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

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Basic information

Entry
Database: PDB / ID: 7pqi
TitleAcinetobacter baumannii DNA gyrase B 23kDa ATPase subdomain complexed with novobiocin
ComponentsDNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / DNA gyrase / GyrB / inhibitor / antibacterial / isomerase
Function / homologyNOVOBIOCIN / :
Function and homology information
Biological speciesAcinetobacter baumannii 1419130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6937
Polymers22,7701
Non-polymers9236
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint21 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.869, 42.869, 256.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA gyrase subunit B


Mass: 22770.273 Da / Num. of mol.: 1
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-NOV / NOVOBIOCIN / 4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside


Mass: 612.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H36N2O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.57 Å3/Da / Density % sol: 52 % / 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: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→256.19 Å / Num. obs: 20179 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.044 / Rrim(I) all: 0.228 / Net I/σ(I): 8.8 / Num. measured all: 530228 / Scaling rejects: 269
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
1.9-1.9427.32.623464912690.8940.5042.6681.2100
9.11-256.1916.70.04645042700.9990.0110.04727.199.9

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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: 6YD9

6yd9


Resolution: 1.9→64.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.142 / SU ML: 0.131 / SU R Cruickshank DPI: 0.1529 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 989 4.9 %RANDOM
Rwork0.2165 ---
obs0.2176 19078 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.53 Å2 / Biso mean: 35.494 Å2 / Biso min: 21.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.97 Å2
Refinement stepCycle: final / Resolution: 1.9→64.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 64 71 1661
Biso mean--36.87 42.82 -
Num. residues----198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131617
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151502
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.6432192
X-RAY DIFFRACTIONr_angle_other_deg1.321.5793436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50221.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24615246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4661512
X-RAY DIFFRACTIONr_chiral_restr0.0610.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 56 -
Rwork0.32 1409 -
all-1465 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.219 Å / Origin y: 5.175 Å / Origin z: 18.915 Å
111213212223313233
T0.1451 Å20.0357 Å2-0.019 Å2-0.0647 Å20.0043 Å2--0.0065 Å2
L1.0174 °2-0.1921 °2-0.0379 °2-1.7926 °2-0.3546 °2--3.3451 °2
S0.0259 Å °0.0203 Å °-0.0503 Å °0.1074 Å °-0.0349 Å °-0.031 Å °0.1357 Å °0.1243 Å °0.0091 Å °

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