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- PDB-6f86: Crystal Structure of E. coli GyraseB 24kDa in complex with 4-(4-b... -

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Basic information

Entry
Database: PDB / ID: 6f86
TitleCrystal Structure of E. coli GyraseB 24kDa in complex with 4-(4-bromo-1H-pyrazol-1-yl)-6-[(ethylcarbamoyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Binding Sites / DNA Gyrase / inhibitors / pyridine-3-carboxamides / topoisomerase IV
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytosol / 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 / 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-CWW / DNA gyrase subunit B / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNarramore, S.K. / Stevenson, C.E.M. / Lawson, D.M. / Maxwell, A. / Fishwick, C.W.G.
CitationJournal: Bioorg.Med.Chem. / Year: 2019
Title: New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.
Authors: Narramore, S. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M. / Fishwick, C.W.G.
History
DepositionDec 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0792
Polymers22,6481
Non-polymers4301
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.340, 99.340, 50.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA gyrase subunit B /


Mass: 22648.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: gyrB, Z5190, ECs4634 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AES7, UniProt: P0AES6*PLUS, EC: 5.99.1.3
#2: Chemical ChemComp-CWW / 4-(4-bromanylpyrazol-1-yl)-6-(ethylcarbamoylamino)-~{N}-pyridin-3-yl-pyridine-3-carboxamide


Mass: 430.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16BrN7O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25-30% PEG400 and 100 mM Hepes pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2016
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→49.67 Å / Num. obs: 22689 / % possible obs: 99.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.065 / Rrim(I) all: 0.205 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.959.61.52716570.5060.5141.61399
8.5-49.6780.0762880.9960.0270.08199.7

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4URO

4uro


Resolution: 1.9→49.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.098 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 1210 5.3 %RANDOM
Rwork0.2031 ---
obs0.2041 21468 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.42 Å2 / Biso mean: 33.643 Å2 / Biso min: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 1.9→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 27 106 1579
Biso mean--32 41.29 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191534
X-RAY DIFFRACTIONr_bond_other_d0.0020.021414
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9622082
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0043265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15523.69973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2981512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 72 -
Rwork0.301 1581 -
all-1653 -
obs--98.69 %
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)
14.7197-2.76120.191910.275-0.00815.2032-0.07810.2292-0.8224-0.01410.19960.5441.1737-0.0816-0.12150.3183-0.1129-0.01140.2882-0.00520.150266.480122.506442.0655
27.0334-2.0412-4.95843.08640.14037.0223-0.05550.1545-0.05560.10680.21010.30150.098-0.6541-0.15460.0621-0.0587-0.03680.19430.03090.111659.550934.072757.3884
31.28041.3246-0.98382.4681-2.23443.3936-0.10670.1231-0.2659-0.24690.09410.05470.4235-0.14230.01260.0647-0.0554-0.00150.1438-0.01840.184167.928527.118860.0004
41.76220.23111.12962.29240.91716.0575-0.07820.0184-0.173-0.01990.0801-0.05880.35560.1654-0.00190.0631-0.03340.02070.074-0.0050.020873.867228.136860.0012
55.79081.8617-1.98081.94312.78339.38210.01550.2421-0.207-0.11430.0809-0.1318-0.2819-0.0762-0.09640.1619-0.0489-0.00660.1756-0.00540.011570.411634.725640.2629
67.8059-0.4587-2.72950.34280.35512.6939-0.16070.179-0.2476-0.13360.12610.11280.185-0.14070.03470.1412-0.0298-0.04070.17540.02540.128556.591341.41148.6088
710.79642.5125-2.7331.9886-0.69113.8680.1876-0.08030.65530.0890.15310.2464-0.4808-0.0738-0.34070.12080.0055-0.00740.11780.03280.092566.158845.231452.7059
88.5043-1.169-3.39952.99670.18143.4532-0.0809-0.2690.2093-0.05410.0260.1414-0.16090.04670.05490.12640.0175-0.0090.13590.01550.131458.36148.746754.7288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 38
2X-RAY DIFFRACTION2A39 - 58
3X-RAY DIFFRACTION3A59 - 120
4X-RAY DIFFRACTION4A121 - 173
5X-RAY DIFFRACTION5A174 - 186
6X-RAY DIFFRACTION6A187 - 197
7X-RAY DIFFRACTION7A198 - 212
8X-RAY DIFFRACTION8A213 - 219

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