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- PDB-2fuf: Crystal structure of the SV40 large T antigen origin-binding domain -

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Basic information

Entry
Database: PDB / ID: 2fuf
TitleCrystal structure of the SV40 large T antigen origin-binding domain
ComponentsLarge T antigenLarge tumor antigen
KeywordsDNA BINDING PROTEIN / Replication origin binding domain / dna replication
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 unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 unwinding involved in DNA replication / DNA replication origin binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / double-stranded DNA binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / hydrolase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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
CITRATE ANION / Large T antigen
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsMeinke, G. / Bullock, P.A. / Bohm, A.
CitationJournal: J.Virol. / Year: 2006
Title: Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
Authors: Meinke, G. / Bullock, P.A. / Bohm, A.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Large T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6982
Polymers15,5081
Non-polymers1891
Water3,063170
1
A: Large T antigen
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)94,18512
Polymers93,0516
Non-polymers1,1356
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655x-y+1,x,z+5/61
crystal symmetry operation2_765-y+2,x-y+1,z+2/31
crystal symmetry operation4_775-x+2,-y+2,z+1/21
crystal symmetry operation3_675-x+y+1,-x+2,z+1/31
crystal symmetry operation5_565y,-x+y+1,z+1/61
Unit cell
Length a, b, c (Å)83.669, 83.669, 35.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations:y,-x+y+1,z+1/6 and -x+y+1,-x+2,z+1/3 and -x+2,-y+2,z+1/2, and -y+2,x-y+1,z+2/3 and x-y+1,x,z+5/6

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Components

#1: Protein Large T antigen / Large tumor antigen


Mass: 15508.424 Da / Num. of mol.: 1 / Fragment: DNA binding domain (residues 131-259)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Gene: SV40 A GENE / Plasmid: pGEX-1lT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03070
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2005 / Details: crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 10.9 % / Av σ(I) over netI: 12.1 / Number: 275942 / Rmerge(I) obs: 0.07 / Χ2: 2.05 / D res high: 1.45 Å / D res low: 50 Å / Num. obs: 25306 / % possible obs: 98.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
3.1250265299.60.055.18110.9
2.483.12258199.70.0643.60410.6
2.172.48254599.50.0742.91211
1.972.172538990.0842.17911.1
1.831.97255099.20.1071.56911.2
1.721.83250598.90.1421.20211.2
1.631.72251698.60.1931.02411.2
1.561.63251398.30.260.92711.2
1.51.56249097.60.3430.83510.9
1.451.5241696.30.4410.799.7
ReflectionResolution: 1.45→50 Å / Num. all: 25306 / Num. obs: 24796 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Χ2: 2.052 / Net I/σ(I): 53.6
Reflection shellResolution: 1.45→1.5 Å / % possible obs: 96.3 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2416 / Num. unique obs: 2416 / Rsym value: 0.441 / Χ2: 0.79 / % possible all: 96.3

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 30 Å / FOM : 0.55 / Reflection: 5094
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se9.5440.5940.0290.0061.647
2Se23.8520.7010.8190.1462.43
Phasing MAD shell
Resolution (Å)FOM Reflection
8.86-300.48251
5.64-8.860.53430
4.42-5.640.53536
3.76-4.420.55628
3.32-3.760.56713
3.01-3.320.56783
2.77-3.010.57837
2.58-2.770.57916
Phasing dmFOM : 0.83 / FOM acentric: 0.85 / FOM centric: 0.62 / Reflection: 5094 / Reflection acentric: 4596 / Reflection centric: 498
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-27.3870.880.920.7522416955
4.5-7.10.880.910.6969759998
3.6-4.50.90.920.785476490
3.1-3.60.860.880.6586478975
2.7-3.10.790.810.5115021386116
2.5-2.70.730.750.4895388964

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: SAD
Starting model: 1TBD

1tbd


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.905 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.065 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1252 4.9 %RANDOM
Rwork0.169 ---
all0.17 25306 --
obs0.17 24796 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 13 170 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221143
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9611558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg65144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.99923.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11215205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.742155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02879
X-RAY DIFFRACTIONr_nbd_refined0.1990.2554
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.221
X-RAY DIFFRACTIONr_mcbond_it0.7161.5705
X-RAY DIFFRACTIONr_mcangle_it1.19521127
X-RAY DIFFRACTIONr_scbond_it1.7913489
X-RAY DIFFRACTIONr_scangle_it2.6714.5429
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 91 -
Rwork0.205 1707 -
obs-1798 96 %
Refinement TLS params.Method: refined / Origin x: 12.636 Å / Origin y: 72.16 Å / Origin z: 0.801 Å
111213212223313233
T-0.051 Å20.0012 Å20.0011 Å2--0.0302 Å2-0.0087 Å2---0.0179 Å2
L1.281 °2-0.0872 °20.2714 °2-0.8212 °2-0.0407 °2--0.8451 °2
S0.0186 Å °0.0698 Å °-0.013 Å °-0.0091 Å °0.0421 Å °-0.008 Å °-0.0298 Å °-0.0374 Å °-0.0607 Å °
Refinement TLS groupSelection: ALL

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