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- PDB-7al1: Cell division protein SepF from Methanobrevibacter smithii -

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Basic information

Entry
Database: PDB / ID: 7al1
TitleCell division protein SepF from Methanobrevibacter smithii
ComponentsCell division protein SepF
KeywordsCELL CYCLE / FtsZ-binding protein Membrane-binding protein
Function / homologyCell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / cell septum assembly / Cell division protein SepF
Function and homology information
Biological speciesMethanobrevibacter smithii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9742
Polymers10,8511
Non-polymers1221
Water1,02757
1
A: Cell division protein SepF
hetero molecules

A: Cell division protein SepF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9474
Polymers21,7032
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.053, 53.053, 53.912
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-348-

HOH

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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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 30% PEG 10K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 1.4→45.95 Å / Num. obs: 17704 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.1
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 1.029 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 846

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 3ZIE

3zie


Resolution: 1.4→34.97 Å / SU ML: 0.1155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 884 5 %
Rwork0.1825 16789 -
obs0.1842 17673 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.38 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms662 0 8 57 727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092702
X-RAY DIFFRACTIONf_angle_d1.0567952
X-RAY DIFFRACTIONf_chiral_restr0.0839115
X-RAY DIFFRACTIONf_plane_restr0.0065120
X-RAY DIFFRACTIONf_dihedral_angle_d18.9164103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.490.25491440.22082746X-RAY DIFFRACTION99.9
1.49-1.60.2371450.2082759X-RAY DIFFRACTION100
1.6-1.760.26641460.19672773X-RAY DIFFRACTION100
1.76-2.020.23851460.17682774X-RAY DIFFRACTION99.97
2.02-2.540.16631490.17862830X-RAY DIFFRACTION99.97
2.54-34.970.22331540.1792907X-RAY DIFFRACTION99.54
Refinement TLS params.Method: refined / Origin x: -4.29269921737 Å / Origin y: -22.3702062537 Å / Origin z: 8.34574490984 Å
111213212223313233
T0.161744024712 Å2-0.018976800801 Å20.0115410230988 Å2-0.182588589369 Å20.00890331244746 Å2--0.192529524707 Å2
L0.482168890831 °2-0.0892177469441 °20.46508982797 °2-1.3292086124 °2-0.381700313415 °2--1.1293976508 °2
S0.0465287058532 Å °-0.0931985426233 Å °0.00297075997274 Å °0.0160879674488 Å °-0.0580051748327 Å °-0.258204156421 Å °0.0312984829032 Å °-0.0266242905909 Å °-0.00119555859279 Å °

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