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- PDB-6yn0: Structure of E. coli PBP1b with a FtsN peptide activating transgl... -

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Basic information

Entry
Database: PDB / ID: 6yn0
TitleStructure of E. coli PBP1b with a FtsN peptide activating transglycosylase activity
Components
  • Cell division protein FtsN
  • Penicillin-binding protein 1B
KeywordsTRANSFERASE / glycosyl transferase / penicillin binding protein / peptidoglycan synthesis
Function / homology
Function and homology information


positive regulation of bipolar cell growth / cell wall repair / division septum / divisome complex / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / peptidoglycan binding / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis ...positive regulation of bipolar cell growth / cell wall repair / division septum / divisome complex / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell septum / peptidoglycan binding / serine-type D-Ala-D-Ala carboxypeptidase / FtsZ-dependent cytokinesis / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / cell division site / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / outer membrane-bounded periplasmic space / regulation of cell shape / cell division / response to antibiotic / proteolysis / membrane / plasma membrane
Similarity search - Function
Cell division protein FtsN / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain ...Cell division protein FtsN / Sporulation-like domain / Sporulation-like domain superfamily / SPOR domain / SPOR domain profile. / Penicillin-binding protein 1B / Bifunctional transglycosylase second domain / Transglycosylase PBP1b, N-terminal transmembrane domain / Transmembrane domain of transglycosylase PBP1 at N-terminal / Bifunctional transglycosylase second domain / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily
Similarity search - Domain/homology
MOENOMYCIN / Penicillin-binding protein 1B / Cell division protein FtsN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKerff, F. / Terrak, M. / Boes, A. / Herman, H. / Charlier, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial cell division protein fragment E FtsN binds to and activates the major peptidoglycan synthase PBP1b.
Authors: Boes, A. / Kerff, F. / Herman, R. / Touze, T. / Breukink, E. / Terrak, M.
History
DepositionApr 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 6, 2021Group: 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 1.3Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1B
B: Cell division protein FtsN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3213
Polymers85,7402
Non-polymers1,5811
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-4 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.143, 283.021, 62.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Penicillin-binding protein 1B / PBP1b / Murein polymerase


Mass: 83280.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: mrcB, pbpF, ponB, b0149, JW0145 / Production host: Escherichia coli (E. coli)
References: UniProt: P02919, peptidoglycan glycosyltransferase, serine-type D-Ala-D-Ala carboxypeptidase
#2: Protein/peptide Cell division protein FtsN /


Mass: 2459.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P29131
#3: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN / Moenomycin family antibiotics


Mass: 1580.567 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H106N5O34P / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: (NH4)2SO4 0.1M, sodium Formate 0.3M, Tris-Hcl 0,1M, low molecular weight poly-glutamic acids (PGA-LM) 3% w/v, PEG 550 MME 20% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.4→47.17 Å / Num. obs: 25830 / % possible obs: 95.5 % / Redundancy: 8.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.25 / Rrim(I) all: 0.265 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.51 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 6891 / CC1/2: 0.279 / Rrim(I) all: 3.81 / % possible all: 85.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HLA

5hla


Resolution: 2.4→47.17 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.857 / SU Rfree Blow DPI: 0.34 / Details: Processing with Staraniso
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1320 5.11 %RANDOM
Rwork0.225 ---
obs0.226 25830 57.3 %-
Displacement parametersBiso max: 195.48 Å2 / Biso mean: 79.06 Å2 / Biso min: 14.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.3941 Å20 Å20 Å2
2---5.4169 Å20 Å2
3---4.0227 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.4→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5525 0 137 55 5717
Biso mean--150.78 36.12 -
Num. residues----702
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2457SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1612HARMONIC5
X-RAY DIFFRACTIONt_it11346HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
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_contact11965SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11346HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg20531HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion16.85
LS refinement shellResolution: 2.4→2.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.262 53 4.84 %
Rwork0.216 1043 -
all0.218 1096 -
obs--21.93 %

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