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- PDB-8f3p: Crystal structure of Penicillin Binding Protein 5 (PBP5) R464A va... -

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Basic information

Entry
Database: PDB / ID: 8f3p
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) R464A 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: 3.09 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

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Assembly

Deposited unit
A: Penicillin binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,90318
Polymers70,0301
Non-polymers1,87317
Water1,78399
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)191.741, 191.741, 156.390
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: 70029.906 Da / Num. of mol.: 1 / Mutation: R464A
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: R464A
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.: 16 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 5.93 Å3/Da / Density % sol: 79.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.085 M Tris pH 8.0, 2.55 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: 3.09→39.68 Å / Num. obs: 31376 / % possible obs: 99.7 % / Redundancy: 19.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.288 / Rpim(I) all: 0.066 / Rrim(I) all: 0.295 / Χ2: 1 / Net I/σ(I): 13.2 / Num. measured all: 622831
Reflection shellResolution: 3.09→3.26 Å / % possible obs: 98.5 % / Redundancy: 20.2 % / Rmerge(I) obs: 2.256 / Num. measured all: 89447 / Num. unique obs: 4435 / CC1/2: 0.865 / Rpim(I) all: 0.508 / Rrim(I) all: 2.314 / Χ2: 1 / Net I/σ(I) obs: 2.3

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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: 3.09→38.1 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 2803 4.8 %
Rwork0.1876 --
obs0.1889 31305 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→38.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 80 99 4918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024879
X-RAY DIFFRACTIONf_angle_d0.4926648
X-RAY DIFFRACTIONf_dihedral_angle_d11.7181715
X-RAY DIFFRACTIONf_chiral_restr0.041760
X-RAY DIFFRACTIONf_plane_restr0.004867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.150.38121510.33662537X-RAY DIFFRACTION92
3.15-3.210.31011550.31022812X-RAY DIFFRACTION100
3.21-3.270.28091500.28252751X-RAY DIFFRACTION100
3.27-3.330.2841280.28182812X-RAY DIFFRACTION100
3.33-3.410.3051220.2572820X-RAY DIFFRACTION100
3.41-3.490.31231530.2352807X-RAY DIFFRACTION100
3.49-3.570.22781410.20932767X-RAY DIFFRACTION100
3.57-3.670.23051370.20152775X-RAY DIFFRACTION100
3.67-3.780.21381530.1872785X-RAY DIFFRACTION100
3.78-3.90.20791200.18432821X-RAY DIFFRACTION100
3.9-4.040.1831230.17822799X-RAY DIFFRACTION100
4.04-4.20.23441650.16222766X-RAY DIFFRACTION100
4.2-4.390.14951320.152790X-RAY DIFFRACTION100
4.39-4.620.16261360.14342803X-RAY DIFFRACTION100
4.62-4.910.16441530.15112789X-RAY DIFFRACTION100
4.91-5.290.19771530.16652773X-RAY DIFFRACTION100
5.29-5.820.20741530.17952784X-RAY DIFFRACTION100
5.82-6.660.20251140.18862830X-RAY DIFFRACTION100
6.66-8.350.2091260.17652791X-RAY DIFFRACTION100
8.37-38.10.18051380.15462807X-RAY DIFFRACTION99

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