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- PDB-4kqv: Topoisomerase iv atp binding domain of francisella tularensis in ... -

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Basic information

Entry
Database: PDB / ID: 4kqv
TitleTopoisomerase iv atp binding domain of francisella tularensis in complex with a small molecule inhibitor
ComponentsTopoisomerase IV, subunit B
KeywordsISOMERASE / ATP-binding / Nucleotide-binding / Topoisomerase / ATP-binding domain / DNA gyrase negatively supercoils closed circular double-stranded DNA
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / metal ion binding
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 / 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 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-DOO / IODIDE ION / DNA topoisomerase 4 subunit B / :
Similarity search - Component
Biological speciesFrancisella tularensis subsp. holarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBensen, D.C. / Akers-Rodriguez, S. / Lam, T. / Tari, L.W.
CitationJournal: To be Published
Title: A new class of type iia topoisomerase inhibitors with broad-spectrum antibacterial activity
Authors: Tari, L.W. / Bensen, D.C. / Finn, J.
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Topoisomerase IV, subunit B
B: Topoisomerase IV, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,78612
Polymers87,9022
Non-polymers1,88410
Water2,324129
1
A: Topoisomerase IV, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1478
Polymers43,9511
Non-polymers1,1967
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Topoisomerase IV, subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6394
Polymers43,9511
Non-polymers6883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.200, 163.160, 72.280
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Topoisomerase IV, subunit B


Mass: 43950.766 Da / Num. of mol.: 2 / Fragment: unp residues 18-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. holarctica (bacteria)
Strain: LVS
Gene: DNA TOPOISOMERASE IV SUBUNIT B PARE, FTL_1726, FTL_1726;
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2A1P5, UniProt: A0A0J9WZF0*PLUS, EC: 5.99.1.3
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-DOO / 6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine


Mass: 434.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23FN8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.4
Details: 10% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE, pH 5.4, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→66.06 Å / Num. all: 142179 / Num. obs: 40074 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.076

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HY1

4hy1


Resolution: 2.38→66.06 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.856 / SU B: 7.204 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29851 2007 5 %RANDOM
Rwork0.2551 ---
all0.259 ---
obs0.25727 37983 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.886 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å2-0.21 Å2
2---1.12 Å20 Å2
3---3.05 Å2
Refinement stepCycle: LAST / Resolution: 2.38→66.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 72 129 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024539
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9786138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52425.879199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86215849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9921512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213327
LS refinement shellResolution: 2.383→2.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 130 -
Rwork0.259 2472 -
obs--86.53 %

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