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- PDB-7on2: SaFtsZ complexed with GDP (soaking in 10 mM CyDTA) -

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Basic information

Entry
Database: PDB / ID: 7on2
TitleSaFtsZ complexed with GDP (soaking in 10 mM CyDTA)
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, GTPase domain / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain ...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, GTPase domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / : / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsFernandez-Tornero, C. / Ruiz, F.M. / Andreu, J.M.
CitationJournal: Plos Biol. / Year: 2022
Title: FtsZ filament structures in different nucleotide states reveal the mechanism of assembly dynamics.
Authors: Ruiz, F.M. / Huecas, S. / Santos-Aledo, A. / Prim, E.A. / Andreu, J.M. / Fernandez-Tornero, C.
History
DepositionMay 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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)32,4844
Polymers31,9401
Non-polymers5443
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-0 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.402, 50.207, 88.050
Angle α, β, γ (deg.)90.000, 111.418, 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: 31940.100 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 BL21(DE3) (bacteria) / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate, 10% (v/v) ethylene glycol, 0.1 M Tris-HCl pH 8.5, and 26% polyethylene glycol 5000 monomethyl ether (+ 10 mM CyDTA for soaking, 23 h)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.69→40.98 Å / Num. obs: 31990 / % possible obs: 96.53 % / Redundancy: 3.2 % / Biso Wilson estimate: 28.63 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.23
Reflection shellResolution: 1.69→1.75 Å / Mean I/σ(I) obs: 1.97 / Num. unique obs: 2889 / CC1/2: 0.882

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RVN

6rvn


Resolution: 1.69→40.98 Å / SU ML: 0.2199 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2471 1550 4.85 %
Rwork0.2039 30425 -
obs0.2061 31975 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.75 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 33 162 2412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092277
X-RAY DIFFRACTIONf_angle_d1.21513081
X-RAY DIFFRACTIONf_chiral_restr0.0657368
X-RAY DIFFRACTIONf_plane_restr0.0077406
X-RAY DIFFRACTIONf_dihedral_angle_d20.1344839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.29371440.26192453X-RAY DIFFRACTION87.41
1.74-1.810.29781380.26322806X-RAY DIFFRACTION98.89
1.81-1.880.33681510.25972785X-RAY DIFFRACTION98.76
1.88-1.960.28381370.25352820X-RAY DIFFRACTION98.04
1.97-2.070.33891300.27532808X-RAY DIFFRACTION97.61
2.07-2.20.36611280.28192801X-RAY DIFFRACTION97.15
2.2-2.370.34381500.2722704X-RAY DIFFRACTION96.03
2.37-2.610.30811260.23962808X-RAY DIFFRACTION96.04
2.61-2.980.2341320.20932745X-RAY DIFFRACTION96.29
2.98-3.760.18671400.17332793X-RAY DIFFRACTION96.89
3.76-40.980.21241740.15312902X-RAY DIFFRACTION98.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1143615953890.055788093244-0.3208606154040.5723218914510.1866426524271.39147082228-0.392623063436-0.1055694725570.7586529008790.20157257680.257948017733-0.1941514491250.088309957515-0.032784629684-0.04082972523750.222945137760.0515116733618-0.1188525899720.241817315155-0.04024239999240.376232302383-1.988934237036.6605506527327.0448756636
20.1424498608460.04037443102850.03181415304410.0598014927716-0.06867506508560.111682588687-0.147703660111-0.1095762691510.600601128053-0.03384785371440.0836614468176-0.217629467576-0.1519395439530.0322408014866-0.0001647190483850.2561132197740.0445255485726-0.1013602015420.264175061723-0.05795706370610.4565648023175.425084840365.1297341955529.7481939123
31.876862064811.3688785345-0.9961523858891.02150146503-0.6238857281911.45356118173-0.363618226639-0.747521957104-0.2726524910470.3203857323890.0109499025038-0.307546078188-0.002888454541280.146268034695-1.081179223520.2915711479170.115277222266-0.1504952293740.373823783573-0.06586233906030.1018433709833.77203273402-7.6505675287738.9910066641
41.13136699270.2554417881970.4998447589660.2470684384720.09496714200480.191343644065-0.245992619142-0.101917781446-0.05369305464950.2453068014130.111027894630.05471340354580.127513820613-0.115413955881-0.002701476870090.2431489343860.0861323055948-0.02424377868950.229654849512-0.02531124582830.153419266384-5.69301049209-4.3194754917828.963498547
50.06835559450570.03572441508920.0431243928130.177283999769-0.05455786421560.203402822615-0.2094255912-0.0683974159274-0.616502316892-0.0111411181287-0.1407818867190.2060281499890.134093724559-0.1256735806090.0003634227547020.2678433435810.03437344658410.02220887481560.260692666874-0.01806337750650.30946442993-5.81527751805-15.274233783725.1338716897
60.349029060779-0.1074197854810.1441206487980.0945048012984-0.1405840127310.175566700145-0.1877164850260.200899907067-0.0888422897898-0.03952716441190.1179056078050.02933010891340.15310759601-0.201607776159-0.002466149628080.2251287621080.0201321074378-0.02162202111620.2820749571-0.02674572508040.210412450525-4.04426174963-5.7420580811412.3541590229
70.259533057288-0.1837305224870.116607185910.1778817289170.1030373196740.3116375910570.08621091301220.1227850710650.00873306844266-0.541996152524-0.04486621949880.110459967691-0.169210861661-0.00451527435133-7.11854283692E-50.2798545225310.0431370586305-0.02871925065810.254964584934-0.0036736200410.277200270141-4.806093926566.1964268932317.2026780108
80.4355174977780.163396986418-0.1664890498470.0814254820191-0.0702498228650.0659818930809-0.0125483960815-0.02232499208780.1910703423620.1675938169150.0168237147490.1067821533110.02203001398010.0386873252704-4.29750266831E-50.2454295971890.0657455865592-0.0171473341750.259083258595-0.01358076651470.298071625559-21.21751257658.6283052441425.7701183551
90.1240458908130.08806166499960.09266626936120.3467170991780.1295354011090.07799437715640.09820197187270.4683202614210.0651047366963-0.215885269558-0.194051633731-0.2891832273460.159424546350.57357485322-0.000944823337020.2608591874730.05517812009530.005590347347260.4430706129380.0263758788220.300740744253-17.13651086889.060648316056.31787122609
100.929085342127-0.8126645719830.08770623223770.7268677096450.1872220348150.7533808070440.02977743502380.230222280875-0.0410946000278-0.05300503284430.009647353252210.0602300583594-0.009156840567930.09073735915435.67923498534E-50.2237718304110.00703869671084-0.03095523226610.289129730845-0.009375552162250.245802413639-22.06320332128.3158899282812.3422633233
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 32 )9 - 321 - 24
22chain 'A' and (resid 33 through 60 )33 - 6025 - 54
33chain 'A' and (resid 61 through 93 )61 - 9355 - 87
44chain 'A' and (resid 94 through 140 )94 - 14088 - 134
55chain 'A' and (resid 141 through 157 )141 - 157135 - 151
66chain 'A' and (resid 158 through 178 )158 - 178152 - 172
77chain 'A' and (resid 179 through 202 )179 - 202173 - 196
88chain 'A' and (resid 203 through 224 )203 - 224197 - 220
99chain 'A' and (resid 225 through 245 )225 - 245221 - 241
1010chain 'A' and (resid 246 through 315 )246 - 315242 - 311

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