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- PDB-8f3y: Crystal structure of Penicillin Binding Protein 5 (PBP5) Poly-Gly... -

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Basic information

Entry
Database: PDB / ID: 8f3y
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) Poly-Gly 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 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 / Beta-lactamase/transpeptidase-like
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 / Resolution: 2.99 Å
AuthorsSchoenle, M.V. / D'Andrea, E.D. / Choy, M.S. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
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 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Oct 16, 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)71,53018
Polymers69,6561
Non-polymers1,87317
Water1,13563
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)193.054, 193.054, 155.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

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Components

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


Mass: 69656.406 Da / Num. of mol.: 1 / Mutation: 624KEKQDVK630-->GGGGGGG
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: 624KEKQDVK630-->GGGGGGG
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.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 6.02 Å3/Da / Density % sol: 79.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.095 M Trisodium citrate pH 5.5, 2.28 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: 2.99→38.97 Å / Num. obs: 34965 / % possible obs: 99.7 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.036 / Rrim(I) all: 0.16 / Χ2: 0.96 / Net I/σ(I): 15.9 / Num. measured all: 686375
Reflection shellResolution: 2.99→3.14 Å / % possible obs: 98.4 % / Redundancy: 19.5 % / Rmerge(I) obs: 2.48 / Num. measured all: 87598 / Num. unique obs: 4502 / CC1/2: 0.643 / Rpim(I) all: 0.563 / Rrim(I) all: 2.545 / Χ2: 0.75 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 2.99→38.97 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1709 4.91 %
Rwork0.2095 --
obs0.2109 34811 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 80 63 4904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024906
X-RAY DIFFRACTIONf_angle_d0.4336678
X-RAY DIFFRACTIONf_dihedral_angle_d12.3161749
X-RAY DIFFRACTIONf_chiral_restr0.04755
X-RAY DIFFRACTIONf_plane_restr0.003875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.080.38951520.40382521X-RAY DIFFRACTION94
3.08-3.180.36781640.33222717X-RAY DIFFRACTION100
3.18-3.290.31751540.28942701X-RAY DIFFRACTION100
3.29-3.430.36631240.27382744X-RAY DIFFRACTION100
3.43-3.580.2861410.25932745X-RAY DIFFRACTION100
3.58-3.770.2671400.2452739X-RAY DIFFRACTION100
3.77-4.010.24871210.22842770X-RAY DIFFRACTION100
4.01-4.310.22381490.18052752X-RAY DIFFRACTION100
4.31-4.750.19191350.17562778X-RAY DIFFRACTION100
4.75-5.430.20961560.17972792X-RAY DIFFRACTION100
5.43-6.840.22641300.19832849X-RAY DIFFRACTION100
6.84-38.970.19881430.17512994X-RAY DIFFRACTION99

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