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- PDB-1qzr: CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIA... -

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Basic information

Entry
Database: PDB / ID: 1qzr
TitleCRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE)
ComponentsDNA topoisomerase II
KeywordsISOMERASE / GHKL ATPASE DOMAIN / ICRF / ICRF-187 / DEXRAZOXANE
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 topoisomerase 2, TOPRIM domain / 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 2, TOPRIM domain / 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 / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-CDX / DNA topoisomerase 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsClassen, S. / Olland, S. / Berger, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187
Authors: Classen, S. / Olland, S. / Berger, J.M.
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionSep 30, 2003ID: 1Q1D
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_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_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_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_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
Remark 600HETEROGEN The electron density for the ethanediyl linker region of CDX (ICRF-187) is not well ...HETEROGEN The electron density for the ethanediyl linker region of CDX (ICRF-187) is not well defined, and the psuedo 2-fold symmetric structure of CDX binds across the 2-fold NCS axis of the Topo II ATPase region. We have therefore modeled CDX in two orientations related by a 180 degree rotation and have assigned them each an occupancy of 0.5.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase II
B: DNA topoisomerase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5277
Polymers96,1982
Non-polymers1,3295
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-36 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.553, 71.444, 215.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA topoisomerase II


Mass: 48098.938 Da / Num. of mol.: 2 / Fragment: N-terminal ATPase Region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TOP2 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS / References: UniProt: P06786, EC: 5.99.1.3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CDX / (S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6-PIPERAZINEDIONE / ICRF-187


Mass: 268.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 47.54 %
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 6.5
Details: PEG 1500, POTASSIUM CHLORIDE, GLYCEROL, SODIUM CACODYLATE, pH 6.5, microbatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2002
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 65576 / Num. obs: 60064 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 28.34 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.298 / % possible all: 59.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PVG

1pvg


Resolution: 1.9→45.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.52 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23741 5512 8.4 %RANDOM
Rwork0.19565 ---
all0.19911 65576 --
obs0.19911 60064 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.203 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å20 Å2
2---0.98 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6110 0 83 766 6959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226326
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.9658555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035754
X-RAY DIFFRACTIONr_chiral_restr0.0810.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024662
X-RAY DIFFRACTIONr_nbd_refined0.1910.23063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2684
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.224
X-RAY DIFFRACTIONr_mcbond_it0.6091.53782
X-RAY DIFFRACTIONr_mcangle_it1.18726160
X-RAY DIFFRACTIONr_scbond_it1.95632544
X-RAY DIFFRACTIONr_scangle_it3.2484.52395
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.287 276
Rwork0.233 2760
obs-2760
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)
10.4844-0.0116-0.29130.83070.09410.9663-0.01970.00840.04860.12440.0385-0.01880.0306-0.0046-0.01880.05690.00660.00210.01080.00110.051831.795745.866945.065
21.51680.2493-0.70750.88560.27311.4830.05750.13430.2068-0.11520.0484-0.0674-0.16410.0187-0.10590.03780.01070.02810.05090.03630.092841.38157.172920.6665
31.1131-0.0288-0.43520.64930.01631.4076-0.06620.2047-0.117-0.0212-0.01350.05890.3163-0.26930.07970.1043-0.08790.00950.1109-0.04880.061626.76822.396617.1464
41.49540.2356-0.7061.16450.1211.2253-0.03580.02370.05380.01250.0743-0.11650.13620.2002-0.03850.01080.0323-0.01070.1024-0.01430.062653.204833.163716.9299
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 25812 - 263
2X-RAY DIFFRACTION2AA276 - 405281 - 410
3X-RAY DIFFRACTION3BB8 - 25813 - 263
4X-RAY DIFFRACTION4BB277 - 405282 - 410

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