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- PDB-6tpi: EnvC bound to the FtsX periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 6tpi
TitleEnvC bound to the FtsX periplasmic domain
Components
  • Cell division protein FtsX
  • Murein hydrolase activator EnvC
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site ...division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / FtsZ-dependent cytokinesis / division septum assembly / cell division site / ATPase complex / positive regulation of cell division / response to radiation / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / cell cycle / cell division / plasma membrane
Similarity search - Function
: / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain / Duplicated hybrid motif / FtsX-like permease family
Similarity search - Domain/homology
Cell division protein FtsX / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsCrow, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust214105/Z/18/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M01116X/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Insights into bacterial cell division from a structure of EnvC bound to the FtsX periplasmic domain.
Authors: Cook, J. / Baverstock, T.C. / McAndrew, M.B.L. / Stansfeld, P.J. / Roper, D.I. / Crow, A.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Murein hydrolase activator EnvC
B: Cell division protein FtsX
C: Cell division protein FtsX


Theoretical massNumber of molelcules
Total (without water)67,6433
Polymers67,6433
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Complex purified using an affinity tag only on FtsX.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-29 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.031, 100.470, 107.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 110 - 205 / Label seq-ID: 3 - 98

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC

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Components

#1: Protein Murein hydrolase activator EnvC / Septal ring factor


Mass: 43117.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: envC, yibP, b3613, JW5646 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P37690
#2: Protein Cell division protein FtsX /


Mass: 12262.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: ftsX, ftsS, b3462, JW3427 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P0AC30
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.68 Å3/Da / Density % sol: 54.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 8000, 20 % Ethylene glycol, 0.1 M Tris/bicine pH8.5, ) 0.12M monosaccarides (glucose, mannose, galactose, fucose, xylose, NAG)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.1→55.823 Å / Num. obs: 43252 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.999 / Rpim(I) all: 0.044 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3494 / CC1/2: 0.767 / Rpim(I) all: 0.577 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BH5 and 4N8O

4bh5

4n8o


Resolution: 2.1→55.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.669 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 2102 4.9 %RANDOM
Rwork0.2148 ---
obs0.2177 41086 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 209.69 Å2 / Biso mean: 58.531 Å2 / Biso min: 25.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.71 Å20 Å20 Å2
2--4.86 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 2.1→55.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 0 229 4729
Biso mean---47.74 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134591
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174310
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.6456186
X-RAY DIFFRACTIONr_angle_other_deg1.2591.5799996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1915583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08322.334287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77215851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8371547
X-RAY DIFFRACTIONr_chiral_restr0.0610.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02948
Refine LS restraints NCS

Ens-ID: 1 / Number: 2391 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.2 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2C
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 152 -
Rwork0.346 2990 -
all-3142 -
obs--99.9 %

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