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- PDB-1bjt: TOPOISOMERASE II RESIDUES 409-1201 -

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Basic information

Entry
Database: PDB / ID: 1bjt
TitleTOPOISOMERASE II RESIDUES 409-1201
ComponentsTOPOISOMERASE II
KeywordsTOPOISOMERASE / QUATERNARY CHANGE / DNA-BINDING / DNA TOPOLOGY
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 / synaptonemal complex / SUMOylation of DNA replication proteins / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / telomere maintenance via recombination ...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 / synaptonemal complex / SUMOylation of DNA replication proteins / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / telomere maintenance via recombination / reciprocal meiotic recombination / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / rRNA transcription / DNA topological change / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus
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 / C-terminal associated domain of TOPRIM / 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 / C-terminal associated domain of TOPRIM / C-terminal associated domain of TOPRIM / DNA topoisomerase II, eukaryotic-type / : / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsFass, D. / Bogden, C.E. / Berger, J.M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.
Authors: Fass, D. / Bogden, C.E. / Berger, J.M.
#1: Journal: Nature / Year: 1996
Title: Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
#2: Journal: Nature / Year: 1996
Title: Erratum. Structure and Mechanism of DNA Topoisomerase II
Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C.
History
DepositionJun 29, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TOPOISOMERASE II


Theoretical massNumber of molelcules
Total (without water)91,8111
Polymers91,8111
Non-polymers00
Water3,909217
1
A: TOPOISOMERASE II

A: TOPOISOMERASE II


Theoretical massNumber of molelcules
Total (without water)183,6212
Polymers183,6212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area67160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.400, 145.700, 161.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein TOPOISOMERASE II


Mass: 91810.602 Da / Num. of mol.: 1 / Fragment: DNA-BINDING AND CLEAVAGE CORE, RESIDUES 409-1201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P06786, EC: 5.99.1.3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11-2 %PEG33501drop
220-40 mMTris-Cl1drop
31-2 %PEG33501reservoir
4250-300 mMammonium acetate1reservoir
520-40 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.1402
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1402 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 41611 / % possible obs: 97.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 29.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.206 / % possible all: 95

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→14 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE B FACTORS FOR RESIDUES 653 - 659 ARE VERY HIGH, BUT THE DENSITY FOR THESE RESIDUES WAS SEEN IN SOLVENT-FLATTENED MIR MAPS. THESE RESIDUES HELPED ASSIGN THE CONNECTIVITY BETWEEN DOMAINS IN THE DIMER.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2905 7.2 %RANDOM
Rwork0.227 ---
obs0.227 40597 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5598 0 0 217 5815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.594
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.164
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3731 373 7.6 %
Rwork0.3487 4515 -
obs--97.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.164

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