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- PDB-6kvp: S. aureus FtsZ in complex with 3-(1-(5-bromo-4-(4-(trifluoromethy... -

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Basic information

Entry
Database: PDB / ID: 6kvp
TitleS. aureus FtsZ in complex with 3-(1-(5-bromo-4-(4-(trifluoromethyl)phenyl)oxazol-2-yl)ethoxy)-2,6-difluorobenzamide (compound 2)
ComponentsCell division protein FtsZ
KeywordsHYDROLASE / GTPase / protein-inhibitor complex
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-ZI1 / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsFerrer-Gonzalez, E. / Fujita, J. / Yoshizawa, T. / Nelson, J.M. / Pilch, A.J. / Hillman, E. / Ozawa, M. / Kuroda, N. / Parhi, A.K. / LaVoie, E.J. ...Ferrer-Gonzalez, E. / Fujita, J. / Yoshizawa, T. / Nelson, J.M. / Pilch, A.J. / Hillman, E. / Ozawa, M. / Kuroda, N. / Parhi, A.K. / LaVoie, E.J. / Matsumura, H. / Pilch, D.S.
Funding support United States, Japan, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118874 United States
Japan Society for the Promotion of Science15J00589 Japan
Japan Society for the Promotion of Science19K16060 Japan
Japan Society for the Promotion of Science17H05732 Japan
Japan Society for the Promotion of Science18K06094 Japan
Japan Society for the Promotion of Science19H04735 Japan
Japan Society for the Promotion of Science19K07582 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101070 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Structure-Guided Design of a Fluorescent Probe for the Visualization of FtsZ in Clinically Important Gram-Positive and Gram-Negative Bacterial Pathogens.
Authors: Ferrer-Gonzalez, E. / Fujita, J. / Yoshizawa, T. / Nelson, J.M. / Pilch, A.J. / Hillman, E. / Ozawa, M. / Kuroda, N. / Al-Tameemi, H.M. / Boyd, J.M. / LaVoie, E.J. / Matsumura, H. / Pilch, D.S.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: 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: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8284
Polymers31,8531
Non-polymers9743
Water6,125340
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 area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.491, 51.739, 86.737
Angle α, β, γ (deg.)90.000, 108.650, 90.000
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 / Fragment: globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: ftsZ / Plasmid: pColdI with TEV protease site / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A031, UniProt: Q6GHP9*PLUS
#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-ZI1 / 3-[(1R)-1-[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]ethoxy]-2,6-bis(fluoranyl)benzamide


Mass: 491.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12BrF5N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.35 Å3/Da / Density % sol: 47.71 % / Mosaicity: 0.715 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 100 mM Tris-HCl, 45% (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: 1.4→50 Å / Num. obs: 58167 / % possible obs: 99.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.032 / Rrim(I) all: 0.079 / Χ2: 1.035 / Net I/σ(I): 8.2 / Num. measured all: 360570
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.426.20.70429230.8710.310.7710.38100
1.42-1.456.20.62129210.8920.2730.6790.385100
1.45-1.486.20.52228940.9150.230.5710.403100
1.48-1.516.20.41229410.940.1810.450.42100
1.51-1.546.20.34228720.9610.150.3740.428100
1.54-1.586.30.27729530.9720.1210.3020.477100
1.58-1.626.20.22329110.9820.0980.2440.49100
1.62-1.666.30.20629000.9820.0890.2250.556100
1.66-1.716.30.17329360.9850.0760.190.619100
1.71-1.766.30.14829250.9880.0650.1620.672100
1.76-1.836.30.1229240.9920.0520.1310.755100
1.83-1.96.30.09829280.9930.0420.1070.88100
1.9-1.996.30.08429320.9950.0370.0921.038100
1.99-2.096.30.07329230.9960.0320.081.272100
2.09-2.226.30.07329220.9960.0320.081.877100
2.22-2.396.30.06629240.9970.0280.0722.187100
2.39-2.636.30.05929440.9970.0260.0642.141100
2.63-3.026.30.05329600.9980.0230.0582.023100
3.02-3.860.0529450.9980.0220.0551.89299.3
3.8-5050.06125890.9940.030.0692.09685.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0151refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 1.4→41.09 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.03 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.177 2861 4.9 %RANDOM
Rwork0.1449 ---
obs0.1465 55292 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.59 Å2 / Biso mean: 21.114 Å2 / Biso min: 6.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.4→41.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 59 340 2610
Biso mean--14.57 34.83 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192501
X-RAY DIFFRACTIONr_bond_other_d0.0020.022451
X-RAY DIFFRACTIONr_angle_refined_deg1.43423439
X-RAY DIFFRACTIONr_angle_other_deg0.89735692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2545368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1626.765102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86415461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.331511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022949
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02508
X-RAY DIFFRACTIONr_rigid_bond_restr1.0834952
X-RAY DIFFRACTIONr_sphericity_free35.528565
X-RAY DIFFRACTIONr_sphericity_bonded11.00955172
LS refinement shellResolution: 1.4→1.434 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.222 212 -
Rwork0.193 4083 -
obs--99.84 %

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