- PDB-4eey: Crystal structure of human DNA polymerase eta in ternary complex ... -
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Basic information
Entry
Database: PDB / ID: 4eey
Title
Crystal structure of human DNA polymerase eta in ternary complex with a cisplatin DNA adduct
Components
5'-D(*CP*TP*TP*GP*GP*TP*CP*TP*CP*CP*TP*CP*C)-3'
5'-D(*TP*GP*GP*AP*GP*GP*AP*GP*A)-3'
DNA polymerase eta
Keywords
TRANSFERASE/DNA / DNA replication / DNA repair / TRANSFERASE-DNA complex
Function / homology
Function and homology information
response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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 ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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: 2.32→49.25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.707 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23253
1528
7.7 %
RANDOM
Rwork
0.17834
-
-
-
all
0.18247
19764
-
-
obs
0.18247
18206
99.85 %
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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: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 34.458 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.4 Å2
-0.2 Å2
0 Å2
2-
-
-0.4 Å2
0 Å2
3-
-
-
0.6 Å2
Refinement step
Cycle: LAST / Resolution: 2.32→49.25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3255
388
32
116
3791
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
3803
X-RAY DIFFRACTION
r_angle_refined_deg
1.134
2.109
5221
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.028
5
423
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.332
23.65
137
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.103
15
585
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.095
15
26
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
588
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
2673
X-RAY DIFFRACTION
r_mcbond_it
0.299
1.5
2113
X-RAY DIFFRACTION
r_mcangle_it
0.605
2
3383
X-RAY DIFFRACTION
r_scbond_it
1.079
3
1690
X-RAY DIFFRACTION
r_scangle_it
1.618
4.5
1838
LS refinement shell
Resolution: 2.32→2.382 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.347
106
-
Rwork
0.211
1329
-
obs
-
-
98.29 %
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
1.0164
-0.5519
0.358
1.3531
-0.3612
1.0163
0.0484
0.0498
0.0374
-0.0786
-0.0918
-0.0899
0.074
0.1087
0.0434
0.0504
-0.0217
-0
0.0545
-0.0135
0.0477
46.3437
-7.6949
3.9242
2
5.5767
0.2974
-3.0563
6.458
-0.5207
8.0022
0.0216
0.1034
0.0112
-0.0358
-0.0129
0.7368
-0.1119
-1.0154
-0.0087
0.0032
0.0127
0.0058
0.1567
-0.0353
0.1717
21.6426
8.8101
3.1388
3
0.4358
-0.0431
-0.0856
0.8591
-0.0179
0.5358
0.0533
0.0339
0.0024
-0.0158
-0.0388
-0.1262
-0.0115
0.1109
-0.0144
0.0473
0.0044
-0.0007
0.0604
-0.0056
0.0595
45.0946
10.2922
2.0833
4
4.5893
0.5865
2.4093
3.4563
-0.2244
5.35
-0.2049
0.1174
0.0655
-0.052
-0.1834
-0.3829
-0.1757
0.7064
0.3884
0.1108
0.0344
0.0502
0.1398
0.0784
0.1471
69.2113
-6.4266
-9.4137
5
2.0659
2.0183
-0.3513
14.1046
-4.1567
1.5903
0.0689
-0.1916
0.1191
-0.5422
-0.0164
0.418
0.0369
0.1416
-0.0525
0.132
-0.0552
0.0116
0.1323
0.0243
0.1278
59.8447
3.851
-0.8297
6
7.3159
4.3722
-1.4453
7.4015
-1.6336
2.8649
0.0605
-0.4298
0.5026
-0.4824
-0.0937
-0.1717
0.1257
0.6303
0.0331
0.1228
-0.0004
0.0517
0.1692
-0.0233
0.1047
62.3122
8.0811
-3.1008
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 124
2
X-RAY DIFFRACTION
2
A
125 - 187
3
X-RAY DIFFRACTION
3
A
188 - 336
4
X-RAY DIFFRACTION
4
A
337 - 432
5
X-RAY DIFFRACTION
5
T
3 - 13
6
X-RAY DIFFRACTION
6
P
1 - 9
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