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- PDB-6scq: Cell Division Protein SepF in complex with C-terminal domain of FtsZ -

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Basic information

Entry
Database: PDB / ID: 6scq
TitleCell Division Protein SepF in complex with C-terminal domain of FtsZ
ComponentsCell division protein SepF
KeywordsCELL CYCLE / Cell Division protein
Function / homology
Function and homology information


division septum assembly / FtsZ-dependent cytokinesis / metal ion binding / cytoplasm
Similarity search - Function
Cell division protein SepF / SepF-like protein / Cell division protein SepF/SepF-related / SepF-like superfamily / Cell division protein SepF / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division protein SepF
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSogues, A. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0017-01 France
CitationJournal: Nat Commun / Year: 2020
Title: Essential dynamic interdependence of FtsZ and SepF for Z-ring and septum formation in Corynebacterium glutamicum.
Authors: Sogues, A. / Martinez, M. / Gaday, Q. / Ben Assaya, M. / Grana, M. / Voegele, A. / VanNieuwenhze, M. / England, P. / Haouz, A. / Chenal, A. / Trepout, S. / Duran, R. / Wehenkel, A.M. / Alzari, P.M.
History
DepositionJul 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 SepF


Theoretical massNumber of molelcules
Total (without water)16,2952
Polymers16,2952
Non-polymers00
Water1,51384
1
A: Cell division protein SepF

A: Cell division protein SepF


Theoretical massNumber of molelcules
Total (without water)16,2952
Polymers16,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area7700 Å2
MethodPISA
2
B: Cell division protein SepF

B: Cell division protein SepF


Theoretical massNumber of molelcules
Total (without water)16,2952
Polymers16,2952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1510 Å2
ΔGint-7 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.840, 32.270, 74.410
Angle α, β, γ (deg.)90.000, 114.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-204-

HOH

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Components

#1: Protein Cell division protein SepF


Mass: 8147.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: sepF, Cgl2152
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8NNN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6, 20 %w/v PEG MME 2K, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→32.91 Å / Num. obs: 21921 / % possible obs: 95.2 % / Redundancy: 2.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Net I/σ(I): 19.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1127 / CC1/2: 0.985 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSversion Mar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1152 5.26 %RANDOM
Rwork0.211 ---
obs0.211 21918 95 %-
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 39.64 Å2 / Biso min: 9.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.7633 Å20 Å2-1.5838 Å2
2--5.4823 Å20 Å2
3----3.7191 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.5→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 84 1136
Biso mean---36.81 -
Num. residues----140
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d360SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes186HARMONIC5
X-RAY DIFFRACTIONt_it1069HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion142SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1387SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1069HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1447HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion13.33
LS refinement shellResolution: 1.5→1.51 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2609 24 5.47 %
Rwork0.1813 415 -
all0.1862 439 -
obs--96.84 %
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)
12.39950.7321-0.59611.95740.21830.4907-0.0066-0.0718-0.11140.10110.0187-0.14310.01180.0043-0.0121-0.21610.0009-0.0196-0.17960.0127-0.1196-7.96920.25154.8321
23.2310.63185.49032.25226.713132.2278-0.15110.22040.3180.7094-0.50420.30082.71260.41730.65530.20590.04270.1039-0.20240.0303-0.1813-16.59343.420924.525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A65 - 136
2X-RAY DIFFRACTION2{ B|* }B68 - 135

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