- PDB-4fgn: Crystal structure of the SV40 large T-antigen origin bining domai... -
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Basic information
Entry
Database: PDB / ID: 4fgn
Title
Crystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA
Components
(Site I DNA) x 2
Large T antigen
Keywords
DNA BINDING PROTEIN/DNA / origin binding domain / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information
symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / single-stranded DNA binding / double-stranded DNA binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA 3'-5' helicase / DNA unwinding involved in DNA replication / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / DNA replication origin binding / helicase activity / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host innate immune response / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / ATP binding / identical protein binding / metal ion binding Similarity search - Function
Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding ...Replication Protein E1; Chain: A, - #20 / Large T antigen, polyomaviridae / Replication Protein E1; Chain: A, / Large T antigen, polyomavirus, C-terminal / Zinc finger, large T-antigen D1-type / Origin of replication binding protein / Polyomavirus large T antigen C-terminus / Large T-antigen (T-ag) origin-binding domain (OBD) profile. / Zinc finger large T-antigen (T-ag) D1-type profile. / T antigen, Ori-binding / Zinc finger, large T-antigen D1 domain superfamily / Helicase, superfamily 3, DNA virus / Superfamily 3 helicase of DNA viruses domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 15240.476 Da / Num. of mol.: 2 / Fragment: origin binding domain, UNP residues 131-260 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 40 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) References: UniProt: P03070, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain
SiteIDNA
Mass: 6963.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is termed Site 1 in SV40 / Source: (synth.) Simian virus 40
#3: DNA chain
SiteIDNA
Mass: 7158.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This DNA sequence is from sv40 site I / Source: (synth.) Simian virus 40
Resolution: 3.2→47.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 73.091 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.267
444
4.8 %
RANDOM
Rwork
0.188
-
-
-
obs
0.191
8841
99.8 %
-
all
-
9305
-
-
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: 137.11 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.22 Å2
0 Å2
0 Å2
2-
-
-0.13 Å2
0 Å2
3-
-
-
0.35 Å2
Refinement step
Cycle: LAST / Resolution: 3.2→47.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2027
937
0
3
2967
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.017
3132
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.767
1.737
4434
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.224
5
248
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.384
23.061
98
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.75
15
345
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
26.134
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
448
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
2062
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: 3.2→3.28 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.266
29
-
Rwork
0.302
563
-
obs
-
-
97.69 %
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
4.3163
-2.8324
-1.0743
14.3332
2.3666
11.8625
0.0745
-0.2827
-0.9794
0.8123
-0.7172
0.6496
0.5555
-0.3503
0.6427
0.3479
-0.0302
0.2384
0.603
-0.0679
0.8232
1.5594
42.2545
-0.2878
2
10.8722
2.9635
1.3241
11.1175
0.2369
3.7342
0.9076
-0.6183
-0.5681
-0.2245
-0.7337
1.4421
1.6383
-1.9481
-0.1738
1.2112
-0.4074
-0.4374
1.5418
-0.1961
0.7115
3.1383
5.6793
-17.5268
3
4.5856
-5.0544
-0.7161
8.903
3.2412
3.2417
0.6374
0.3198
0.9739
-1.2909
-0.4605
-1.7934
-0.3216
0.3427
-0.1769
1.0534
0.2711
0.1618
0.6879
-0.0419
0.7649
17.6876
27.3756
-20.0936
4
2.5926
-2.6339
1.4469
4.0713
0.4706
4.1954
0.9031
0.5819
0.0307
-1.4441
-0.7736
0.2976
-0.2765
0.1121
-0.1295
0.9832
0.2006
0.2339
0.6251
-0.0533
0.7814
16.4447
29.9636
-20.6853
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
133 - 258
2
X-RAY DIFFRACTION
2
B
134 - 257
3
X-RAY DIFFRACTION
3
Z
1 - 23
4
X-RAY DIFFRACTION
4
Y
1 - 23
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