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

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Basic information

Entry
Database: PDB / ID: 9fzo
TitlePseudomonas aeruginosa penicillin binding protein 3 in complex with ceftazidime
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 / division septum assembly / serine-type D-Ala-D-Ala carboxypeptidase activity / 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 (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 5, 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)56,9587
Polymers56,0081
Non-polymers9506
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-41 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.326, 83.183, 89.886
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 resides are 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane pH 8.5, 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: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→54.39 Å / Num. obs: 47543 / % possible obs: 98.7 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.038 / Net I/σ(I): 12.4
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2374 / CC1/2: 0.612 / Rpim(I) all: 0.393

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.53 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2374 5.02 %
Rwork0.1873 --
obs0.189 47304 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3867 0 62 630 4559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.678
X-RAY DIFFRACTIONf_dihedral_angle_d14.1841547
X-RAY DIFFRACTIONf_chiral_restr0.048614
X-RAY DIFFRACTIONf_plane_restr0.006732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.30831420.27182561X-RAY DIFFRACTION97
1.84-1.880.31711240.25582573X-RAY DIFFRACTION97
1.88-1.920.27731410.23372583X-RAY DIFFRACTION97
1.92-1.970.25871280.22542592X-RAY DIFFRACTION98
1.97-2.020.25131290.21342632X-RAY DIFFRACTION98
2.02-2.080.24481440.21442547X-RAY DIFFRACTION96
2.08-2.150.25631440.21212547X-RAY DIFFRACTION96
2.15-2.220.25321310.20132630X-RAY DIFFRACTION99
2.23-2.310.23981350.19212639X-RAY DIFFRACTION98
2.31-2.420.25211510.19252643X-RAY DIFFRACTION99
2.42-2.550.21661450.18442650X-RAY DIFFRACTION99
2.55-2.710.25831600.18372642X-RAY DIFFRACTION99
2.71-2.920.20231390.18642706X-RAY DIFFRACTION100
2.92-3.210.20511340.18182696X-RAY DIFFRACTION100
3.21-3.670.1981420.17172711X-RAY DIFFRACTION100
3.67-4.630.18121360.15292693X-RAY DIFFRACTION97
4.63-45.530.20321490.17952885X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.231 Å / Origin y: 21.3562 Å / Origin z: 0.6877 Å
111213212223313233
T0.1063 Å2-0.0107 Å20.0032 Å2-0.1396 Å20.0115 Å2--0.1688 Å2
L0.1581 °20.0487 °20.1679 °2-0.4368 °20.4486 °2--1.608 °2
S-0.0077 Å °-0.0647 Å °0.0117 Å °0.0624 Å °0.0203 Å °-0.0108 Å °0.03 Å °0.0315 Å °-0.0167 Å °
Refinement TLS groupSelection details: chain A

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