- PDB-4g3i: Crystal structure of Dpo4 in complex with DNA duplex -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4g3i
Title
Crystal structure of Dpo4 in complex with DNA duplex
Components
(DNA) x 2
DNA polymerase IV
Keywords
TRANSFERASE/DNA / DNA synthesis / TRANSFERASE-DNA complex
Function / homology
Function and homology information
error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / : / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / : / DNA polymerase IV / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 2.5→95.81 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.882 / SU B: 25.325 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29363
1650
5.1 %
RANDOM
Rwork
0.24067
-
-
-
all
0.24337
34376
-
-
obs
0.24337
30884
97.1 %
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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: 33.155 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.09 Å2
2.12 Å2
0.02 Å2
2-
-
0 Å2
-1.51 Å2
3-
-
-
1.47 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→95.81 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5494
722
2
20
6238
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
6378
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.923
2.135
8720
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.753
5
681
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.424
23.636
242
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.407
15
1127
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.341
15
48
X-RAY DIFFRACTION
r_chiral_restr
0.118
0.2
997
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
4410
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
1.151
1.5
3403
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.026
2
5532
X-RAY DIFFRACTION
r_scbond_it
2.689
3
2975
X-RAY DIFFRACTION
r_scangle_it
4.116
4.5
3188
X-RAY DIFFRACTION
r_rigid_bond_restr
1.556
3
6378
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
2744
MEDIUMPOSITIONAL
0.51
0.5
1
A
2744
MEDIUMTHERMAL
0.9
2
2
C
198
MEDIUMPOSITIONAL
0.5
0.5
2
C
198
MEDIUMTHERMAL
0.62
2
3
D
163
MEDIUMPOSITIONAL
0.44
0.5
3
D
163
MEDIUMTHERMAL
0.75
2
LS refinement shell
Resolution: 2.5→2.565 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.334
117
-
Rwork
0.261
2231
-
obs
-
-
96.07 %
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
0.911
-0.4644
-0.1971
1.6181
-0.6315
0.9739
0.0665
0.1139
0.0151
-0.2584
0.013
0.1674
0.1883
-0.0096
-0.0795
0.3183
-0.0622
-0.0022
0.1768
0.0049
0.1875
19.1199
9.5501
-22.911
2
1.5128
-0.2439
0.2922
0.5881
0.078
0.0781
0.0264
-0.0097
-0.0056
-0.0031
0.0104
-0.0629
-0.0471
-0.0035
-0.0368
0.1596
-0.0306
0.0014
0.2611
-0.0154
0.1449
-5.4278
12.2608
15.4297
3
3.7112
-3.9417
1.7117
6.8951
0.1713
0.1455
0.6536
0.2319
-0.0909
-1.1353
-0.482
-0.3911
0.1681
0.2568
-0.1717
0.5662
0.0099
0.174
0.5256
0.1294
0.2294
13.1818
19.821
-29.9825
4
2.0005
-6.9668
3.2818
14.9457
-1.5956
3.1203
0.5325
0.0296
-0.2906
-2.2116
-0.8018
-0.3065
-0.1384
-0.0938
0.2693
0.8566
0.1606
0.2858
0.2691
0.118
0.4019
14.539
16.8256
-26.4996
5
-0.4182
-0.0494
-1.9072
1.3247
1.3892
1.4677
-0.2256
-0.1836
-0.0743
0.3896
0.2828
-0.3533
0.2454
0.3185
-0.0573
0.3366
0.0491
-0.123
0.3185
-0.0049
0.3054
2.2338
2.7972
22.8284
6
9.3977
-6.2509
-6.2174
3.8749
4.7373
3.0981
-0.2863
-0.8364
0.7756
0.4684
0.6178
-0.1305
0.3314
0.2982
-0.3315
0.2491
0.1379
-0.1284
0.5063
-0.1811
0.3445
-0.1129
4.8398
19.4446
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 341
2
X-RAY DIFFRACTION
2
B
1 - 341
3
X-RAY DIFFRACTION
3
C
4 - 13
4
X-RAY DIFFRACTION
4
D
5 - 12
5
X-RAY DIFFRACTION
5
E
4 - 13
6
X-RAY DIFFRACTION
6
F
5 - 12
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