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- PDB-5xdt: Staphylococcus aureus FtsZ 12-316 complexed with TXA707 -

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Basic information

Entry
Database: PDB / ID: 5xdt
TitleStaphylococcus aureus FtsZ 12-316 complexed with TXA707
ComponentsCell division protein FtsZ
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Cell division / GTPase / Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


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 / 1-methylpyrrolidin-2-one / Chem-ZI7 / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsFujita, J. / Maeda, Y. / Mizohata, E. / Inoue, T. / Kaul, M. / Parhi, A.K. / LaVoie, E.J. / Pilch, D.S. / Matsumura, H.
Funding support United States, Japan, 6items
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 Science24109017 Japan
Japan Society for the Promotion of Science15H04443 Japan
Japan Society for the Promotion of Science26102526 Japan
Japan Society for the Promotion of Science16H00783 Japan
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structural Flexibility of an Inhibitor Overcomes Drug Resistance Mutations in Staphylococcus aureus FtsZ
Authors: Fujita, J. / Maeda, Y. / Mizohata, E. / Inoue, T. / Kaul, M. / Parhi, A.K. / LaVoie, E.J. / Pilch, D.S. / Matsumura, H.
History
DepositionMar 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 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 1.3Nov 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)32,9246
Polymers31,8531
Non-polymers1,0715
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.553, 51.193, 86.449
Angle α, β, γ (deg.)90.000, 108.680, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

MB3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cell division protein FtsZ /


Mass: 31853.025 Da / Num. of mol.: 1 / Fragment: UNP residues 12-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MRSA252) (bacteria)
Strain: MRSA252 / Gene: ftsZ, SAR1162 / Plasmid: pCold / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6GHP9

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Non-polymers , 5 types, 309 molecules

#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-ZI7 / 2,6-bis(fluoranyl)-3-[[6-(trifluoromethyl)-[1,3]thiazolo[5,4-b]pyridin-2-yl]methoxy]benzamide


Mass: 389.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H8F5N3O2S
#5: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one / N-Methyl-2-pyrrolidone


Mass: 99.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 47.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 100mM Tris-HCl, 41% w/v PEP629, 300mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 11, 2016
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: 71548 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Χ2: 1.038 / Net I/σ(I): 8.6 / Num. measured all: 503253
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.326.90.7636200.8410.3110.8230.651100
1.32-1.3570.68435250.8720.2790.740.648100
1.35-1.376.90.57835650.8910.2370.6260.663100
1.37-1.470.50835950.9190.2070.5490.684100
1.4-1.4370.41935600.9470.1710.4530.691100
1.43-1.4670.37235980.9520.1510.4020.705100
1.46-1.570.28835950.9680.1170.3110.761100
1.5-1.5470.23635700.9770.0960.2550.83100
1.54-1.597.10.18835470.9860.0760.2040.889100
1.59-1.647.10.16135830.9880.0650.1730.89100
1.64-1.77.10.12935970.9920.0520.1390.898100
1.7-1.767.10.10536160.9940.0430.1140.943100
1.76-1.847.10.08535630.9960.0340.0911.02100
1.84-1.947.10.07535890.9970.030.0811.249100
1.94-2.067.10.06836180.9970.0280.0741.692100
2.06-2.227.20.05736060.9980.0230.0611.673100
2.22-2.457.20.04635910.9980.0180.0491.457100
2.45-2.87.20.04136160.9990.0160.0441.407100
2.8-3.537.10.03536200.9990.0140.0381.39399.7
3.53-506.40.03533740.9980.0160.0391.6190.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3VOA

3voa


Resolution: 1.3→40.95 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1681 3484 4.9 %RANDOM
Rwork0.1361 ---
obs0.1377 68064 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.78 Å2 / Biso mean: 25.435 Å2 / Biso min: 10.11 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.3→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 69 304 2584
Biso mean--22.58 39.11 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192518
X-RAY DIFFRACTIONr_bond_other_d00.022498
X-RAY DIFFRACTIONr_angle_refined_deg1.7462.0043460
X-RAY DIFFRACTIONr_angle_other_deg3.64335799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92626.733101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19115470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5831511
X-RAY DIFFRACTIONr_chiral_restr0.090.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022963
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02511
X-RAY DIFFRACTIONr_rigid_bond_restr11.36535016
X-RAY DIFFRACTIONr_sphericity_free35.363561
X-RAY DIFFRACTIONr_sphericity_bonded12.58155203
LS refinement shellResolution: 1.299→1.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 251 -
Rwork0.207 4953 -
all-5204 -
obs--98.64 %

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