / : / Monooxygenase / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
A: DNA polymerase T: DNA (5'-D(*TP*CP*GP*TP*CP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') P: DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*G)-3') hetero molecules
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→45.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.783 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21317
3850
5.1 %
RANDOM
Rwork
0.17859
-
-
-
all
0.1803
76223
-
-
obs
0.1803
72335
97.09 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 28.999 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.28 Å2
-0 Å2
-0 Å2
2-
-
0.76 Å2
0 Å2
3-
-
-
-0.48 Å2
Refinement step
Cycle: LAST / Resolution: 2.02→45.66 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7355
629
36
502
8522
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.019
8271
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.059
1.887
11314
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.224
5
900
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.547
24.155
373
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.39
15
1347
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.846
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.077
0.2
1168
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
6100
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.019→2.071 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.244
259
-
Rwork
0.211
4912
-
obs
-
-
90.37 %
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
0.2671
-0.1006
0.0215
0.0589
-0.0134
0.0388
-0.1369
-0.0119
0.1333
0.0405
0.0572
-0.0564
0.0211
-0.0106
0.0796
0.1057
-0.0206
-0.0147
0.1139
-0.0154
0.1809
17.011
-2.888
35.649
2
0.0498
-0.126
-0.0565
0.8587
0.3181
0.1513
0.01
-0.0181
0.0235
-0.0452
-0.0325
0.0742
-0.0017
-0.0124
0.0225
0.0601
0.0055
-0.0134
0.0246
-0.0227
0.0882
-25.061
2.428
33.722
3
0.2419
-0.262
0.0285
0.5303
0.0278
0.7573
0.0192
0.021
0.0223
-0.0644
-0.0447
0.0124
0.0274
0.0687
0.0254
0.054
0.0088
-0.0143
0.0179
0.0049
0.0315
-10.644
-22.13
14.887
4
0.5521
-0.3356
-0.1767
0.7348
0.0149
0.1125
-0.0608
-0.2391
0.0476
0.0995
0.0956
-0.0114
0.0121
0.0874
-0.0348
0.0787
0.0373
-0.0139
0.1126
-0.0256
0.0127
3.674
-6.813
60.529
5
0.4242
-0.0835
-0.0451
1.9563
-0.3173
0.1389
-0.0543
-0.0946
-0.0928
-0.0899
0.0137
0.0483
0.0315
-0.0255
0.0406
0.0779
-0.0006
0.0234
0.0479
0.0124
0.048
-9.395
-26.118
47.158
6
1.3571
0.5147
-0.6545
0.5403
-0.5868
1.1592
0.0343
-0.0618
-0.0621
0.0524
0.0369
0.0469
-0.0012
0.0568
-0.0711
0.0769
0.0395
0.0125
0.0415
0.0225
0.0409
9.365
-23.011
48.293
7
1.4053
0.0557
0.2104
0.2698
-0.3861
1.1243
-0.0853
0.2341
-0.1236
-0.0162
0.0981
-0.0571
-0.0008
0.0565
-0.0128
0.0397
-0.0225
0.0178
0.1115
-0.0593
0.0426
22.313
-20.825
27.979
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
T
1 - 18
2
X-RAY DIFFRACTION
1
P
103 - 115
3
X-RAY DIFFRACTION
1
A
1001
4
X-RAY DIFFRACTION
2
A
1 - 105
5
X-RAY DIFFRACTION
2
A
340 - 389
6
X-RAY DIFFRACTION
3
A
106 - 339
7
X-RAY DIFFRACTION
4
A
390 - 468
8
X-RAY DIFFRACTION
4
A
576 - 706
9
X-RAY DIFFRACTION
5
A
469 - 575
10
X-RAY DIFFRACTION
6
A
707 - 737
11
X-RAY DIFFRACTION
7
A
738 - 901
+
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