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- PDB-2rgr: Topoisomerase IIA bound to G-segment DNA -

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Basic information

Entry
Database: PDB / ID: 2rgr
TitleTopoisomerase IIA bound to G-segment DNA
Components
  • (DNA) x 2
  • DNA topoisomerase 2
KeywordsIsomerase/DNA / protein-DNA complex / ATP-binding / DNA-binding / Isomerase / Nucleotide-binding / Nucleus / Phosphoprotein / Topoisomerase / Isomerase-DNA COMPLEX
Function / homology
Function and homology information


replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ...replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / DNA topological change / rRNA transcription / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM ...Dna Ligase; domain 1 - #30 / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / DNA topoisomerase 2, TOPRIM domain / Rossmann fold - #670 / Gyrase A; domain 2 - #40 / DNA topoisomerase II, eukaryotic-type / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Gyrase A; domain 2 / Dna Ligase; domain 1 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsDong, K.C. / Berger, J.M.
CitationJournal: Nature / Year: 2007
Title: Structural basis for gate-DNA recognition and bending by type IIA topoisomerases.
Authors: Dong, K.C. / Berger, J.M.
History
DepositionOct 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA
D: DNA
A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,6894
Polymers98,6643
Non-polymers241
Water86548
1
C: DNA
D: DNA
A: DNA topoisomerase 2
hetero molecules

C: DNA
D: DNA
A: DNA topoisomerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,3778
Polymers197,3296
Non-polymers492
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.435, 126.801, 223.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: DNA chain DNA


Mass: 4659.036 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA


Mass: 5757.710 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA topoisomerase 2 / DNA topoisomerase II


Mass: 88247.617 Da / Num. of mol.: 1
Fragment: DNA binding and cleavage domain (residues 419-1177)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOP2, TOR3 / Plasmid: pGAL / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123 / References: UniProt: P06786, EC: 5.99.1.3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A PRO -> LEU SEQUENCE CONFLICT AT RESIDUE 547 IN UNIPROT DATABASE.

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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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-20% PEG 1000, 100-250 mM MgCl2, 100 mM sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 100011
2MgCl211
3sodium cacodylate11
4PEG 100012
5MgCl212
6sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.3776 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006
RadiationMonochromator: DOUBLE CRYSTAL, Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3776 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 49135 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.086 / Χ2: 1.024 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3-3.112.20.43846220.9198.4
3.11-3.232.20.32446931.06999.7
3.23-3.382.20.23547191.076100
3.38-3.562.20.16347340.989100
3.56-3.782.20.12946331.06299.6
3.78-4.072.20.08847051.084100
4.07-4.482.20.06747001.053100
4.48-5.132.20.05146890.989100
5.13-6.462.20.05247070.92799.9
6.46-502.20.02846581.07298.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å43.87 Å
Translation3 Å43.87 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1BGW, 1I7D

1bgw

1i7d


Resolution: 3→43.873 Å / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(I): 1.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2380 5.09 %RANDOM
Rwork0.229 ---
obs0.231 49135 99.34 %-
all-49135 --
Solvent computationShrinkage radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.37 Å2
Baniso -1Baniso -2Baniso -3
1--4.48 Å22.957 Å21.527 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3→43.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 690 1 48 6668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg0.01
X-RAY DIFFRACTIONf_bond_d1.402
LS refinement shellResolution: 3→3.11 Å
RfactorNum. reflection% reflection
Rfree0.335 120 -
Rwork0.324 --
obs-2539 96.69 %

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