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- PDB-6f96: Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(et... -

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Basic information

Entry
Database: PDB / ID: 6f96
TitleCrystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-[(4-methoxyphenyl)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) 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 / 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-D0K / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 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)24,6852
Polymers24,2781
Non-polymers4061
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.200, 100.200, 50.270
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: 24278.258 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, EC: 5.99.1.3
#2: Chemical ChemComp-D0K / 6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide


Mass: 406.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H22N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25-30% PEG 400 and 100 mM Hepes pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2016
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50.27 Å / Num. obs: 10325 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.063 / Rrim(I) all: 0.197 / Net I/σ(I): 10.6 / Num. measured all: 101076
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.579.81.6917350.5280.5671.785100
11.18-50.277.70.0471370.9970.0170.0599.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6F86

6f86


Resolution: 2.5→50.27 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.476 / SU ML: 0.204 / SU R Cruickshank DPI: 0.3543 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.243
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 498 4.8 %RANDOM
Rwork0.2074 ---
obs0.2088 9812 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.96 Å2 / Biso mean: 47.287 Å2 / Biso min: 28.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.94 Å2
Refinement stepCycle: final / Resolution: 2.5→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 30 74 1551
Biso mean--50.36 47.95 -
Num. residues----187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191537
X-RAY DIFFRACTIONr_bond_other_d0.0020.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9622083
X-RAY DIFFRACTIONr_angle_other_deg0.9663.0063259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4523.69973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9921512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 42 -
Rwork0.3 687 -
all-729 -
obs--99.86 %
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)
14.14970.1892-0.551611.42890.12892.6179-0.16670.2465-0.62440.11380.12930.33330.815-0.06880.03740.2656-0.06210.01860.1739-0.04280.126366.874123.107942.2192
25.5341-1.7148-3.38751.65010.10868.8912-0.07730.06-0.28750.02080.00130.4552-0.0385-0.58270.0760.0715-0.058-0.03360.11920.01790.158360.011334.617557.5155
30.7361.0042-0.68582.3379-2.15093.3312-0.0046-0.0061-0.1249-0.2102-0.09230.02620.3904-0.12620.09690.06340.0019-0.0040.0993-0.03250.128168.352627.68259.9915
42.8983-0.1330.90632.09560.22625.8886-0.02010.0341-0.05540.04150.0501-0.19410.24530.2797-0.02990.0346-0.011-0.01290.03830.00730.037274.309328.90660.1982
56.89940.4481-4.7011.77512.92969.1980.15310.6134-0.0344-0.0192-0.025-0.0865-0.153-0.5316-0.12810.1194-0.0302-0.03440.16410.04480.025770.855735.452940.3169
610.7462-4.9217-5.10612.26822.31872.45520.01080.1818-0.3095-0.0612-0.07740.1950.0703-0.08950.06660.2372-0.0181-0.16830.17710.03440.25256.970841.915348.6454
78.40770.3346-1.30475.0374-0.19692.92830.2068-0.22830.71560.04210.01150.0191-0.37860.1028-0.21830.11350.0059-0.01460.0694-0.01950.102966.479945.756952.8419
817.4092-0.9257-3.58091.3412-0.54654.1780.1761-0.22610.2007-0.0298-0.02480.1421-0.34130.0188-0.15130.1205-0.0114-0.01410.0255-0.00920.098958.555249.196754.7773
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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