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- PDB-9fz8: Pseudomonas aeruginosa penicillin binding protein 3 -

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Open data


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Basic information

Entry
Database: PDB / ID: 9fz8
TitlePseudomonas aeruginosa penicillin binding protein 3
ComponentsPeptidoglycan D,D-transpeptidase FtsI
KeywordsHYDROLASE / Transpeptidase / Penicillin binding protein / 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
Peptidoglycan D,D-transpeptidase FtsI
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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 Grant (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


Theoretical massNumber of molelcules
Total (without water)56,0081
Polymers56,0081
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.920, 84.005, 89.542
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: Residues that were disordered 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 46.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Sodium citrate pH 5.5, 20 % w/v PEG 3000

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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 EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.11→54.14 Å / Num. obs: 30196 / % possible obs: 99.8 % / Redundancy: 10.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.046 / Net I/σ(I): 6.9
Reflection shellResolution: 2.11→2.17 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2387 / CC1/2: 0.815 / Rpim(I) all: 0.416 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→45.49 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0.93 / Phase error: 32.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 2793 4.92 %
Rwork0.2238 --
obs0.2256 28399 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.11→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 0 215 4039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.485
X-RAY DIFFRACTIONf_dihedral_angle_d11.9941459
X-RAY DIFFRACTIONf_chiral_restr0.042595
X-RAY DIFFRACTIONf_plane_restr0.004699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.150.33771230.3622711X-RAY DIFFRACTION99
2.15-2.190.39761380.34032721X-RAY DIFFRACTION100
2.19-2.230.41551330.30432731X-RAY DIFFRACTION100
2.23-2.270.33871420.32022681X-RAY DIFFRACTION100
2.27-2.320.36411390.29162673X-RAY DIFFRACTION100
2.32-2.380.33021580.2822674X-RAY DIFFRACTION100
2.38-2.440.30341460.26812669X-RAY DIFFRACTION99
2.44-2.50.30371400.27672702X-RAY DIFFRACTION99
2.5-2.580.30611260.26112658X-RAY DIFFRACTION99
2.58-2.660.2991300.25062723X-RAY DIFFRACTION100
2.66-2.750.27281590.25642677X-RAY DIFFRACTION100
2.75-2.860.30621210.25972750X-RAY DIFFRACTION100
2.86-2.990.3461280.25882718X-RAY DIFFRACTION100
2.99-3.150.31171330.25172663X-RAY DIFFRACTION100
3.15-3.350.25641560.23212704X-RAY DIFFRACTION100
3.35-3.610.25281980.22562674X-RAY DIFFRACTION100
3.61-3.970.22281270.19772711X-RAY DIFFRACTION100
3.97-4.540.20751240.16342715X-RAY DIFFRACTION100
4.55-5.720.19631140.17522723X-RAY DIFFRACTION100
5.73-45.490.20661580.17082691X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.393 Å / Origin y: 22.9438 Å / Origin z: 1.4494 Å
111213212223313233
T0.3382 Å2-0.0203 Å2-0.0347 Å2-0.279 Å20.036 Å2--0.3221 Å2
L0.2988 °20.173 °20.1055 °2-0.6174 °20.4712 °2--2.6091 °2
S-0.0077 Å °-0.1416 Å °-0.0265 Å °0.1514 Å °-0.0157 Å °-0.0071 Å °-0.0166 Å °0.0931 Å °0.0072 Å °
Refinement TLS groupSelection details: chain A

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