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- PDB-8f3n: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485A va... -

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Basic information

Entry
Database: PDB / ID: 8f3n
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) T485A variant with S466 insertion penicillin bound form from Enterococcus faecium
ComponentsPenicillin binding protein 5
KeywordsANTIBIOTIC / Penicillin binding / antibiotic resistance / ANTIBIOTICS
Function / homology
Function and homology information


penicillin binding / 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 / molecular replacement / Resolution: 2.99 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Penicillin binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,33521
Polymers70,1731
Non-polymers2,16220
Water54030
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)192.264, 192.264, 156.952
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-801-

HOH

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Components

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


Mass: 70173.078 Da / Num. of mol.: 1 / Mutation: T485A, S466 insertion
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, S466 insertion
Source method: isolated from a genetically manipulated source
Formula: C16H20N2O4S / References: serine-type D-Ala-D-Ala carboxypeptidase / Comment: antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 5.97 Å3/Da / Density % sol: 79.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid pH 5.0, 3.0 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: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.99→39.24 Å / Num. obs: 34774 / % possible obs: 99.6 % / Redundancy: 13.1 % / CC1/2: 0.971 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.04 / Rrim(I) all: 0.137 / Χ2: 0.84 / Net I/σ(I): 13.5 / Num. measured all: 455452
Reflection shellResolution: 2.99→3.14 Å / % possible obs: 99 % / Redundancy: 13 % / Rmerge(I) obs: 0.542 / Num. measured all: 58701 / Num. unique obs: 4522 / CC1/2: 0.964 / Rpim(I) all: 0.206 / Rrim(I) all: 0.591 / Χ2: 0.6 / Net I/σ(I) obs: 2.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.66 Å39.24 Å
Translation7.66 Å39.24 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XDSdata reduction
Aimless0.6.3data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 2.99→38.2 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.218 3096 4.9 %
Rwork0.1983 --
obs0.1993 33794 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 95 30 4832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0014859
X-RAY DIFFRACTIONf_angle_d0.4146627
X-RAY DIFFRACTIONf_dihedral_angle_d12.6341688
X-RAY DIFFRACTIONf_chiral_restr0.04755
X-RAY DIFFRACTIONf_plane_restr0.003865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.040.48651550.4292668X-RAY DIFFRACTION96
3.04-3.090.34981850.35142791X-RAY DIFFRACTION100
3.09-3.140.31861690.29832792X-RAY DIFFRACTION99
3.14-3.20.32971070.27521970X-RAY DIFFRACTION70
3.2-3.260.29961210.27591957X-RAY DIFFRACTION70
3.26-3.330.24971160.25012766X-RAY DIFFRACTION99
3.33-3.40.27351300.25122862X-RAY DIFFRACTION100
3.4-3.480.26471580.23592810X-RAY DIFFRACTION100
3.48-3.570.22151340.22692835X-RAY DIFFRACTION100
3.57-3.660.27451440.22552784X-RAY DIFFRACTION100
3.66-3.770.23211560.1992849X-RAY DIFFRACTION100
3.77-3.890.22831200.18912821X-RAY DIFFRACTION100
3.89-4.030.18511250.17552838X-RAY DIFFRACTION100
4.03-4.190.21281580.17762789X-RAY DIFFRACTION99
4.19-4.380.18591410.16562837X-RAY DIFFRACTION100
4.39-4.620.17231330.16292826X-RAY DIFFRACTION100
4.62-4.90.16871490.15562820X-RAY DIFFRACTION100
4.91-5.280.1931610.18122804X-RAY DIFFRACTION100
5.28-5.810.19941520.1912794X-RAY DIFFRACTION99
5.81-6.640.18651190.20342840X-RAY DIFFRACTION100
6.65-8.360.20621250.19192832X-RAY DIFFRACTION99
8.37-38.20.19721380.16562813X-RAY DIFFRACTION99

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