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- PDB-9fz7: Pseudomonas aeruginosa penicillin binding protein 3 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9fz7
TitlePseudomonas aeruginosa penicillin binding protein 3 in complex with cefiderocol
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Transpeptidase / penicillin binding protein 3 / PBP3
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
ACYLATED CEFTAZIDIME / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSmith, H.G. / Allen, M.D. / Basak, S. / Aniebok, V. / Beech, M.J. / Alshref, F.M. / Farley, A.J.M. / Schofield, C.J.
Funding support1items
OrganizationGrant numberCountry
Other privateIneos Oxford Institute Core Fund (UK)
CitationJournal: Chem Sci / Year: 2024
Title: Structural basis of Pseudomonas aeruginosa penicillin binding protein 3 inhibition by the siderophore-antibiotic cefiderocol.
Authors: Smith, H.G. / Basak, S. / Aniebok, V. / Beech, M.J. / Alshref, F.M. / Allen, M.D. / Farley, A.J.M. / Schofield, C.J.
History
DepositionJul 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,4772
Polymers56,0081
Non-polymers4691
Water9,062503
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-1 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.051, 82.965, 90.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 56007.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Disordered residues were not modelled / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ftsI, pbpB, PA4418 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: G3XD46, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium formate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→61.07 Å / Num. obs: 48820 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.026 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 1.068 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2358 / CC1/2: 0.812 / Rpim(I) all: 0.306 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.11 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 1986 4.08 %
Rwork0.1891 --
obs0.1903 48724 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3913 0 0 503 4416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.663
X-RAY DIFFRACTIONf_dihedral_angle_d14.7411576
X-RAY DIFFRACTIONf_chiral_restr0.047620
X-RAY DIFFRACTIONf_plane_restr0.005751
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.33811440.30333223X-RAY DIFFRACTION98
1.84-1.890.33841550.29713282X-RAY DIFFRACTION100
1.89-1.950.29161530.24853287X-RAY DIFFRACTION100
1.95-2.010.2341540.21333286X-RAY DIFFRACTION100
2.01-2.080.27121370.20463310X-RAY DIFFRACTION100
2.08-2.170.25461330.20593329X-RAY DIFFRACTION100
2.17-2.270.2481310.20863307X-RAY DIFFRACTION100
2.27-2.380.23931160.20153350X-RAY DIFFRACTION100
2.38-2.530.2291320.19283319X-RAY DIFFRACTION99
2.53-2.730.21431340.19043344X-RAY DIFFRACTION100
2.73-30.20341480.19583377X-RAY DIFFRACTION100
3-3.440.19971550.1843362X-RAY DIFFRACTION100
3.44-4.330.19781640.16323390X-RAY DIFFRACTION100
4.33-45.110.18731300.16553572X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -5.3331 Å / Origin y: 21.2503 Å / Origin z: -1.022 Å
111213212223313233
T0.1737 Å20.0103 Å20.0011 Å2-0.1959 Å2-0.0166 Å2--0.2388 Å2
L0.1061 °2-0.0328 °20.1229 °2-0.4696 °2-0.5666 °2--1.8546 °2
S-0.0037 Å °0.0665 Å °-0.0063 Å °-0.0878 Å °0.0231 Å °-0.0082 Å °0.0988 Å °-0.052 Å °-0.0184 Å °
Refinement TLS groupSelection details: chain A

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