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- PDB-6ttg: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

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Basic information

Entry
Database: PDB / ID: 6ttg
TitleCrystal structure of the ATP binding domain of S. aureus GyrB complexed with LMD62
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA GYRASE / GYRB
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
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. ...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-, 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
Similarity search - Domain/homology
IMIDAZOLE / Chem-NWK / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWelin, M. / Kimbung, R. / Focht, D.
Funding support Slovenia, 1items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0208 Slovenia
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens.
Authors: Durcik, M. / Nyerges, A. / Skok, Z. / Skledar, D.G. / Trontelj, J. / Zidar, N. / Ilas, J. / Zega, A. / Cruz, C.D. / Tammela, P. / Welin, M. / Kimbung, Y.R. / Focht, D. / Benek, O. / Revesz, ...Authors: Durcik, M. / Nyerges, A. / Skok, Z. / Skledar, D.G. / Trontelj, J. / Zidar, N. / Ilas, J. / Zega, A. / Cruz, C.D. / Tammela, P. / Welin, M. / Kimbung, Y.R. / Focht, D. / Benek, O. / Revesz, T. / Draskovits, G. / Szili, P.E. / Daruka, L. / Pal, C. / Kikelj, D. / Masic, L.P. / Tomasic, T.
History
DepositionDec 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,72514
Polymers47,8632
Non-polymers1,86212
Water3,837213
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9538
Polymers23,9321
Non-polymers1,0227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7726
Polymers23,9321
Non-polymers8405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.700, 55.360, 50.810
Angle α, β, γ (deg.)90.000, 100.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-306-

CA

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B


Mass: 23931.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DELTA 105-127 / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Plasmid: PET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2
References: UniProt: P0A0K8, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 7 types, 225 molecules

#2: Chemical ChemComp-NWK / 2-[[3,4-bis(chloranyl)-5-methyl-1~{H}-pyrrol-2-yl]carbonylamino]-4-(2-morpholin-4-ylethoxy)-1,3-benzothiazole-6-carboxylic acid


Mass: 499.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20Cl2N4O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/MOPS pH 7.5 0.03 M magnesium chloride 0.03 M calcium chloride 25 % v/v MPD 25% v/v PEG 1000 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→51.5 Å / Num. obs: 42170 / % possible obs: 98 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.6
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.433 / Mean I/σ(I) obs: 1 / Num. unique obs: 2060 / CC1/2: 0.475 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cph

5cph


Resolution: 1.7→51.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.443 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.108
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2031 4.8 %RANDOM
Rwork0.1861 ---
obs0.1873 40138 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.72 Å2 / Biso mean: 35.721 Å2 / Biso min: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å2-2.98 Å2
2--0.67 Å20 Å2
3---1.42 Å2
Refinement stepCycle: final / Resolution: 1.7→51.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 118 213 3380
Biso mean--58.78 47.2 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133271
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173024
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.6834442
X-RAY DIFFRACTIONr_angle_other_deg1.3641.5997005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77522.99194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7161524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023647
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02669
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 154 -
Rwork0.313 2899 -
all-3053 -
obs--96.92 %
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)
10.7891-0.23180.41160.18090.04060.4661-0.10420.14750.03090.0774-0.04880.086-0.00330.08680.15310.0657-0.04040.03690.04430.00320.083911.67611.687-5.157
20.8246-0.03560.26540.6456-0.01470.2873-0.0845-0.04820.11020.0536-0.0242-0.16610.0401-0.08010.10870.09190.00490.01850.035-0.01510.087-20.928-12.633-27.567
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 230
2X-RAY DIFFRACTION2B20 - 231

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