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- PDB-6kvq: S. aureus FtsZ in complex with BOFP (compound 3) -

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Basic information

Entry
Database: PDB / ID: 6kvq
TitleS. aureus FtsZ in complex with BOFP (compound 3)
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
Chem-DVX / GUANOSINE-5'-DIPHOSPHATE / Cell division protein FtsZ / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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)33,1184
Polymers31,8531
Non-polymers1,2653
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-12 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.268, 49.686, 88.592
Angle α, β, γ (deg.)90.000, 111.240, 90.000
Int Tables number5
Space group name H-MC121
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: 31853.025 Da / Num. of mol.: 1
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


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-DVX / [(2R)-2-[3-aminocarbonyl-2,4-bis(fluoranyl)phenoxy]-2-[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]ethyl] 3-[2,2-bis(fluoranyl)-10,12-dimethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.0^{3,7}]dodeca-1(12),4,6,8,10-pentaen-4-yl]propanoate


Mass: 781.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H25BBrF7N4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM HEPES, 39% (w/v) PEP629

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→36.091 Å / Num. obs: 38774 / % possible obs: 99.8 % / Redundancy: 6.838 % / Biso Wilson estimate: 24.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 0.985 / Net I/σ(I): 15.09 / Num. measured all: 265154
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.647.0530.8811.9920250287428710.7150.9599.9
1.64-1.696.9850.6912.6919629281228100.8030.74699.9
1.69-1.746.8880.5783.218349266526640.8820.626100
1.74-1.796.7610.4683.9917566260225980.9310.50799.8
1.79-1.856.5430.3515.2216895259025820.9560.38299.7
1.85-1.916.4170.2616.915786246724600.9720.28599.7
1.91-1.986.7060.1999.1716000239023860.9840.21699.8
1.98-2.077.2260.15512.1316496229022830.9910.16799.7
2.07-2.167.1620.1214.7415648218821850.9940.12999.9
2.16-2.267.0560.09617.5714839210321030.9960.104100
2.26-2.397.0220.08120.1314009200319950.9970.08799.6
2.39-2.536.810.07122.0512932190118990.9970.07799.9
2.53-2.76.3650.06524.0311387179717890.9970.07199.6
2.7-2.926.7530.05727.9511305167816740.9970.06299.8
2.92-3.27.1320.05232.8110791151715130.9980.05699.7
3.2-3.586.9950.04735.199856141014090.9970.05199.9
3.58-4.136.7420.045378299123612310.9980.04999.6
4.13-5.066.3020.04136.586529104510360.9980.04599.1
5.06-7.166.70.04137.655218288240.9990.04499.5
7.16-36.0916.6390.0339.4430674704620.9990.03398.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOA

3voa


Resolution: 1.6→36.091 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2135 1939 5 %
Rwork0.1899 36834 -
obs0.1911 38773 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.73 Å2 / Biso mean: 32.0202 Å2 / Biso min: 15.39 Å2
Refinement stepCycle: final / Resolution: 1.6→36.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2223 0 80 165 2468
Biso mean--27.04 37.75 -
Num. residues----308
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.640.34141390.29452628100
1.64-1.68440.26911380.25852628100
1.6844-1.73390.2761370.25462593100
1.7339-1.78990.28371360.23662591100
1.7899-1.85390.25971390.22712639100
1.8539-1.92810.25181380.20982628100
1.9281-2.01580.22251380.20042626100
2.0158-2.12210.2521370.1962596100
2.1221-2.2550.2031390.19192642100
2.255-2.42910.2341390.1942636100
2.4291-2.67350.24681380.19272619100
2.6735-3.06020.20751400.18972654100
3.0602-3.85480.22341390.17382646100
3.8548-36.0910.15651420.1688270899

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