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- PDB-2nov: Breakage-reunion domain of S.pneumoniae topo IV: crystal structur... -

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Basic information

Entry
Database: PDB / ID: 2nov
TitleBreakage-reunion domain of S.pneumoniae topo IV: crystal structure of a gram-positive quinolone target
ComponentsDNA topoisomerase 4 subunit A
KeywordsISOMERASE / protein / ParC / topo IV / gram-positive bacteria / quinolone target / DNA binding / DNA cleavage
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / 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 subunit A, Gram-positive / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : / DNA gyrase C-terminal domain, beta-propeller / 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-like domain superfamily
Similarity search - Domain/homology
DNA topoisomerase 4 subunit A / DNA topoisomerase (ATP-hydrolyzing)
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Achari, A. / Yang, C. / Ferrara, J.D. / Fisher, L.M. / Sanderson, M.R.
Citation
Journal: PLoS ONE / Year: 2007
Title: Breakage-Reunion Domain of Streptococcus pneumoniae Topoisomerase IV: Crystal Structure of a Gram-Positive Quinolone Target.
Authors: Laponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Achari, A. / Yang, C. / Ferrara, J.D. / Fisher, L.M. / Sanderson, M.R.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 2005
Title: The Structure of the ParC Subunit of Topoisomerase IV from Streptococcus pneumoniae
Authors: Laponogov, I. / Veselkov, D.A. / Sohi, M.K. / Pan, X.S. / Fisher, L.M. / Sanderson, M.R.
History
DepositionOct 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit A
C: DNA topoisomerase 4 subunit A
D: DNA topoisomerase 4 subunit A


Theoretical massNumber of molelcules
Total (without water)225,8224
Polymers225,8224
Non-polymers00
Water43224
1
A: DNA topoisomerase 4 subunit A
B: DNA topoisomerase 4 subunit A


Theoretical massNumber of molelcules
Total (without water)112,9112
Polymers112,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-11 kcal/mol
Surface area40740 Å2
MethodPISA
2
C: DNA topoisomerase 4 subunit A
D: DNA topoisomerase 4 subunit A


Theoretical massNumber of molelcules
Total (without water)112,9112
Polymers112,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-11 kcal/mol
Surface area42120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.920, 137.850, 326.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe biological assembly is a dimer generated by a) A and B chains b) C and D chains (two biological dimers in the asymmetric unit)

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Components

#1: Protein
DNA topoisomerase 4 subunit A / Topoisomerase IV subunit A


Mass: 56455.434 Da / Num. of mol.: 4 / Fragment: 55-kDa N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: 7785 / Gene: parC / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: P72525, UniProt: Q3HYJ3*PLUS, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.4 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were ...Details: The purified ParC55 protein was dialyzed against 20 mM Tris-HCl, pH 7.0, 200 mM NaCl, 10% glycerol, 1 mM beta-mercaptoethanol, 0.05% NaN3 then concentrated to 3-4 mg/ml. Hanging drops were formed by mixing equal volumes of protein and crystallization solutions (100 mM Tris-HCl, pH 5.5, 200 mM NaCl, 1 mM beta-mercaptoethanol, 0.05% NaN3 and 10% of 1:1 ethanol-isopropanol as precipitant). , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.91694 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: two cylindrical parabolic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91694 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: k,-h,l / Fraction: 0.323
ReflectionHighest resolution: 2.67 Å / Num. obs: 85197 / Redundancy: 5.4 % / Rsym value: 0.093

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AB4

1ab4


Resolution: 2.67→500 Å
Details: Refinement was performed using twinning operator (k,-h,l) and twinning fraction of 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 8219 9.4 %RANDOM
Rwork0.2235 ---
obs-85197 97.2 %-
Solvent computationBsol: 13.223 Å2
Displacement parametersBiso mean: 64.915 Å2
Baniso -1Baniso -2Baniso -3
1--7.871 Å20 Å20 Å2
2---6.113 Å20 Å2
3---13.983 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.73 Å
Refinement stepCycle: LAST / Resolution: 2.67→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13620 0 0 24 13644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1631.5
X-RAY DIFFRACTIONc_scbond_it1.3372
X-RAY DIFFRACTIONc_mcangle_it2.0752
X-RAY DIFFRACTIONc_scangle_it2.2242.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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