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- PDB-6yd1: SaFtsZ-DFMBA -

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Basic information

Entry
Database: PDB / ID: 6yd1
TitleSaFtsZ-DFMBA
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / Cell division protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...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-like protein FtsZ/CetZ / 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 / : / 2,6-difluoro-3-methoxybenzamide / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFernandez-Tornero, C. / Ruiz, F.M. / Andreu, J.M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Targeting the FtsZ Allosteric Binding Site with a Novel Fluorescence Polarization Screen, Cytological and Structural Approaches for Antibacterial Discovery.
Authors: Huecas, S. / Araujo-Bazan, L. / Ruiz, F.M. / Ruiz-Avila, L.B. / Martinez, R.F. / Escobar-Pena, A. / Artola, M. / Vazquez-Villa, H. / Martin-Fontecha, M. / Fernandez-Tornero, C. / Lopez- ...Authors: Huecas, S. / Araujo-Bazan, L. / Ruiz, F.M. / Ruiz-Avila, L.B. / Martinez, R.F. / Escobar-Pena, A. / Artola, M. / Vazquez-Villa, H. / Martin-Fontecha, M. / Fernandez-Tornero, C. / Lopez-Rodriguez, M.L. / Andreu, J.M.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4074
Polymers31,7381
Non-polymers6693
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-5 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.334, 51.139, 87.823
Angle α, β, γ (deg.)90.000, 110.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Cell division protein FtsZ


Mass: 31737.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ftsZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A031
#2: Chemical ChemComp-GDP / GUANOSINE-5'-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-OLQ / 2,6-difluoro-3-methoxybenzamide / 2,6-bis(fluoranyl)-3-methoxy-benzamide


Mass: 187.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7F2NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG5K MME, 10% EthGly, 0.2 M Li2SO4, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97901 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 1.7→41.15 Å / Num. obs: 32199 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 25.49 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.03 / Net I/σ(I): 13.79
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 3208 / CC1/2: 0.84 / Rpim(I) all: 0.34 / Rrim(I) all: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 1.7→41.15 Å / SU ML: 0.2171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9661
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2187 1550 4.82 %
Rwork0.1719 30632 -
obs0.1742 32182 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.91 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 42 207 2451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01582279
X-RAY DIFFRACTIONf_angle_d1.47743085
X-RAY DIFFRACTIONf_chiral_restr0.0965366
X-RAY DIFFRACTIONf_plane_restr0.0095407
X-RAY DIFFRACTIONf_dihedral_angle_d21.7001843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.34541360.27862783X-RAY DIFFRACTION98.28
1.75-1.820.30971200.24952764X-RAY DIFFRACTION98.9
1.82-1.890.27571360.23442788X-RAY DIFFRACTION98.38
1.89-1.980.30571180.21922788X-RAY DIFFRACTION97.85
1.98-2.080.26461340.19022792X-RAY DIFFRACTION98.65
2.08-2.210.26011460.17942801X-RAY DIFFRACTION98.99
2.21-2.380.23441490.17892743X-RAY DIFFRACTION98.17
2.38-2.620.21991360.18012776X-RAY DIFFRACTION97.36
2.62-30.21781760.17822772X-RAY DIFFRACTION98.79
3-3.780.19351420.15762758X-RAY DIFFRACTION96.6
3.78-41.150.18491570.13872867X-RAY DIFFRACTION98.34

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