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- PDB-7pqm: Acinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain compl... -

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Basic information

Entry
Database: PDB / ID: 7pqm
TitleAcinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain complexed with EBL2888
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / DNA gyrase / GyrB / inhibitor / antibacterial / isomerase
Function / homologyChem-80S / :
Function and homology information
Biological speciesAcinetobacter baumannii 1419130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 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)46,5615
Polymers45,5412
Non-polymers1,0213
Water6,377354
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3013
Polymers22,7701
Non-polymers5302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2612
Polymers22,7701
Non-polymers4901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.634, 48.293, 82.692
Angle α, β, γ (deg.)90.000, 123.850, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 30 - 231 / Label seq-ID: 3 - 204

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

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Components

#1: Protein DNA gyrase subunit B


Mass: 22770.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: corresponds to residues 28-233 of full-length wild-type protein
Source: (gene. exp.) Acinetobacter baumannii 1419130 (bacteria)
Gene: gyrB, J518_2757 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A009KIJ4, 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NULL

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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: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→43.5 Å / Num. obs: 57543 / % possible obs: 99.9 % / Redundancy: 10.9 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.11 / Net I/σ(I): 8.9
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
1.55-1.5811.11.553073927770.660.4821.6250.599
8.49-43.510.50.04540163840.9980.0140.04748.699.3

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PQI

7pqi


Resolution: 1.55→43.54 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.05 / SU ML: 0.135 / SU R Cruickshank DPI: 0.1063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 2969 5.2 %RANDOM
Rwork0.18 ---
obs0.1823 54572 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.43 Å2 / Biso mean: 31.638 Å2 / Biso min: 23.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å22.55 Å2
2---5.57 Å20 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 1.55→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 65 354 3311
Biso mean--34.85 44.51 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133096
X-RAY DIFFRACTIONr_bond_other_d0.0050.0152803
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.6354231
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5756440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19322.067179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36415485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.21524
X-RAY DIFFRACTIONr_chiral_restr0.0590.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
X-RAY DIFFRACTIONr_rigid_bond_restr6.71835899
Refine LS restraints NCS

Ens-ID: 1 / Number: 6097 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 205 -
Rwork0.342 3982 -
all-4187 -
obs--99.36 %

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