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

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Basic information

Entry
Database: PDB / ID: 9fzp
TitlePseudomonas aeruginosa penicillin binding protein 3 in complex with cefepime
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
CEFOTAXIME, C3' cleaved, open, bound form / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 (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)56,4052
Polymers56,0081
Non-polymers3971
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-1 kcal/mol
Surface area22390 Å2
Unit cell
Length a, b, c (Å)67.303, 88.467, 82.008
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-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.01 M Zinc chloride, 0.1 M MES pH 6.0, 20 % w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.7→53.59 Å / Num. obs: 12157 / % possible obs: 87.8 % / Redundancy: 7.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.108 / Rrim(I) all: 0.319 / Net I/σ(I): 4.2
Reflection shellResolution: 2.7→2.84 Å / Rmerge(I) obs: 1.529 / Num. unique obs: 1620 / CC1/2: 0.546 / Rpim(I) all: 0.558 / Rrim(I) all: 1.635

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→53.56 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2955 690 5.73 %
Rwork0.2501 --
obs0.2527 12048 86.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 0 31 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.201
X-RAY DIFFRACTIONf_dihedral_angle_d13.067590
X-RAY DIFFRACTIONf_chiral_restr0.065595
X-RAY DIFFRACTIONf_plane_restr0.009699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.34471370.32842252X-RAY DIFFRACTION87
2.91-3.210.41471220.30482287X-RAY DIFFRACTION88
3.21-3.670.33311420.27672268X-RAY DIFFRACTION88
3.67-4.620.27361540.21962258X-RAY DIFFRACTION86
4.62-53.560.25021350.22212293X-RAY DIFFRACTION83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4375-1.0786-0.0267.87910.72930.5550.0901-0.0412-0.05270.24050.0956-0.6170.03250.1152-0.16710.4772-0.04190.00820.491-0.02110.5065-9.2075-9.2616.8429
20.5253-0.14690.15983.627-1.0621.36570.00570.1109-0.1178-0.02710.0432-0.07430.30060.0978-0.00070.3150.04160.01090.339-0.04490.3579-11.156124.3225-2.8799
31.4810.5848-0.03462.3421-0.38031.23830.01320.0303-0.0572-0.09310.0274-0.02840.0955-0.0432-0.02440.33120.0201-0.03980.35410.00860.3237-13.44437.2078-4.4367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 301 )
3X-RAY DIFFRACTION3chain 'A' and (resid 302 through 513 )

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