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- PDB-3igc: Smallpox virus topoisomerase-DNA transition state -

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Basic information

Entry
Database: PDB / ID: 3igc
TitleSmallpox virus topoisomerase-DNA transition state
Components
  • 5'-D(*AP*TP*TP*CP*C)-3'
  • 5'-D(*CP*GP*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
  • 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
  • DNA topoisomerase 1
KeywordsIsomerase/DNA / topoisomerase / protein-dna complex / poxvirus / isomerase / ATP-binding / DNA-binding / Late protein / Nucleotide-binding / Isomerase-DNA COMPLEX
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / virion component / DNA binding
Similarity search - Function
DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. ...DNA topoisomerase I, N-terminal, viral / Viral DNA topoisomerase I, N-terminal / Viral Topoisomerase I / DNA topoisomerase I domain / DNA topoisomerase I, N-terminal / Topoisomerase (Topo) IB-type catalytic domain profile. / Topoisomerase I; Chain A, domain 3 / Topoisomerase I; Chain A, domain 3 / DNA topoisomerase I, active site / Topoisomerase (Topo) IB-type active site signature. / DNA topoisomerase I / DNA topoisomerase I, catalytic core, eukaryotic-type / DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type / Eukaryotic DNA topoisomerase I, catalytic core / DNA breaking-rejoining enzyme, catalytic core / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesVariola virus (smallpox virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPerry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
CitationJournal: Structure / Year: 2010
Title: Insights from the Structure of a Smallpox Virus Topoisomerase-DNA Transition State Mimic.
Authors: Perry, K. / Hwang, Y. / Bushman, F.D. / Van Duyne, G.D.
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 1
B: 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'
C: 5'-D(*AP*TP*TP*CP*C)-3'
D: 5'-D(*CP*GP*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4855
Polymers46,3704
Non-polymers1151
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-30 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.999, 103.999, 93.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA topoisomerase 1 / DNA topoisomerase I


Mass: 36617.449 Da / Num. of mol.: 1 / Mutation: C100S,C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variola virus (smallpox virus) / Strain: Western Reserve / Gene: H6R, I6R, TOP1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P32989, EC: 5.99.1.2

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DNA chain , 3 types, 3 molecules BCD

#2: DNA chain 5'-D(*GP*TP*GP*TP*CP*GP*CP*CP*CP*TP*T)-3'


Mass: 3316.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide Synthesized by Yale Keck Facility
#3: DNA chain 5'-D(*AP*TP*TP*CP*C)-3'


Mass: 1454.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide Synthesized by Yale Keck Facility
#4: DNA chain 5'-D(*CP*GP*GP*AP*AP*TP*AP*AP*GP*GP*GP*CP*GP*AP*CP*A)-3'


Mass: 4981.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide Synthesized by Yale Keck Facility

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Non-polymers , 2 types, 427 molecules

#5: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 294 K / pH: 7.4
Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2007
RadiationMonochromator: KOHZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27692 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.5
Reflection shellResolution: 2→2.15 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H7G EXCLUDING DNA DOWNSTREAM OF CLEAVAGE SITE AND AMINO ACID RESIDUES 240-314

2h7g


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.758 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1490 5.1 %RANDOM
Rwork0.177 ---
obs0.18 27692 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 647 3 426 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223371
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.742.2054678
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80923.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87415506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2321515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212277
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7151.51569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26122570
X-RAY DIFFRACTIONr_scbond_it2.10331802
X-RAY DIFFRACTIONr_scangle_it2.9174.52108
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 121 -
Rwork0.203 2044 -
obs--98.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.68420.9131.77461.41970.05033.8655-0.1875-0.00960.17150.01790.13680.2210.0191-0.22650.05070.1558-0.01250.00750.02870.01790.11018.3383-13.367911.4861
24.141-1.65971.12342.3162-0.4873.0408-0.2663-0.23810.03250.24310.0355-0.1924-0.07130.31520.23080.18990.01030.01260.06820.03480.046736.9491-16.411135.3506
32.77470.33190.46025.3890.83854.8227-0.5186-0.80720.92690.79370.10590.0805-1.04-0.33310.41260.58760.2189-0.23940.2789-0.24840.381426.40734.029141.3075
45.20030.41691.01614.4763-0.42784.14920.1252-0.0078-0.187-0.255-0.2310.28430.07130.10270.10570.11470.01260.00270.0135-0.0120.041124.1357-14.639521.5881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A75 - 219
3X-RAY DIFFRACTION3A219 - 314
4X-RAY DIFFRACTION4A501 - 532

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