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- PDB-5hld: E. coli PBP1b in complex with acyl-CENTA and moenomycin -

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Basic information

Entry
Database: PDB / ID: 5hld
TitleE. coli PBP1b in complex with acyl-CENTA and moenomycin
ComponentsPenicillin-binding protein 1B
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / penicillin-binding protein / inhibitor complex / transpeptidase / transglycosylase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape ...positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / membrane / plasma membrane
Similarity search - Function
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 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : ...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 / Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-63V / MOENOMYCIN / Penicillin-binding protein 1B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKing, D.T. / Strynadka, N.C.J.
Funding support Canada, United States, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Howard Hughes Medical Institute (HHMI) United States
Canadian Foundation for Innovation Canada
British Columbia Knowledge Development Fund Canada
Canada Research Chair Programs Canada
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition.
Authors: King, D.T. / Wasney, G.A. / Nosella, M. / Fong, A. / Strynadka, N.C.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,1993
Polymers83,2801
Non-polymers1,9192
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint2 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 63.940, 294.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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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)
Strain: K12 / Gene: mrcB, pbpF, ponB, b0149, JW0145 / Production host: Escherichia coli (E. coli)
References: UniProt: P02919, peptidoglycan glycosyltransferase, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-63V / (2S)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 338.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14N2O4S2
#3: Chemical ChemComp-M0E / MOENOMYCIN / MOENOMYCIN


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


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Drops contained 1uL of protein solution (20mg/mL protein, 100uM moenomycin and 2mM CENTA) mixed with an equal volume of precipitant (20% w/v PEG 3350, 0.2M potassium/sodium tartate, 0.1M Bis Tris pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→62.49 Å / Num. obs: 48263 / % possible obs: 92.5 % / Redundancy: 4 % / Biso Wilson estimate: 42.99 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.5
Reflection shellResolution: 2.31→2.37 Å / Rmerge(I) obs: 0.41

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMA

3vma


Resolution: 2.31→33.82 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.8036 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.272 / SU Rfree Blow DPI: 0.22 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 2384 4.94 %RANDOM
Rwork0.2534 ---
obs0.2547 48242 91.25 %-
Displacement parametersBiso mean: 61.56 Å2
Baniso -1Baniso -2Baniso -3
1-8.2237 Å20 Å20 Å2
2--14.0314 Å20 Å2
3----22.2551 Å2
Refine analyzeLuzzati coordinate error obs: 0.464 Å
Refinement stepCycle: 1 / Resolution: 2.31→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5063 0 99 187 5349
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095262HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117145HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1827SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes749HARMONIC5
X-RAY DIFFRACTIONt_it5262HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.28
X-RAY DIFFRACTIONt_other_torsion19.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion696SEMIHARMONIC5
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_contact5843SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2936 169 5.18 %
Rwork0.262 3096 -
all0.2637 3265 -
obs--91.25 %

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