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- PDB-3fv5: Crystal Structure of E. coli Topoisomerase IV co-complexed with i... -

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Basic information

Entry
Database: PDB / ID: 3fv5
TitleCrystal Structure of E. coli Topoisomerase IV co-complexed with inhibitor
ComponentsDNA topoisomerase 4 subunit B
KeywordsISOMERASE / topoisomerase IV B subunit complex / Antibiotic resistance / ATP-binding / Nucleotide-binding / Topoisomerase
Function / homology
Function and homology information


plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / sister chromatid cohesion / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome organization / chromosome segregation / chromosome ...plasmid partitioning / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / sister chromatid cohesion / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome organization / chromosome segregation / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
DNA topoisomerase IV, subunit B, Gram-negative / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 ...DNA topoisomerase IV, subunit B, Gram-negative / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / 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
Chem-1EU / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWei, Y. / Charifson, P. / LeTiran, A.
CitationJournal: To be Published
Title: Design and syntheses of novel C7-derived-aminobenzimidazole ureas: bacterial gyrase/topoisomerase IV inhibitors with potent Gram-positve antibacterial activity
Authors: Wei, Y. / Letiran, A.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: DNA topoisomerase 4 subunit B
B: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3514
Polymers44,7042
Non-polymers6472
Water7,837435
1
A: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6762
Polymers22,3521
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA topoisomerase 4 subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6762
Polymers22,3521
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.420, 72.840, 70.970
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 22352.160 Da / Num. of mol.: 2 / Fragment: topoisomerase IV subunit B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: parE, nfxD, b3030, JW2998 / Production host: Escherichia coli (E. coli)
References: UniProt: P20083, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses
#2: Chemical ChemComp-1EU / 1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea


Mass: 323.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15% PEG 4000, 0.1M MES, pH=5.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2003 / Details: mirrors
RadiationMonochromator: Ni mirrors + Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 33331 / % possible obs: 81.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.12 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.033

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNX2005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S14

1s14


Resolution: 1.8→19.75 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2167981.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1675 5.1 %RANDOM
Rwork0.197 ---
all0.199 33267 --
obs0.199 33150 82.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.3431 Å2 / ksol: 0.379115 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.8 Å20 Å2-0.48 Å2
2---0 Å2
3----6.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 48 435 3325
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it3.872.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 128 4.6 %
Rwork0.246 2635 -
obs--41.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2751107.par751107.top
X-RAY DIFFRACTION3water_rep.parwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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