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- PDB-6y6u: Structure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 ... -

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Basic information

Entry
Database: PDB / ID: 6y6u
TitleStructure of Pseudomonas aeruginosa Penicillin-Binding Protein 3 (PBP3) in complex with Compound 6
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / PBP3 / Penicillin Binding Proteins / Peptidoglycan production / transpeptidation
Function / homology
Function and homology information


peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / division septum assembly / FtsZ-dependent cytokinesis / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane
Similarity search - Function
Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Chem-ODZ / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsNewman, H. / Bellini, D. / Dowson, C.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Chem Sci / Year: 2020
Title: Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion
Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / ...Authors: Kidd, S.L. / Fowler, E. / Reinhardt, T. / Compton, T. / Mateu, N. / Newman, H. / Bellini, D. / Talon, R. / McLoughlin, J. / Krojer, T. / Aimon, A. / Bradley, A. / Fairhead, M. / Brear, P. / Diaz-Saez, L. / McAuley, K. / Sore, H.F. / Madin, A. / O'Donovan, D.H. / Huber, K.V.M. / Hyvonen, M. / Dowson, C.G. / Spring, D.R.
History
DepositionFeb 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan D,D-transpeptidase FtsI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1557
Polymers56,4311
Non-polymers7246
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-0 kcal/mol
Surface area22570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.568, 83.128, 90.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidoglycan D,D-transpeptidase FtsI / Penicillin-binding protein 3 / PBP-3


Mass: 56431.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ODZ / 2-(4-hydroxyphenyl)-~{N}-[(2~{S})-2-methyl-4-oxidanyl-1-oxidanylidene-pent-4-en-2-yl]ethanamide


Mass: 263.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.92 % / Mosaicity: 0.08 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 25% (w/v) polyethylene glycol 3 350, 0.1 M Bis-Tris propane pH 7.8 and 1% (w/v) protamine sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2018 / Details: mirrors
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→61.09 Å / Num. obs: 56715 / % possible obs: 95.5 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Net I/σ(I): 17.5
Reflection shellResolution: 1.55→1.69 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.179 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2836 / CC1/2: 0.705 / Rpim(I) all: 0.448 / % possible all: 64.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS20171111data reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
STARANISO1.10.15data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HZR

6hzr


Resolution: 1.55→61.09 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.95 / SU B: 10.417 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1403 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2775 4.9 %RANDOM
Rwork0.1567 ---
obs0.16 53940 75.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 450.53 Å2 / Biso mean: 38.566 Å2 / Biso min: 19.03 Å2
Baniso -1Baniso -2Baniso -3
1--9.38 Å20 Å2-0 Å2
2--5.94 Å20 Å2
3---3.44 Å2
Refinement stepCycle: final / Resolution: 1.55→61.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 49 358 4170
Biso mean--53.32 54.29 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133955
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173798
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.6525377
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5798790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79520.922206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91115661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461537
X-RAY DIFFRACTIONr_chiral_restr0.0830.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02831
X-RAY DIFFRACTIONr_rigid_bond_restr18.82837753
LS refinement shellResolution: 1.552→1.592 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 17 -
Rwork0.341 285 -
all-302 -
obs--5.5 %

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