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- PDB-7ptg: Pseudomonas aeruginosa DNA gyrase B 24kDa ATPase subdomain comple... -

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Basic information

Entry
Database: PDB / ID: 7ptg
TitlePseudomonas aeruginosa DNA gyrase B 24kDa ATPase subdomain complexed with EBL2888
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / DNA gyrase / GyrB / inhibitor / antibacterial / isomerase
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 / 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-, 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
Chem-80S / DNA gyrase subunit B
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCotman, A.E. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P. / Mundy, J.E.A. / Stevenson, C.E.M. / Burton, N. / Lawson, D.M. ...Cotman, A.E. / Zega, A. / Zidar, N. / Ilas, J. / Tomasic, T. / Masic, L.P. / Mundy, J.E.A. / Stevenson, C.E.M. / Burton, N. / Lawson, D.M. / Maxwell, A. / Kikelj, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme115583 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery and Hit-to-Lead Optimization of Benzothiazole Scaffold-Based DNA Gyrase Inhibitors with Potent Activity against Acinetobacter baumannii and Pseudomonas aeruginosa.
Authors: Cotman, A.E. / Durcik, M. / Benedetto Tiz, D. / Fulgheri, F. / Secci, D. / Sterle, M. / Mozina, S. / Skok, Z. / Zidar, N. / Zega, A. / Ilas, J. / Peterlin Masic, L. / Tomasic, T. / Hughes, D. ...Authors: Cotman, A.E. / Durcik, M. / Benedetto Tiz, D. / Fulgheri, F. / Secci, D. / Sterle, M. / Mozina, S. / Skok, Z. / Zidar, N. / Zega, A. / Ilas, J. / Peterlin Masic, L. / Tomasic, T. / Hughes, D. / Huseby, D.L. / Cao, S. / Garoff, L. / Berruga Fernandez, T. / Giachou, P. / Crone, L. / Simoff, I. / Svensson, R. / Birnir, B. / Korol, S.V. / Jin, Z. / Vicente, F. / Ramos, M.C. / de la Cruz, M. / Glinghammar, B. / Lenhammar, L. / Henderson, S.R. / Mundy, J.E.A. / Maxwell, A. / Stevenson, C.E.M. / Lawson, D.M. / Janssen, G.V. / Sterk, G.J. / Kikelj, D.
History
DepositionSep 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)50,0564
Polymers49,0752
Non-polymers9812
Water1,65792
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0282
Polymers24,5371
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0282
Polymers24,5371
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.572, 47.865, 75.287
Angle α, β, γ (deg.)90.000, 93.460, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 19 - 218 / Label seq-ID: 19 - 218

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein DNA gyrase subunit B /


Mass: 24537.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: corresponds to residues 1-221 of full-length wild-type protein
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: gyrB, PA0004 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9I7C2, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical ChemComp-80S / 2-[[3,4-bis(chloranyl)-5-methyl-1H-pyrrol-2-yl]carbonylamino]-4-[(1S)-1-phenylethoxy]-1,3-benzothiazole-6-carboxylic acid


Mass: 490.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17Cl2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.3 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→41.86 Å / Num. obs: 19239 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.091 / Rrim(I) all: 0.237 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.276.51.1931068916380.6460.5021.2961.5100
9.07-41.8660.06918133010.9940.030.0751798.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PTF

7ptf


Resolution: 2.2→41.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.936 / SU ML: 0.188 / SU R Cruickshank DPI: 0.3019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.302 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 953 5 %RANDOM
Rwork0.1941 ---
obs0.1962 18270 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.83 Å2 / Biso mean: 31.095 Å2 / Biso min: 8.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-1.61 Å2
2---0.25 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.2→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2843 0 64 93 3000
Biso mean--30.96 31.23 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132981
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152707
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6364050
X-RAY DIFFRACTIONr_angle_other_deg1.351.5786220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7985364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05721.875160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36115472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4661521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02671
Refine LS restraints NCS

Ens-ID: 1 / Number: 5523 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 80 -
Rwork0.278 1315 -
all-1395 -
obs--99.71 %
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)
11.6641-0.4818-0.51992.60340.11981.34470.01320.04250.0085-0.0502-0.0086-0.04080.0401-0.0781-0.00460.06290.0058-0.02950.1559-0.00820.0159-14.2211-6.6234-0.3165
22.13820.54570.91522.9427-0.27652.79830.0081-0.17770.06470.0189-0.07610.16140.0515-0.070.0680.16450.0327-0.01340.2457-0.02070.0134-9.91684.275127.4587
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 301
2X-RAY DIFFRACTION2B19 - 301

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