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- PDB-4zvi: GYRASE B IN COMPLEX WITH 4,5-DIBROMOPYRROLAMIDE-BASED INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4zvi
TitleGYRASE B IN COMPLEX WITH 4,5-DIBROMOPYRROLAMIDE-BASED INHIBITOR
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Gyrase B / Inhibitor / GyrB / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 / 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-4S4 / IODIDE ION / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZidar, N. / Macut, H. / Tomasic, T. / Brvar, M. / Montalvao, S. / Tammela, P. / Solmajer, T. / Peterlin Masic, L. / Ilas, J. / Kikelj, D.
CitationJournal: J.Med.Chem. / Year: 2015
Title: N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation.
Authors: Zidar, N. / Macut, H. / Tomasic, T. / Brvar, M. / Montalvao, S. / Tammela, P. / Solmajer, T. / Peterlin Masic, L. / Ilas, J. / Kikelj, D.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3894
Polymers41,6901
Non-polymers6993
Water1,35175
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.878, 50.546, 71.344
Angle α, β, γ (deg.)90.000, 93.530, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DNA gyrase subunit B /


Mass: 41689.965 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 16-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AES7, EC: 5.99.1.3
#2: Chemical ChemComp-4S4 / N-(4-{[(4,5-dibromo-1H-pyrrol-2-yl)carbonyl]amino}benzoyl)glycine


Mass: 445.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11Br2N3O4
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: 15-25% PEG3350 / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→71.21 Å / Num. obs: 20677 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.45 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.435 / Rejects: 0 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.2→71.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 18.609 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1403 6.8 %RANDOM
Rwork0.2242 ---
obs0.2281 19273 95.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.94 Å2 / Biso mean: 63.312 Å2 / Biso min: 33.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å2-0 Å22.77 Å2
2---1.09 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 2.2→71.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 21 76 2881
Biso mean--79.28 58.28 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192743
X-RAY DIFFRACTIONr_bond_other_d0.0010.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9523724
X-RAY DIFFRACTIONr_angle_other_deg2.68235843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0525354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.01724.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1261516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023170
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02621
X-RAY DIFFRACTIONr_mcbond_it2.6824.5891425
X-RAY DIFFRACTIONr_mcbond_other2.6814.5881424
X-RAY DIFFRACTIONr_mcangle_it3.8067.741776
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 112 -
Rwork0.362 1401 -
all-1513 -
obs--96.25 %
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)
13.0167-0.5828-0.62893.6932-1.05692.88110.2665-0.16290.51580.0318-0.06250.1293-0.59080.0026-0.20410.13490.00190.05590.3092-0.05150.1072-16.69611.23314.811
22.4758-1.38431.06622.7115-1.23482.27140.0627-0.0653-0.3184-0.08250.0283-0.06160.18610.059-0.0910.0208-0.0427-0.00180.4938-0.02270.073411.486-8.24222.916
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 222
2X-RAY DIFFRACTION2A223 - 392

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