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- PDB-8f3s: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485M T4... -

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Basic information

Entry
Database: PDB / ID: 8f3s
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) T485M T499I 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 / Resolution: 3.5 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)71,93617
Polymers70,1581
Non-polymers1,77716
Water28816
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)193.338, 193.338, 156.986
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: 70158.172 Da / Num. of mol.: 1 / Mutation: T485M T499I
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: T485M T499I
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.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 6.04 Å3/Da / Density % sol: 79.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 2.9 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: 3.5→38.41 Å / Num. obs: 22247 / % possible obs: 99.3 % / Redundancy: 19.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.507 / Rpim(I) all: 0.117 / Rrim(I) all: 0.521 / Χ2: 0.97 / Net I/σ(I): 11.2 / Num. measured all: 436622
Reflection shellResolution: 3.5→3.78 Å / % possible obs: 99.7 % / Redundancy: 19.9 % / Rmerge(I) obs: 4.077 / Num. measured all: 89790 / Num. unique obs: 4509 / CC1/2: 0.846 / Rpim(I) all: 0.93 / Rrim(I) all: 4.184 / Χ2: 0.88 / Net I/σ(I) obs: 3.9

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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: 3.5→37.31 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1933 4.73 %
Rwork0.1835 --
obs0.185 22060 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→37.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 75 16 4811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014856
X-RAY DIFFRACTIONf_angle_d0.4026613
X-RAY DIFFRACTIONf_dihedral_angle_d11.2491706
X-RAY DIFFRACTIONf_chiral_restr0.041753
X-RAY DIFFRACTIONf_plane_restr0.003864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.32461340.28922686X-RAY DIFFRACTION95
3.59-3.680.34071350.26192808X-RAY DIFFRACTION100
3.68-3.790.26711560.23912805X-RAY DIFFRACTION100
3.79-3.910.27181230.22092806X-RAY DIFFRACTION100
3.91-4.050.26041190.20872775X-RAY DIFFRACTION97
4.05-4.220.26371570.18532639X-RAY DIFFRACTION94
4.22-4.410.20251350.16822826X-RAY DIFFRACTION100
4.41-4.640.15681340.15092808X-RAY DIFFRACTION100
4.64-4.930.16761460.14662826X-RAY DIFFRACTION100
4.93-5.310.19541630.16172790X-RAY DIFFRACTION100
5.31-5.840.18771510.18582810X-RAY DIFFRACTION100
5.84-6.680.21741160.1932764X-RAY DIFFRACTION97
6.68-8.40.18961280.18692832X-RAY DIFFRACTION100
8.4-37.310.1921360.15382781X-RAY DIFFRACTION98

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