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- PDB-8f3f: Crystal structure of Penicillin Binding Protein 5 (PBP5) T485M va... -

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Basic information

Entry
Database: PDB / ID: 8f3f
TitleCrystal structure of Penicillin Binding Protein 5 (PBP5) T485M variant apo 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
Penicillin binding protein 5
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å
AuthorsD'Andrea, E.D. / Choy, M.S. / Hunashal, Y. / 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

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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)71,68317
Polymers70,1461
Non-polymers1,53716
Water1,982110
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)192.665, 192.665, 155.862
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-900-

HOH

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Components

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


Mass: 70146.117 Da / Num. of mol.: 1 / Mutation: T485M
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.95 Å3/Da / Density % sol: 79.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 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: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.84→39.79 Å / Num. obs: 40522 / % possible obs: 99.4 % / Redundancy: 15.1 % / CC1/2: 0.865 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.053 / Rrim(I) all: 0.194 / Net I/σ(I): 12.2 / Num. measured all: 610210
Reflection shellResolution: 2.84→2.96 Å / % possible obs: 95.1 % / Redundancy: 14.9 % / Rmerge(I) obs: 2.006 / Num. measured all: 64046 / Num. unique obs: 4307 / CC1/2: 0.744 / Rpim(I) all: 0.523 / Rrim(I) all: 2.075 / Net I/σ(I) obs: 2.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.67 Å39.79 Å
Translation7.67 Å39.79 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKA

6mka


Resolution: 2.84→39.79 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.44 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 3617 4.94 %
Rwork0.1734 --
obs0.1751 39038 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.84→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 80 110 4978
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054926
X-RAY DIFFRACTIONf_angle_d0.6966692
X-RAY DIFFRACTIONf_dihedral_angle_d12.3851773
X-RAY DIFFRACTIONf_chiral_restr0.046759
X-RAY DIFFRACTIONf_plane_restr0.004870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.880.39651580.37152505X-RAY DIFFRACTION90
2.88-2.920.3621520.3192753X-RAY DIFFRACTION100
2.92-2.960.3581340.28382787X-RAY DIFFRACTION100
2.96-3.010.32271360.27732811X-RAY DIFFRACTION100
3.01-3.050.3351750.27452739X-RAY DIFFRACTION100
3.05-3.10.36031210.27571650X-RAY DIFFRACTION60
3.1-3.160.3261600.25562734X-RAY DIFFRACTION100
3.16-3.210.3132870.26241431X-RAY DIFFRACTION52
3.21-3.280.24261510.23882755X-RAY DIFFRACTION100
3.28-3.340.25231330.23032800X-RAY DIFFRACTION100
3.34-3.410.29471240.23062803X-RAY DIFFRACTION100
3.41-3.490.21411460.1872797X-RAY DIFFRACTION100
3.49-3.580.18621440.17212761X-RAY DIFFRACTION100
3.58-3.680.18591430.16682774X-RAY DIFFRACTION100
3.68-3.790.18851430.1582797X-RAY DIFFRACTION100
3.79-3.910.21961240.16412802X-RAY DIFFRACTION100
3.91-4.050.19581220.14812804X-RAY DIFFRACTION100
4.05-4.210.2071650.14422781X-RAY DIFFRACTION100
4.21-4.40.18761300.13422785X-RAY DIFFRACTION100
4.4-4.630.16091340.13112799X-RAY DIFFRACTION100
4.63-4.920.14411520.13422755X-RAY DIFFRACTION100
4.92-5.30.15291510.13622793X-RAY DIFFRACTION100
5.3-5.830.16871530.16062766X-RAY DIFFRACTION100
5.83-6.680.18041150.16342834X-RAY DIFFRACTION100
6.68-8.390.19731260.15862790X-RAY DIFFRACTION100
8.4-39.790.17171380.14022797X-RAY DIFFRACTION100

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