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- PDB-7omp: SaFtsZ complexed with GDPPCP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7omp
TitleSaFtsZ complexed with GDPPCP and Mg2+
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cell division protein FtsZ
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 24, 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)32,6726
Polymers31,9401
Non-polymers7325
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint2 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.583, 51.949, 87.779
Angle α, β, γ (deg.)90.000, 110.105, 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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
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 8.8, and 22% polyethylene glycol 5000 monomethyl ether (+20 mM MgCl2 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: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.52→41.22 Å / Num. obs: 45499 / % possible obs: 98.71 % / Redundancy: 4.5 % / Biso Wilson estimate: 17.93 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.62
Reflection shellResolution: 1.52→1.57 Å / Mean I/σ(I) obs: 1.82 / Num. unique obs: 4545 / CC1/2: 0.792

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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: 1.52→41.22 Å / SU ML: 0.1548 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1767 2152 4.73 %
Rwork0.1518 43330 -
obs0.153 45482 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.66 Å2
Refinement stepCycle: LAST / Resolution: 1.52→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 45 287 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872334
X-RAY DIFFRACTIONf_angle_d1.16923157
X-RAY DIFFRACTIONf_chiral_restr0.0588373
X-RAY DIFFRACTIONf_plane_restr0.0067417
X-RAY DIFFRACTIONf_dihedral_angle_d17.9942854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.560.291560.27772874X-RAY DIFFRACTION98.57
1.56-1.590.26811520.22212840X-RAY DIFFRACTION98.91
1.59-1.640.23321560.20582868X-RAY DIFFRACTION98.89
1.64-1.690.23261490.19082895X-RAY DIFFRACTION99.28
1.69-1.740.22411450.1852863X-RAY DIFFRACTION99.21
1.74-1.80.24051470.17682900X-RAY DIFFRACTION99.12
1.8-1.870.20771430.17272855X-RAY DIFFRACTION98.13
1.87-1.960.17121390.1552889X-RAY DIFFRACTION99.18
1.96-2.060.16441280.14712912X-RAY DIFFRACTION99.22
2.06-2.190.17741590.14162898X-RAY DIFFRACTION98.77
2.19-2.360.17641400.13722844X-RAY DIFFRACTION98
2.36-2.60.15681300.13712918X-RAY DIFFRACTION98.74
2.6-2.970.15311200.14442914X-RAY DIFFRACTION99.02
2.98-3.750.16341390.14022892X-RAY DIFFRACTION97.37
3.75-41.220.15391490.1422968X-RAY DIFFRACTION98.36
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)
11.00159506644-0.2384778344770.1927700064290.4139984093890.09770813024380.610263533433-0.0567268581066-0.02830781900960.1087856586670.05795673092860.00801761087004-0.0401570099035-0.05892624014830.00458974778512-0.0009354018248150.1501866354240.0200567639197-0.001382617419380.119566584252-0.003468331678140.1416713232691.00281506047-1.9211658436831.1158465597
20.05266199283970.0879599315601-0.03038193488660.152322264694-0.06766456301270.05622700593920.0605333454705-0.0881224270333-0.1879725319550.0311771217142-0.1716911834620.0916044149680.0532949146895-0.0253335531802-0.000993259840180.165929156220.019104152822-0.0009411604221780.137788081809-0.01155649772140.208221770881-5.40863362965-16.413088797425.5112534157
30.243964798364-0.13163505022-0.000276646709710.0681762508130.03049071108120.0824421899834-0.02877945070570.0548649595360.0575153821026-0.009474901675110.009987776987440.0179301091764-0.000615688885142-0.01950593398151.06076791433E-50.1671331762420.0303367173716-0.0009243641085540.15718405834-0.0006467870361530.152680192784-8.758812158691.988882094717.7470072265
40.431244385812-0.375307551630.1927518213620.352882453557-0.08766143645880.2443555099740.1286469155490.142181139714-0.0682347300109-0.0918888162977-0.09144560133280.08796327963610.05174741816090.1392353493771.0878354837E-50.1806368385640.03646029058910.005148711390220.218516280365-0.002915757775660.183088353131-20.00839051647.1879836199210.8741409355
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 140 )9 - 1401 - 133
22chain 'A' and (resid 141 through 157 )141 - 157134 - 150
33chain 'A' and (resid 158 through 223 )158 - 223151 - 219
44chain 'A' and (resid 224 through 315 )224 - 315220 - 313

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