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- PDB-7al2: Cell division protein SepF from Methanobrevibacter smithii in com... -

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Basic information

Entry
Database: PDB / ID: 7al2
TitleCell division protein SepF from Methanobrevibacter smithii in complex with FtsZ-CTD
Components
  • Cell division protein FtsZ
  • Cell division protein SepF
KeywordsCELL CYCLE / FtsZ-binding protein Membrane-binding protein
Function / homology
Function and homology information


cell septum assembly / FtsZ-dependent cytokinesis / division septum assembly / cell division site / protein polymerization / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / 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 ...Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / 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
Cell division protein SepF / Cell division protein FtsZ
Similarity search - Component
Biological speciesMethanobrevibacter smithii (archaea)
Methanobrevibacter smithii DSM 2375 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsSogues, A. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE11-0017 France
CitationJournal: Nat Commun / Year: 2021
Title: SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system.
Authors: Pende, N. / Sogues, A. / Megrian, D. / Sartori-Rupp, A. / England, P. / Palabikyan, H. / Rittmann, S.K.R. / Grana, M. / Wehenkel, A.M. / Alzari, P.M. / Gribaldo, S.
History
DepositionOct 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

Deposited unit
A: Cell division protein SepF
B: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)12,0342
Polymers12,0342
Non-polymers00
Water00
1
A: Cell division protein SepF
B: Cell division protein FtsZ

A: Cell division protein SepF
B: Cell division protein FtsZ


Theoretical massNumber of molelcules
Total (without water)24,0684
Polymers24,0684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4750 Å2
ΔGint-24 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.847, 64.847, 107.924
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Cell division protein SepF


Mass: 10851.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanobrevibacter smithii (strain ATCC 35061 / DSM 861 / OCM 144 / PS) (archaea)
Strain: ATCC 35061 / DSM 861 / OCM 144 / PS / Gene: Msm_0406 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5UK83
#2: Protein/peptide Cell division protein FtsZ


Mass: 1182.280 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Methanobrevibacter smithii DSM 2375 (archaea)
References: UniProt: B9AGF7

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 30% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.7→38.91 Å / Num. obs: 3807 / % possible obs: 95.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.4
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 493

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AL1

7al1


Resolution: 2.701→38.91 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.601 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.733 / SU Rfree Blow DPI: 0.317 / SU Rfree Cruickshank DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 181 -RANDOM
Rwork0.2292 ---
obs0.2305 3806 94 %-
Displacement parametersBiso mean: 61.24 Å2
Baniso -1Baniso -2Baniso -3
1--9.0585 Å20 Å20 Å2
2---9.0585 Å20 Å2
3---18.117 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.701→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 0 0 0 746
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008754HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.021015HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d277SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes126HARMONIC5
X-RAY DIFFRACTIONt_it754HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion103SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact574SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion17.3
LS refinement shellResolution: 2.701→2.81 Å
RfactorNum. reflection% reflection
Rfree0.2641 24 -
Rwork0.2228 --
obs--95.42 %
Refinement TLS params.Origin x: 21.3515 Å / Origin y: -14.3187 Å / Origin z: 1.8725 Å
111213212223313233
T-0.1901 Å2-0.0114 Å2-0.0283 Å2--0.1825 Å2-0.0611 Å2---0.2923 Å2
L2.8126 °20.6224 °2-0.5347 °2-5.5861 °2-1.8769 °2--9.0063 °2
S-0.1198 Å °0.0221 Å °-0.3857 Å °0.0221 Å °0.0025 Å °-0.4482 Å °-0.3857 Å °-0.4482 Å °0.1173 Å °
Refinement TLS groupSelection details: { A|* }

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