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- PDB-8f3l: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485A va... -

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Basic information

Entry
Database: PDB / ID: 8f3l
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) T485A variant penicillin bound form from Enterococcus faecium
ComponentsPenicillin binding protein 5
KeywordsANTIBIOTIC / Penicillin binding / antibiotic resistance / ANTIBIOTICS
Function / homology
Function and homology information


peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily ...NTF2-like; domain 1 / NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Penicillin binding protein 5
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsD'Andrea, E.D. / Choy, M.S. / Schoenle, M.V. / Page, R. / Peti, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: The Molecular Basis for Resistance of E. faecium PBP5 to beta-lactam Antibiotics
Authors: Hunashal, Y. / Kumar, G.S. / Choy, M.S. / Da Silva Santiago, A. / D'Andrea, E.D. / Schoenle, M.V. / Arthur, M. / Rice, L.B. / Page, R. / Peti, W.
History
DepositionNov 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,19110
Polymers70,0861
Non-polymers1,1059
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.182, 193.182, 156.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Penicillin binding protein 5 / Penicillin-binding protein Pbp5


Mass: 70086.000 Da / Num. of mol.: 1 / Mutation: T485A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: pbp5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G5CKR9
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 1 / Mutation: T485A
Source method: isolated from a genetically manipulated source
Formula: C16H20N2O4S / References: serine-type D-Ala-D-Ala carboxypeptidase
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 6.01 Å3/Da / Density % sol: 79.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.08 M HEPES pH 7.0, 2.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.39→39.1 Å / Num. obs: 24307 / % possible obs: 99.7 % / Redundancy: 19.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.064 / Rrim(I) all: 0.283 / Χ2: 0.94 / Net I/σ(I): 10.7 / Num. measured all: 476902
Reflection shellResolution: 3.39→3.63 Å / % possible obs: 98.5 % / Redundancy: 20.1 % / Rmerge(I) obs: 3.385 / Num. measured all: 85299 / Num. unique obs: 4254 / CC1/2: 0.662 / Rpim(I) all: 0.769 / Rrim(I) all: 3.473 / Χ2: 0.89 / Net I/σ(I) obs: 2.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.91 Å39.1 Å
Translation7.91 Å39.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 3.4→39.1 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 2144 4.77 %
Rwork0.1806 --
obs0.1814 24201 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 40 22 4684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024729
X-RAY DIFFRACTIONf_angle_d0.4366461
X-RAY DIFFRACTIONf_dihedral_angle_d11.4041621
X-RAY DIFFRACTIONf_chiral_restr0.04753
X-RAY DIFFRACTIONf_plane_restr0.003854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.36921490.32232718X-RAY DIFFRACTION96
3.48-3.560.30361470.28892848X-RAY DIFFRACTION100
3.56-3.660.30761450.27232873X-RAY DIFFRACTION100
3.66-3.770.28611560.24052836X-RAY DIFFRACTION100
3.77-3.890.24461280.22492868X-RAY DIFFRACTION100
3.89-4.030.23021200.20252887X-RAY DIFFRACTION100
4.03-4.190.22811610.18392830X-RAY DIFFRACTION100
4.19-4.380.20551500.16942875X-RAY DIFFRACTION100
4.38-4.610.15151360.15842877X-RAY DIFFRACTION100
4.61-4.90.14121450.15372826X-RAY DIFFRACTION100
4.9-5.270.19931650.16232842X-RAY DIFFRACTION100
5.27-5.80.18561450.18362860X-RAY DIFFRACTION100
5.8-6.640.20951290.18872873X-RAY DIFFRACTION100
6.64-8.350.16221260.17542893X-RAY DIFFRACTION100
8.35-39.10.15961420.14062857X-RAY DIFFRACTION100

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