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- PDB-14uo: Crystal Structure of FtsZ with F3308-1098 -

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Basic information

Entry
Database: PDB / ID: 14uo
TitleCrystal Structure of FtsZ with F3308-1098
ComponentsCell division protein FtsZ
KeywordsCELL CYCLE / tuberculosis / FtsZ / cell division
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
FtsZ protein signature 2. / 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. / Tubulin-like protein FtsZ/CetZ / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal ...FtsZ protein signature 2. / 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. / 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
: / PHOSPHATE ION / Cell division protein FtsZ
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsMeeks, K.R. / Kreitler, D.F. / Lazo, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1605010 United States
CitationJournal: To be published
Title: Crystal Structure of FtsZ with F3308-1098
Authors: Meeks, K.R. / Kreitler, D.F. / Lazo, E.O.
History
DepositionJul 15, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: 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
B: Cell division protein FtsZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9024
Polymers77,5812
Non-polymers3202
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.729, 88.729, 178.884
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell division protein FtsZ


Mass: 38790.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Gene: ftsZ, MT2209 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WN94
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-A1DNY / 4-methyl-2-(thiophen-2-yl)-1,3-thiazole-5-carboxylic acid


Mass: 225.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M ammonium sulfate, 15.6% (w/v) PEG 3350, 0.1 M Bis-Tris pH 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919764 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2025 / Details: KB
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919764 Å / Relative weight: 1
ReflectionResolution: 1.948→44.364 Å / Num. obs: 58059 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.061 / Rrim(I) all: 0.223 / Net I/σ(I): 8 / Num. measured all: 773645
Reflection shellResolution: 1.948→1.982 Å / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 2.346 / Num. measured all: 39436 / Num. unique obs: 2940 / CC1/2: 0.339 / Rpim(I) all: 0.664 / Rrim(I) all: 2.439

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0430refinement
autoPROC1.0.5data reduction
Aimlessdata scaling
XDSdata reduction
DIMPLEphasing
PHASERphasing
Cootmodel building
gemmi0.7.3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.948→44.404 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.174 / SU B: 4.075 / SU ML: 0.108 / Average fsc free: 0.9627 / Average fsc work: 0.9707 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2097 2921 5.032 %
Rwork0.1809 55133 -
all0.182 --
obs-58054 99.967 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.003 Å2-0.001 Å2-0 Å2
2---0.003 Å20 Å2
3---0.009 Å2
Refinement stepCycle: LAST / Resolution: 1.948→44.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 19 307 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124606
X-RAY DIFFRACTIONr_bond_other_d0.0050.0164545
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.7826240
X-RAY DIFFRACTIONr_angle_other_deg0.6011.73410425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4436.05338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9210765
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4610179
X-RAY DIFFRACTIONr_chiral_restr0.0790.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025585
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02959
X-RAY DIFFRACTIONr_nbd_refined0.2190.2968
X-RAY DIFFRACTIONr_symmetry_nbd_other0.4940.25413
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1170.22442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1640.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.216
X-RAY DIFFRACTIONr_nbd_other0.1980.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.212
X-RAY DIFFRACTIONr_mcbond_it2.953.2782546
X-RAY DIFFRACTIONr_mcbond_other2.9493.2772545
X-RAY DIFFRACTIONr_mcangle_it4.3065.8783186
X-RAY DIFFRACTIONr_mcangle_other4.3055.8783187
X-RAY DIFFRACTIONr_scbond_it4.7753.92060
X-RAY DIFFRACTIONr_scbond_other4.7643.8972057
X-RAY DIFFRACTIONr_scangle_it7.3016.8983054
X-RAY DIFFRACTIONr_scangle_other7.36.8983055
X-RAY DIFFRACTIONr_lrange_it8.48533.3135100
X-RAY DIFFRACTIONr_lrange_other8.46933.2535035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.948-1.9990.3252190.30140900.30243100.9180.93399.97680.303
1.999-2.0530.2971970.28939490.2941480.9310.93999.95180.29
2.053-2.1130.2571880.26438780.26440670.9490.95199.97540.26
2.113-2.1780.2581600.23937690.2439290.9590.961000.23
2.178-2.2490.2781790.22336490.22638290.9490.96699.97390.211
2.249-2.3280.2391880.20335040.20536920.9640.9741000.186
2.328-2.4150.2282350.1833210.18335560.970.981000.163
2.415-2.5140.2251940.18432270.18634210.9710.981000.164
2.514-2.6250.2231680.1831540.18233220.970.9811000.161
2.625-2.7530.211660.17129630.17331290.9730.9831000.153
2.753-2.9010.2151540.16728630.16930170.9740.9841000.149
2.901-3.0760.1931410.1727110.17128520.9750.9821000.159
3.076-3.2870.2121260.17225250.17326510.970.9821000.165
3.287-3.5490.1871230.17823660.17824890.9820.9831000.176
3.549-3.8850.2051140.16321530.16522670.9740.9861000.166
3.885-4.340.149860.14619990.14620850.9870.9871000.158
4.34-5.0030.166890.13817420.13918310.9850.9891000.155
5.003-6.1080.197950.1714510.17215460.9820.9861000.186
6.108-8.5580.172700.14611450.14812150.9830.9891000.168
8.558-44.4040.211290.1756740.1767030.9550.9791000.204

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