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- PDB-8htb: Staphylococcus aureus FtsZ 12-316 complexed with TXH9179 -

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Basic information

Entry
Database: PDB / ID: 8htb
TitleStaphylococcus aureus FtsZ 12-316 complexed with TXH9179
ComponentsCell division protein FtsZ
KeywordsHYDROLASE / GTPase / protein-inhibitor complex / antibacterial agent
Function / homology
Function and homology information


chloroplast fission / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...Tubulin-like protein FtsZ/CetZ / Cell division protein FtsZ / Cell division protein FtsZ, conserved site / Cell division protein FtsZ, C-terminal / FtsZ family, C-terminal domain / FtsZ protein signature 1. / FtsZ protein signature 2. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-ZI9 / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBryan, E. / Ferrer-Gonzalez, E. / Sagong, H.Y. / Fujita, J. / Mark, L. / Kaul, M. / LaVoie, E.J. / Matsumura, H. / Pilch, D.S.
Funding support United States, Japan, 11items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118874 United States
Japan Society for the Promotion of Science (JSPS)15J00589 Japan
Japan Society for the Promotion of Science (JSPS)16H00783 Japan
Japan Society for the Promotion of Science (JSPS)18K06094 Japan
Japan Society for the Promotion of Science (JSPS)19H04735 Japan
Japan Society for the Promotion of Science (JSPS)19K07582 Japan
Takeda Science Foundation Japan
The Promotion and Mutual Aid Corporation for Private Schools of Japan Japan
Institute for Protein Research, Osaka UniversityCR-18-05 Japan
Institute for Protein Research, Osaka UniversityCR-19-05 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101070 Japan
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Structural and Antibacterial Characterization of a New Benzamide FtsZ Inhibitor with Superior Bactericidal Activity and In Vivo Efficacy Against Multidrug-Resistant Staphylococcus aureus.
Authors: Bryan, E. / Ferrer-Gonzalez, E. / Sagong, H.Y. / Fujita, J. / Mark, L. / Kaul, M. / LaVoie, E.J. / Matsumura, H. / Pilch, D.S.
History
DepositionDec 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6824
Polymers31,8531
Non-polymers8293
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.445, 51.540, 86.292
Angle α, β, γ (deg.)90.00, 108.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell division protein FtsZ /


Mass: 31853.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ, SAR1162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GHP9
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ZI9 / 3-[(6-ethynyl-[1,3]thiazolo[5,4-b]pyridin-2-yl)methoxy]-2,6-bis(fluoranyl)benzamide


Mass: 345.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H9F2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: 100 mM Tris-HCl, 43% (w/v) PEP629, 300 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 69235 / % possible obs: 95.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.048 / Χ2: 1.01 / Net I/σ(I): 34.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Χ2% possible all
1.3-1.324.70.8042.234670.8280.71994.5
1.32-1.354.80.69833760.72294.7
1.35-1.374.80.58134250.72494.8
1.37-1.44.80.50534210.74395.2
1.4-1.434.80.42434170.75195.2
1.43-1.464.80.34934900.73195.6
1.46-1.54.80.2734290.76195.8
1.5-1.544.80.21334680.75595.9
1.54-1.594.80.16634450.77696.2
1.59-1.644.80.13835030.79396.3
1.64-1.74.80.10934870.79696.6
1.7-1.764.80.08735420.80797
1.76-1.844.80.06935000.86997.2
1.84-1.944.80.05735230.99397.3
1.94-2.064.70.04735451.15397.7
2.06-2.224.70.0435591.32898
2.22-2.454.70.03635821.48598.3
2.45-2.84.70.03335871.63598.4
2.8-3.534.50.03335631.9397.1
3.53-504.10.04129062.07277.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 1.3→34.05 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18555 3448 5 %RANDOM
Rwork0.15467 ---
obs0.15625 65787 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.106 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.3→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 53 341 2605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132472
X-RAY DIFFRACTIONr_bond_other_d0.0350.0162433
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.663394
X-RAY DIFFRACTIONr_angle_other_deg2.3761.5895640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80925.045111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66715454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661511
X-RAY DIFFRACTIONr_chiral_restr0.120.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022915
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5162.1131287
X-RAY DIFFRACTIONr_mcbond_other1.5112.1111286
X-RAY DIFFRACTIONr_mcangle_it2.0553.1791623
X-RAY DIFFRACTIONr_mcangle_other2.0573.1811624
X-RAY DIFFRACTIONr_scbond_it1.762.5491185
X-RAY DIFFRACTIONr_scbond_other1.762.5491186
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.223.6661740
X-RAY DIFFRACTIONr_long_range_B_refined3.26226.6242753
X-RAY DIFFRACTIONr_long_range_B_other3.1626.4132728
X-RAY DIFFRACTIONr_rigid_bond_restr12.88334905
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.332 Å
RfactorNum. reflection% reflection
Rfree0.268 262 -
Rwork0.249 4732 -
obs--93.03 %

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