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

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Basic information

Entry
Database: PDB / ID: 9fze
TitlePseudomonas aeruginosa penicillin binding protein 3 in complex with meropenem
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
Chem-MER / Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
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)56,3932
Polymers56,0081
Non-polymers3851
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.697, 89.076, 83.452
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 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-MER / (4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid / Meropenem, bound form


Mass: 385.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
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: 0.99763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99763 Å / Relative weight: 1
ReflectionResolution: 2.1→60.89 Å / Num. obs: 56238 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.055 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 1.246 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2486 / CC1/2: 0.782 / Rpim(I) all: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.54 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 2849 5.07 %
Rwork0.2127 --
obs0.2147 56238 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 0 344 4186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.494
X-RAY DIFFRACTIONf_dihedral_angle_d10.3421488
X-RAY DIFFRACTIONf_chiral_restr0.043611
X-RAY DIFFRACTIONf_plane_restr0.004719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.33591200.28612773X-RAY DIFFRACTION100
2.14-2.180.31151420.28572708X-RAY DIFFRACTION100
2.18-2.210.3331370.31622240X-RAY DIFFRACTION98
2.22-2.260.56371390.44212100X-RAY DIFFRACTION86
2.26-2.310.40271510.35992526X-RAY DIFFRACTION93
2.31-2.370.3381460.25922765X-RAY DIFFRACTION100
2.37-2.430.35191640.26852660X-RAY DIFFRACTION100
2.43-2.490.30291370.2592749X-RAY DIFFRACTION100
2.49-2.560.28061420.2522718X-RAY DIFFRACTION100
2.56-2.650.3291390.22932782X-RAY DIFFRACTION100
2.65-2.740.23171370.22322735X-RAY DIFFRACTION100
2.74-2.850.24791640.2292733X-RAY DIFFRACTION100
2.85-2.980.25071150.22612782X-RAY DIFFRACTION100
2.98-3.140.20871360.2162703X-RAY DIFFRACTION100
3.14-3.330.23661470.20562742X-RAY DIFFRACTION100
3.33-3.590.22011750.19662726X-RAY DIFFRACTION100
3.59-3.950.21681150.18642735X-RAY DIFFRACTION100
3.95-4.520.21361260.15422775X-RAY DIFFRACTION100
4.53-5.70.19321440.15772731X-RAY DIFFRACTION100
5.7-44.540.19481730.16382706X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.8835 Å / Origin y: 23.6934 Å / Origin z: 1.7164 Å
111213212223313233
T0.2371 Å2-0.0034 Å20.032 Å2-0.2872 Å20.0163 Å2--0.2645 Å2
L0.1118 °2-0.2616 °2-0.0147 °2-2.1715 °20.3718 °2--0.3716 °2
S0.0116 Å °0.0259 Å °0.0809 Å °-0.0175 Å °-0.0287 Å °0.0375 Å °-0.0741 Å °-0.0262 Å °0.0178 Å °
Refinement TLS groupSelection details: chain A

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